diff --git a/Project.toml b/Project.toml index a0de4fc6..9ecc01f1 100644 --- a/Project.toml +++ b/Project.toml @@ -4,6 +4,7 @@ DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f" +Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" diff --git a/examples/censored.jl b/examples/censored.jl index 9e97118f..d7250b9c 100644 --- a/examples/censored.jl +++ b/examples/censored.jl @@ -12,7 +12,7 @@ md""" # Censored -Researchers are studying a new drug designed to cure a specific type of skin condition. They monitor 15 patients undergoing treatment for five months, recording the time it takes for patients to show no signs of the disease. Of the 15, seven were cured in the five-month study period, at `[2.1, 4.7, 1.6, 2.8, 4.3, 1.9, 4.2]` months. Eight patients might not achieve remission within the five-year study period (this is censored data). You may assume that these persons were cured at some later, unspecified time after the five-year period. Given a Gamma prior on the rate parameter $\lambda$, what is its posterior distribution? +Researchers are studying a new drug designed to cure a specific type of skin condition. They monitor 15 patients undergoing treatment for five months, recording the time it takes for patients to show no signs of the condition. Of the 15, seven were cured in the five-month study period, at `[2.1, 4.7, 1.6, 2.8, 4.3, 1.9, 4.2]` months. Eight patients were not achieve cured within the five-month study period (this is censored data). You may assume that these persons were cured at some later, unspecified time after the five-month trial. Given a Gamma prior on the rate parameter $\lambda$, what is its posterior distribution? Give a 95% credibility interval. diff --git a/examples/citations.jl b/examples/citations.jl new file mode 100644 index 00000000..6da0023b --- /dev/null +++ b/examples/citations.jl @@ -0,0 +1,99 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# ╔═╡ 2fb807d8-f555-41cf-a374-8ff9cadf9533 +using Pkg; Pkg.activate("..") + +# ╔═╡ 6613efca-d42c-11ef-0e77-716f85ded3df +using Turing, PlutoUI, StatsPlots + +# ╔═╡ e89d9c26-0ffe-48ca-ad39-93655d6868a4 +md"Consider the following model:" + +# ╔═╡ 19fcf183-322a-44c4-8c3c-987f667d882e +@model function citations() + X ~ Normal(0, 1) + Y ~ Normal(1, 2) + Z ~ Poisson(exp(0.8X + 1.2Y + 0.2X*Y)) +end + +# ╔═╡ 8197a2a1-86fb-44eb-a09f-d4e8511167b2 +md"Generate a sample of 10,000 observations of this distribution. + +Use this sample to create a histogram of `Z` and compute its quantiles. Additionally, compute the 99% quantile (this is the top-1% value of `Z`). + +Next, compute the correlation between `X` and `Y` and draw a scatter plot. Does this match your observation? +" + +# ╔═╡ aa73f4fa-23ca-41ff-b3cf-4bab0740d157 +prior = sample(citations(), Prior(), 10_000) + +# ╔═╡ e40b92ad-2a9a-414e-b8ee-cc658d505212 +summarize(prior) + +# ╔═╡ fba7efbd-8ad0-4fa3-aeb9-5a674e0295ce +histogram(prior[:Z]) + +# ╔═╡ a737c4c1-c27d-4800-9d0a-e71d4503025b +histogram(prior[:Z], yscale=:log10) + +# ╔═╡ b1d4d0a6-6d1d-4cf2-b21e-51705c167b86 +quantile(prior, q = [0.025, 0.25, 0.5, 0.75, 0.975, 0.99]) + +# ╔═╡ 4196765c-b2bd-4093-963b-82fb0ec2e343 +cor(prior[:X], prior[:Y]) + +# ╔═╡ 5b4ef7a2-790e-46ba-89f1-136a1c9e7fdb +scatter(prior[:X], prior[:Y], xlab="X", ylab="Y") + +# ╔═╡ b0bef20d-a10c-457b-ac8c-1e8caddc54e1 +md"Now, make a conditional model `high_citation` in which you fix `Z = 100`. Use the No-U-Turn sampler to obtain 10,000 posterior samples. + +Using this conditional sample, again compute the correlation between `X` and `Y` together with the scatter plot. What do you observe? +" + +# ╔═╡ bb1681c5-ff86-497c-8cb8-f5e2bd638536 +high_citation = citations() | (Z=100,) + +# ╔═╡ 03f48a27-f0ce-46e7-989d-ab57cfc5babe +post = sample(high_citation, NUTS(), 10_000) + +# ╔═╡ d5e6bd69-6a49-4d6a-8c37-9cda7fb97bb5 +quantile(post) + +# ╔═╡ 72577ba4-e20c-4eb1-af34-1d702957f1e3 +cor(post[:X], post[:Y]) + +# ╔═╡ 0a64b09b-fd71-4628-8b7d-7df3c4b45a15 +scatter(post[:X], post[:Y], xlabel="X", ylabel="Y") + +# ╔═╡ bf8ac4d6-5a6e-49ff-b75e-6a0f7ad7ff4d +md"Now for some context, the model is represents the number of citations a journal article can attract after being published (`Z`). `X` represents a metric of **quality**, how well the study was done and whether everything was done correctly. `Y` represents the spectacularity or excitedness of the claims, i.e., whether its results would be of general interest. Re-interpret you results in light of this new information." + +# ╔═╡ 830e9980-3f01-4f54-b29f-7247bb4531f4 +plot(post) + +# ╔═╡ Cell order: +# ╠═6613efca-d42c-11ef-0e77-716f85ded3df +# ╠═2fb807d8-f555-41cf-a374-8ff9cadf9533 +# ╠═e89d9c26-0ffe-48ca-ad39-93655d6868a4 +# ╠═19fcf183-322a-44c4-8c3c-987f667d882e +# ╠═8197a2a1-86fb-44eb-a09f-d4e8511167b2 +# ╠═aa73f4fa-23ca-41ff-b3cf-4bab0740d157 +# ╠═e40b92ad-2a9a-414e-b8ee-cc658d505212 +# ╠═fba7efbd-8ad0-4fa3-aeb9-5a674e0295ce +# ╠═a737c4c1-c27d-4800-9d0a-e71d4503025b +# ╠═b1d4d0a6-6d1d-4cf2-b21e-51705c167b86 +# ╠═4196765c-b2bd-4093-963b-82fb0ec2e343 +# ╠═5b4ef7a2-790e-46ba-89f1-136a1c9e7fdb +# ╠═b0bef20d-a10c-457b-ac8c-1e8caddc54e1 +# ╠═bb1681c5-ff86-497c-8cb8-f5e2bd638536 +# ╠═03f48a27-f0ce-46e7-989d-ab57cfc5babe +# ╠═d5e6bd69-6a49-4d6a-8c37-9cda7fb97bb5 +# ╠═72577ba4-e20c-4eb1-af34-1d702957f1e3 +# ╠═0a64b09b-fd71-4628-8b7d-7df3c4b45a15 +# ╠═bf8ac4d6-5a6e-49ff-b75e-6a0f7ad7ff4d +# ╠═830e9980-3f01-4f54-b29f-7247bb4531f4 diff --git a/examples/insuline_sensitivity backup 1.jl b/examples/insuline_sensitivity backup 1.jl new file mode 100644 index 00000000..89bf4a58 --- /dev/null +++ b/examples/insuline_sensitivity backup 1.jl @@ -0,0 +1,372 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). +macro bind(def, element) + #! format: off + quote + local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local el = $(esc(element)) + global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) + el + end + #! format: on +end + +# ╔═╡ 7bc363b0-9415-4954-807f-81a308bde531 +begin + import Pkg + Pkg.activate("..") +end + +# ╔═╡ 52b28a4c-b0bb-11ef-2841-17ecfb596676 +using Plots, PlutoUI, DifferentialEquations, ForwardDiff, Catalyst + +# ╔═╡ 77860f25-1b30-4cf1-812a-03ff2100bacd +using Turing + +# ╔═╡ c897d6e6-0b33-4dfb-89f3-f7e05bb9f73b +using StatsPlots, Optim + +# ╔═╡ e96779da-57c0-4c11-b3ab-40dc5ae81bee +using StatsBase + +# ╔═╡ bfcc4b4e-073e-401e-851c-d01ef828028a +md""" +# The minimal glucose model and dynamic compensation + +The Minimal Model of Glucose Regulation is a mathematical model used to describe how the body regulates glucose (sugar) levels in the blood. It was developed by Richard Bergman and Claudio Cobelli in the late 1970s and has become a cornerstone in diabetes research. + +We will use this exercise to study insulin sensitivity. + +The basic model considers only the concentration of glucose $G(t)$ in nM and the concentration of insulin $I(t)$ in nM: + +- glucose is added to a system with a zeroth-order rate of $m$ (later $m(t)$ if we model a non-fixed input); +- glucose is removed from the blood with a rate of $sGI$, where $s$ is the insulin sensitivity; +- insulin decays according to first-order kinetics with a rate parameter $\gamma$ +- $\beta$-cells produce insulin as a response to higher glucose concentrations. This is according to a saturated process, so it is well approximated using a Hill function ($n=2$). The rate of insulin production is given by $qBf(G)$, with $B$ the amount of $\beta$-cells and $q$ the maximal rate of insulin production/unit of cells. + +The following plot gives a fairly realistic response of insulin production as a function of glucose concentration in the blood. +""" + +# ╔═╡ e93bc1a5-e0b1-425c-b069-d5ce80756e60 +f_insulin(G) = hill(G, 1, 5, 2) + +# ╔═╡ 2ac43184-a393-4d39-9c3b-c299c3371b09 +plot(f_insulin, 0, 30, xlab="G nm", ylab="f(G)", title="Insulin production rate") + +# ╔═╡ 75a5b5d9-f8d7-4728-83dc-03dde502dcfb +md"Below is a reaction network implementing this model. All parameters are set to 1 for didactic purposes." + +# ╔═╡ f62c2b4a-a9e8-472b-b07b-44072da08ee8 +glucose_insuline_circuit = @reaction_network begin + @parameters q=1 s=1 γ=1 m=1 B=1 Ks=1.0 + m, 0 --> G + s * I, G --> 0 + B * hill(G, q, Ks, 2), 0 --> I + γ, I --> 0 +end + +# ╔═╡ 99ccbd1b-b9e4-4afc-8d9a-8c1055bcce0f +convert(ODESystem, glucose_insuline_circuit) + +# ╔═╡ c319ae6e-2f02-4a7e-a0b0-4a3f57fdcb66 +md"You can set initial values of glucose and insulin here." + +# ╔═╡ 7623a596-d6d4-4e0a-b29c-f2f7de0d2940 +G0 = 5.0 + +# ╔═╡ 0621968c-b39a-4346-a86a-42fa2cde724c +I0 = 0.0 + +# ╔═╡ 3c1465d2-0886-4b74-baee-55c7dad41f9a +md"Simulate the system over a time interval of 0 to 10 hours with $m=1$. Plot the results. What are the steady state concentrations for the two species? Does this depend on initial glucose levels (given enough time)?" + +# ╔═╡ bbbc3335-4190-4bc7-91ba-e96476a75751 +@unpack t, G, I = glucose_insuline_circuit + +# ╔═╡ afc40964-0a97-43a6-ab27-5fe96ecd319b +oprob1 = ODEProblem(glucose_insuline_circuit, [G=>G0, I=>I0], (0., 10.), [:m=>1.0]) + +# ╔═╡ f050b32e-1a14-4d5e-9fb3-5dbc4dfbf79c +sol1 = solve(oprob1, Tsit5()); + +# ╔═╡ 7e35b56b-44a0-46df-a812-f5fb437b672e +plot(sol1) + +# ╔═╡ 00db9d76-c4dd-450d-b7e3-cf87f8bfeffb +plot(sol1, idxs=(G, I)) + +# ╔═╡ aab02fef-6d84-4f53-aff5-6f94bf2bd460 +md"Now simulate the system but rather than with $m$ being a constant glucose input, we give in a pulse of glucose (i.e., drinking a soda) with a peak at $t=5$h. Note that our parameter now depends on the time!" + +# ╔═╡ 8a5ce760-55bb-4610-9226-32c3d8376748 +glucose_pulse(t) = .5 + exp(-(t-5)^2) + +# ╔═╡ a2fb8c21-c594-44f3-92df-99e6d3afeba1 +plot(glucose_pulse, 0, 10, label="G [nm]", xlab="t") + +# ╔═╡ ba68f740-ba8b-4efa-be2d-ac50c77dfa1a +glucose_pulse(t) + +# ╔═╡ 31aaced7-1fe4-4117-80f3-0fa70035822a +md"Up to now, we set $s$, the insulin sensitivity to 1. This parameter represents how sensitive the body is to insuline in taking up glucose. Aging and obesity increase glucose resistance ($1/s$), resulting in diabetes! Explore the effect of this parameter on your plots below." + +# ╔═╡ 69e21e9b-7d0e-44e3-8b33-ee7102dadadf +@bind s Slider(0.1:0.1:5, default=1, show_value=true) + +# ╔═╡ 6890e3ec-0875-423e-89c1-988411c869e3 +oprob2 = ODEProblem(glucose_insuline_circuit, [G=>0., I=>0.0], (0., 10.), [:m=>glucose_pulse(t), :s=>s]) + +# ╔═╡ fb439f9d-ee88-43cd-b91b-44ed8013b27d +sol2 = solve(oprob2, Tsit5()); + +# ╔═╡ 095e359a-2ec4-4637-8477-93510bef23ed +plot(sol2) + +# ╔═╡ b4073e81-6db8-4be6-a2d1-afa01640dbcf +s + +# ╔═╡ 4d58a832-9157-42fe-b578-c3fc29f01ea8 +md"We have made a function here that computes the steady state glucose concentration after 100 hours. Plot this as a function of s." + +# ╔═╡ 7cf11e6f-7ef4-478f-8cc7-eae93374cc58 +function glucose_steady_state(s) + oprob = ODEProblem(glucose_insuline_circuit, [G=>0., I=>0.0], (0., 100.), [:m=>1/2, :s=>s]) + sol = solve(oprob, Tsit5()) + return sol[G][end] +end + +# ╔═╡ 5eda8c4a-2baa-4987-b408-dbe7383abe95 +glucose_steady_state(s) + +# ╔═╡ 34788b1d-1530-4b88-8690-03fe9af52a8b +plot(glucose_steady_state, 0.1, 5, xlab="s", ylab="Gss") + +# ╔═╡ f616da2f-b51e-4328-bd3c-47e6d7377cbb +md"Using automatic differentiation (ForwardDiff), compute the absolute and relative sensitity indices. Is this system sensitive to the insuline sensitivity?" + +# ╔═╡ 97636a73-4732-4377-b760-c36cef13904b +fsens(s) = ForwardDiff.derivative(glucose_steady_state, s) + +# ╔═╡ a67d70ee-c8b5-4f22-926c-f48c5dcf9815 +fsens(s) + +# ╔═╡ 1bb5834a-6a4e-40ec-82c1-f2c505ecfeb8 +frelsens(s) = ForwardDiff.derivative(glucose_steady_state, s) * glucose_steady_state(s) / s + +# ╔═╡ a3156073-07bd-4f13-be5e-d19483fbad28 +frelsens(s) + +# ╔═╡ 0ae57436-0b8c-41ce-9d9d-8c48ed59b820 +md""" +We see that the final glucose concentration is highly dependent on $s$! This seems to be a flaw in the model, as we can imagine that the physiological parameters can greatly differ from person to person (for example, a person can have a large pancreas). + +A mechanism that stabilizes this is called *dynamic compensation*. Simply put, we have assumed here that the amount of beta cells ($B$) is fixed. However, in practice, these cells are capable of dividing, growing, and thus producing more insulin. Their growth rate depends on the concentration of glucose, creating an additional feedback loop that stabilizes the physiological circuit. The growth rate of the $\beta$-cells follows a sigmoid shape, being negative when $G$ is smaller than a threshold and positive if $G$ exceeds this threshold. + +```julia +μ(G), B --> 2B +``` + +This curve is plotted below. +""" + +# ╔═╡ 87d9c826-56af-409a-a884-d784cfa16a64 +μ(G) = 0.3atan(0.5(G-1)) + +# ╔═╡ 4d95e77b-fab0-454b-8319-1fe83e12f9e9 +plot(μ, 0, 30, xlab="G", label="μ(G)", title="Glucose-dependend growth rate") + +# ╔═╡ ea46f5f9-47a8-4641-a7e3-08a1a29cd04f +md"Add dynamic compensation to the model and show that this greatly reduces the sentitivty w.r.t. $s$." + +# ╔═╡ 870e9229-374a-40b8-97f7-1a84d1a857e9 +md""" +Robust version with dynamic compensation +```julia +glucose_insuline_circuit = @reaction_network begin + @parameters q=1 s=1 γ=1 m=1 Ks=1.0 + @species B(t)=1 + m, 0 --> G + s * I, G --> 0 + q * B * hill(G, 1, Ks, 2), 0 --> I + γ, I --> 0 + μ(G), B --> 2B +end +``` +""" + +# ╔═╡ e37ce327-504b-4fe4-baea-493cda834b4a +md" this does not work yet. Split and use different model: https://allendowney.github.io/ModSimPy/chap18.html" + +# ╔═╡ e66378f7-8ec8-4f7f-ab40-5c64479f865e +tmeas = 0:2:8 + +# ╔═╡ bcafb5c2-4f3c-47f4-b786-8f656969abe6 +length(tmeas) + +# ╔═╡ 08d3cf6e-dc0b-4a56-a241-0d0033e79fad +Gmeas = [92, 350, 287, 251, 240] + +# ╔═╡ c0d39fc8-d779-465e-91c1-3a6f9b694ee3 +Imeas = [11, 26, 130, 85, 51] + +# ╔═╡ c2c18077-add0-4ff9-a122-f248dbd1da79 +begin + scatter(tmeas, Gmeas, xlab="t [h]", label="G [mg/dL]") + scatter!(tmeas, Imeas, label="I [μU/mL]") +end + +# ╔═╡ e93a2495-aa5b-46f6-ae3c-b94559583c60 +@model function glucose_inference(tmeas, Gmeas, Imeas) + @assert length(tmeas) == length(Gmeas) == length(Imeas) + N = length(tmeas) + σGsq ~ Gamma(5) + σIsq ~ Gamma(3) + q~10LogNormal() + s~10LogNormal() + γ~10LogNormal() + B=1 + m~10LogNormal() + Ks~10LogNormal() + G0~100LogNormal() + I0~1LogNormal() + prob = remake(oprob1; u0=[G=>G0, I=>I0], tspan=(0., 8.), + p=[:m=>m, :q=>q, :s=>s, + :γ=>γ, :Ks=>Ks, :B=>B]) + sol = solve(prob, saveat=tmeas) + for i in 1:N + Gmeas[i] ~ Normal(sol[G][i], sqrt(σGsq)) + Imeas[i] ~ Normal(sol[I][i], sqrt(σIsq)) + end + return sol +end + +# ╔═╡ 55e4db93-f376-4cbb-829d-fea9ce3f3998 +glucose_inference(tmeas, Gmeas, Imeas)() + +# ╔═╡ 8989e653-e3e8-4e4f-8fc2-596e931ed21c +mod_data = glucose_inference(tmeas, Gmeas, Imeas) + +# ╔═╡ b763bb0c-581e-46ec-8104-53df25369642 +mod_data() |> plot + +# ╔═╡ 5e187f36-3883-4f08-b08c-a55d24e409cd +chain1 = sample(mod_data, NUTS(), 100) + +# ╔═╡ 2bf57ee8-ac1d-412f-a4c8-6e4ce87a74c5 +summarize(chain1) + +# ╔═╡ aa32db53-c944-442a-88df-5937f380b54c +#=╠═╡ +plot(chain1) + ╠═╡ =# + +# ╔═╡ 7b247ff1-f873-4b00-90c3-4c7a87485fb2 +#=╠═╡ +scatter(chain1[:q], chain1[:B]) + ╠═╡ =# + +# ╔═╡ e591eff0-fd70-43d3-bf2a-34309a8ecd62 +#=╠═╡ +begin + p = scatter(tmeas, Gmeas, xlab="t [h]", label="G [mg/dL]") + scatter!(tmeas, Imeas, label="I [μU/mL]") + N = length(sample_sols) + for i in 1:10 + n = rand(1:N) + plot!(sample_sols[n], lw=0.5, alpha=0.8, label="", color=[:blue :orange]) + end + p +end + ╠═╡ =# + +# ╔═╡ 04d6078e-f46b-43f2-988c-d91252b26747 +#=╠═╡ +sample_sols = generated_quantities(mod_data, chain1); + ╠═╡ =# + +# ╔═╡ 851e6a2f-3569-489d-b375-149329c68a7c +mapGI = optimize(mod_data, MAP(), NelderMead()) + +# ╔═╡ 246a06ba-ef48-47ba-aef0-51f07ceb96e4 + + +# ╔═╡ 403f6e68-e827-4885-830b-cb0d7f872ee0 +coeftable(mapGI) + +# ╔═╡ 2f992357-4608-40e6-9954-8306f31e9768 + + +# ╔═╡ 6ecda2c4-2a1d-4d24-b7b8-ec956a3e8d70 +#coeftable(mapG) + +# ╔═╡ Cell order: +# ╠═52b28a4c-b0bb-11ef-2841-17ecfb596676 +# ╠═7bc363b0-9415-4954-807f-81a308bde531 +# ╠═bfcc4b4e-073e-401e-851c-d01ef828028a +# ╠═e93bc1a5-e0b1-425c-b069-d5ce80756e60 +# ╠═2ac43184-a393-4d39-9c3b-c299c3371b09 +# ╟─75a5b5d9-f8d7-4728-83dc-03dde502dcfb +# ╠═f62c2b4a-a9e8-472b-b07b-44072da08ee8 +# ╠═99ccbd1b-b9e4-4afc-8d9a-8c1055bcce0f +# ╠═c319ae6e-2f02-4a7e-a0b0-4a3f57fdcb66 +# ╠═7623a596-d6d4-4e0a-b29c-f2f7de0d2940 +# ╠═0621968c-b39a-4346-a86a-42fa2cde724c +# ╠═3c1465d2-0886-4b74-baee-55c7dad41f9a +# ╠═afc40964-0a97-43a6-ab27-5fe96ecd319b +# ╠═bbbc3335-4190-4bc7-91ba-e96476a75751 +# ╠═f050b32e-1a14-4d5e-9fb3-5dbc4dfbf79c +# ╠═7e35b56b-44a0-46df-a812-f5fb437b672e +# ╠═00db9d76-c4dd-450d-b7e3-cf87f8bfeffb +# ╠═aab02fef-6d84-4f53-aff5-6f94bf2bd460 +# ╠═8a5ce760-55bb-4610-9226-32c3d8376748 +# ╟─a2fb8c21-c594-44f3-92df-99e6d3afeba1 +# ╠═ba68f740-ba8b-4efa-be2d-ac50c77dfa1a +# ╠═6890e3ec-0875-423e-89c1-988411c869e3 +# ╠═fb439f9d-ee88-43cd-b91b-44ed8013b27d +# ╠═095e359a-2ec4-4637-8477-93510bef23ed +# ╠═31aaced7-1fe4-4117-80f3-0fa70035822a +# ╠═69e21e9b-7d0e-44e3-8b33-ee7102dadadf +# ╠═b4073e81-6db8-4be6-a2d1-afa01640dbcf +# ╠═4d58a832-9157-42fe-b578-c3fc29f01ea8 +# ╠═7cf11e6f-7ef4-478f-8cc7-eae93374cc58 +# ╠═5eda8c4a-2baa-4987-b408-dbe7383abe95 +# ╠═34788b1d-1530-4b88-8690-03fe9af52a8b +# ╠═f616da2f-b51e-4328-bd3c-47e6d7377cbb +# ╠═97636a73-4732-4377-b760-c36cef13904b +# ╠═a67d70ee-c8b5-4f22-926c-f48c5dcf9815 +# ╠═1bb5834a-6a4e-40ec-82c1-f2c505ecfeb8 +# ╠═a3156073-07bd-4f13-be5e-d19483fbad28 +# ╠═0ae57436-0b8c-41ce-9d9d-8c48ed59b820 +# ╠═87d9c826-56af-409a-a884-d784cfa16a64 +# ╠═4d95e77b-fab0-454b-8319-1fe83e12f9e9 +# ╠═ea46f5f9-47a8-4641-a7e3-08a1a29cd04f +# ╟─870e9229-374a-40b8-97f7-1a84d1a857e9 +# ╠═e37ce327-504b-4fe4-baea-493cda834b4a +# ╠═e66378f7-8ec8-4f7f-ab40-5c64479f865e +# ╠═bcafb5c2-4f3c-47f4-b786-8f656969abe6 +# ╠═08d3cf6e-dc0b-4a56-a241-0d0033e79fad +# ╠═c0d39fc8-d779-465e-91c1-3a6f9b694ee3 +# ╠═c2c18077-add0-4ff9-a122-f248dbd1da79 +# ╠═77860f25-1b30-4cf1-812a-03ff2100bacd +# ╠═e93a2495-aa5b-46f6-ae3c-b94559583c60 +# ╠═55e4db93-f376-4cbb-829d-fea9ce3f3998 +# ╠═8989e653-e3e8-4e4f-8fc2-596e931ed21c +# ╠═b763bb0c-581e-46ec-8104-53df25369642 +# ╠═5e187f36-3883-4f08-b08c-a55d24e409cd +# ╠═2bf57ee8-ac1d-412f-a4c8-6e4ce87a74c5 +# ╠═c897d6e6-0b33-4dfb-89f3-f7e05bb9f73b +# ╠═aa32db53-c944-442a-88df-5937f380b54c +# ╠═7b247ff1-f873-4b00-90c3-4c7a87485fb2 +# ╠═e591eff0-fd70-43d3-bf2a-34309a8ecd62 +# ╠═04d6078e-f46b-43f2-988c-d91252b26747 +# ╠═851e6a2f-3569-489d-b375-149329c68a7c +# ╠═246a06ba-ef48-47ba-aef0-51f07ceb96e4 +# ╠═e96779da-57c0-4c11-b3ab-40dc5ae81bee +# ╠═403f6e68-e827-4885-830b-cb0d7f872ee0 +# ╠═2f992357-4608-40e6-9954-8306f31e9768 +# ╠═6ecda2c4-2a1d-4d24-b7b8-ec956a3e8d70 diff --git a/examples/insuline_sensitivity.jl b/examples/insuline_sensitivity.jl index 89bf4a58..d63feea8 100644 --- a/examples/insuline_sensitivity.jl +++ b/examples/insuline_sensitivity.jl @@ -25,15 +25,6 @@ end # ╔═╡ 52b28a4c-b0bb-11ef-2841-17ecfb596676 using Plots, PlutoUI, DifferentialEquations, ForwardDiff, Catalyst -# ╔═╡ 77860f25-1b30-4cf1-812a-03ff2100bacd -using Turing - -# ╔═╡ c897d6e6-0b33-4dfb-89f3-f7e05bb9f73b -using StatsPlots, Optim - -# ╔═╡ e96779da-57c0-4c11-b3ab-40dc5ae81bee -using StatsBase - # ╔═╡ bfcc4b4e-073e-401e-851c-d01ef828028a md""" # The minimal glucose model and dynamic compensation @@ -199,111 +190,12 @@ end ``` """ -# ╔═╡ e37ce327-504b-4fe4-baea-493cda834b4a -md" this does not work yet. Split and use different model: https://allendowney.github.io/ModSimPy/chap18.html" - -# ╔═╡ e66378f7-8ec8-4f7f-ab40-5c64479f865e -tmeas = 0:2:8 - -# ╔═╡ bcafb5c2-4f3c-47f4-b786-8f656969abe6 -length(tmeas) - -# ╔═╡ 08d3cf6e-dc0b-4a56-a241-0d0033e79fad -Gmeas = [92, 350, 287, 251, 240] - -# ╔═╡ c0d39fc8-d779-465e-91c1-3a6f9b694ee3 -Imeas = [11, 26, 130, 85, 51] - -# ╔═╡ c2c18077-add0-4ff9-a122-f248dbd1da79 -begin - scatter(tmeas, Gmeas, xlab="t [h]", label="G [mg/dL]") - scatter!(tmeas, Imeas, label="I [μU/mL]") -end - -# ╔═╡ e93a2495-aa5b-46f6-ae3c-b94559583c60 -@model function glucose_inference(tmeas, Gmeas, Imeas) - @assert length(tmeas) == length(Gmeas) == length(Imeas) - N = length(tmeas) - σGsq ~ Gamma(5) - σIsq ~ Gamma(3) - q~10LogNormal() - s~10LogNormal() - γ~10LogNormal() - B=1 - m~10LogNormal() - Ks~10LogNormal() - G0~100LogNormal() - I0~1LogNormal() - prob = remake(oprob1; u0=[G=>G0, I=>I0], tspan=(0., 8.), - p=[:m=>m, :q=>q, :s=>s, - :γ=>γ, :Ks=>Ks, :B=>B]) - sol = solve(prob, saveat=tmeas) - for i in 1:N - Gmeas[i] ~ Normal(sol[G][i], sqrt(σGsq)) - Imeas[i] ~ Normal(sol[I][i], sqrt(σIsq)) - end - return sol -end - -# ╔═╡ 55e4db93-f376-4cbb-829d-fea9ce3f3998 -glucose_inference(tmeas, Gmeas, Imeas)() - -# ╔═╡ 8989e653-e3e8-4e4f-8fc2-596e931ed21c -mod_data = glucose_inference(tmeas, Gmeas, Imeas) - -# ╔═╡ b763bb0c-581e-46ec-8104-53df25369642 -mod_data() |> plot - -# ╔═╡ 5e187f36-3883-4f08-b08c-a55d24e409cd -chain1 = sample(mod_data, NUTS(), 100) - -# ╔═╡ 2bf57ee8-ac1d-412f-a4c8-6e4ce87a74c5 -summarize(chain1) - -# ╔═╡ aa32db53-c944-442a-88df-5937f380b54c -#=╠═╡ -plot(chain1) - ╠═╡ =# - -# ╔═╡ 7b247ff1-f873-4b00-90c3-4c7a87485fb2 -#=╠═╡ -scatter(chain1[:q], chain1[:B]) - ╠═╡ =# - -# ╔═╡ e591eff0-fd70-43d3-bf2a-34309a8ecd62 -#=╠═╡ -begin - p = scatter(tmeas, Gmeas, xlab="t [h]", label="G [mg/dL]") - scatter!(tmeas, Imeas, label="I [μU/mL]") - N = length(sample_sols) - for i in 1:10 - n = rand(1:N) - plot!(sample_sols[n], lw=0.5, alpha=0.8, label="", color=[:blue :orange]) - end - p -end - ╠═╡ =# - -# ╔═╡ 04d6078e-f46b-43f2-988c-d91252b26747 -#=╠═╡ -sample_sols = generated_quantities(mod_data, chain1); - ╠═╡ =# - -# ╔═╡ 851e6a2f-3569-489d-b375-149329c68a7c -mapGI = optimize(mod_data, MAP(), NelderMead()) - # ╔═╡ 246a06ba-ef48-47ba-aef0-51f07ceb96e4 -# ╔═╡ 403f6e68-e827-4885-830b-cb0d7f872ee0 -coeftable(mapGI) - # ╔═╡ 2f992357-4608-40e6-9954-8306f31e9768 -# ╔═╡ 6ecda2c4-2a1d-4d24-b7b8-ec956a3e8d70 -#coeftable(mapG) - # ╔═╡ Cell order: # ╠═52b28a4c-b0bb-11ef-2841-17ecfb596676 # ╠═7bc363b0-9415-4954-807f-81a308bde531 @@ -346,27 +238,5 @@ coeftable(mapGI) # ╠═4d95e77b-fab0-454b-8319-1fe83e12f9e9 # ╠═ea46f5f9-47a8-4641-a7e3-08a1a29cd04f # ╟─870e9229-374a-40b8-97f7-1a84d1a857e9 -# ╠═e37ce327-504b-4fe4-baea-493cda834b4a -# ╠═e66378f7-8ec8-4f7f-ab40-5c64479f865e -# ╠═bcafb5c2-4f3c-47f4-b786-8f656969abe6 -# ╠═08d3cf6e-dc0b-4a56-a241-0d0033e79fad -# ╠═c0d39fc8-d779-465e-91c1-3a6f9b694ee3 -# ╠═c2c18077-add0-4ff9-a122-f248dbd1da79 -# ╠═77860f25-1b30-4cf1-812a-03ff2100bacd -# ╠═e93a2495-aa5b-46f6-ae3c-b94559583c60 -# ╠═55e4db93-f376-4cbb-829d-fea9ce3f3998 -# ╠═8989e653-e3e8-4e4f-8fc2-596e931ed21c -# ╠═b763bb0c-581e-46ec-8104-53df25369642 -# ╠═5e187f36-3883-4f08-b08c-a55d24e409cd -# ╠═2bf57ee8-ac1d-412f-a4c8-6e4ce87a74c5 -# ╠═c897d6e6-0b33-4dfb-89f3-f7e05bb9f73b -# ╠═aa32db53-c944-442a-88df-5937f380b54c -# ╠═7b247ff1-f873-4b00-90c3-4c7a87485fb2 -# ╠═e591eff0-fd70-43d3-bf2a-34309a8ecd62 -# ╠═04d6078e-f46b-43f2-988c-d91252b26747 -# ╠═851e6a2f-3569-489d-b375-149329c68a7c # ╠═246a06ba-ef48-47ba-aef0-51f07ceb96e4 -# ╠═e96779da-57c0-4c11-b3ab-40dc5ae81bee -# ╠═403f6e68-e827-4885-830b-cb0d7f872ee0 # ╠═2f992357-4608-40e6-9954-8306f31e9768 -# ╠═6ecda2c4-2a1d-4d24-b7b8-ec956a3e8d70 diff --git a/examples/iris_models.jl b/examples/iris_models.jl new file mode 100644 index 00000000..dce1ac9f --- /dev/null +++ b/examples/iris_models.jl @@ -0,0 +1,2733 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# ╔═╡ 8ff3f3a2-b954-11ef-36c3-b7ee53f18169 +using Statistics, DataFrames, CSV + +# ╔═╡ 442ba9c0-8889-4042-b762-12e712a39454 +using PlutoUI, Turing, Plots + +# ╔═╡ 511b6a4e-9f71-4f5c-a339-7180ed5a49d6 +path = joinpath(pkgdir(DataFrames), "docs", "src", "assets", "iris.csv"); + +# ╔═╡ 73e46529-bee5-4441-9032-21875fed3205 + iris = CSV.read(path, DataFrame) + +# ╔═╡ faa90341-f1c9-4ba2-9402-2bd90beb1582 +for (df) in groupby(iris, :Species) + println(describe(df)) +end + +# ╔═╡ e3b62465-67b8-437b-a2f1-c6d25d35be7c +setosa = iris[1:50,1:5] + +# ╔═╡ cc4db3e7-53f6-4a5c-b02c-fc614dd863ae +describe(setosa) + +# ╔═╡ 186cd276-e053-46b8-b78a-cb11527665ba +Matrix(setosa[!,1:4]) |> cov + +# ╔═╡ a2071b91-7731-4892-9c5c-f42def71be78 +sqrt(0.12 - 0.01/0.14) + +# ╔═╡ 1be97aba-fbd0-4e33-af34-277a25258e09 +cond_pars(μa,μb,Σaa, Σab, Σbb) = μa + Σab / Σbb * + +# ╔═╡ f9c475fb-6290-41a3-8adc-74b7978c3794 +@model function iris_setosa() + Sl ~ Normal(5, 0.35) + Sw ~ Normal(3.4+(Sl-5)*0.1/0.12, 0.22) + Pl ~ Uniform(1, 2) + Pw ~ Uniform(0.1, 0.6) +end + +# ╔═╡ 03050492-060c-4d96-8f13-928471c14661 +rand(iris_setosa()) + +# ╔═╡ f356378e-a3ee-40b0-b552-f3895aca3115 +versicolor = iris[51:100,1:5] + +# ╔═╡ 4a42186e-5047-4dac-9bb7-7e06c7998fd9 +describe(versicolor) + +# ╔═╡ 76b747a8-a35a-492c-9054-dc03ad847eef +cov(Matrix(versicolor[:,1:4])) + +# ╔═╡ 5b0e3a81-efb2-4678-abd3-a98dde3ce19c +@model function iris_versicolor() + Sl ~ Normal(5.93, 0.27) + Sw ~ Normal(2.77+0.085/0.098*(Sl-5.93), √(0.098 - 0.085^2/0.27)) + Pl ~ Normal(4.26+18(Sl-5.93)/27, √(0.22-0.18^2/0.26)) + Pw ~ Normal(1.33+0.073(Pl-4.26)/0.22, √(0.03-0.073^2/0.22)) +end + +# ╔═╡ f7cba63e-ea70-4f56-a33f-4fb50d026d87 +√(0.098 - 0.085^2/0.27) + +# ╔═╡ a679613f-c714-4722-ba8f-7f82109a2230 +rand(iris_versicolor()) + +# ╔═╡ 999da0e9-f80c-4da9-82a7-6449f22dfc90 +virginica = iris[101:150,1:5] + +# ╔═╡ 09b1610a-bf64-4db5-a95c-57f952b586d4 +describe(virginica) + +# ╔═╡ 1034df52-a8cf-4a96-904a-b3c5844bd587 +cov(Matrix(virginica[:,1:4])) + +# ╔═╡ 43c431de-cb55-4f3e-89c4-123bceb81ba2 +@model function iris_virginica() + Sl ~ Normal(6.588, 0.4) + Sw ~ Normal(2.2+0.094/0.4*(Sl-6.588), √(0.1 - 0.094^2/0.4)) + Pl ~ Normal(5.5+0.3(Sl-6.6)/0.4, √(0.3-0.3^2/0.4)) + Pw ~ Normal(1.4+0.04(Pl-5.5)/0.3, √(0.07-0.05^2/0.3)) +end + +# ╔═╡ a93ae961-5eea-4dbe-b16a-f3f54aa18f20 +rand(iris_virginica()) + +# ╔═╡ 475f7447-c1d7-40e7-a523-1f981ccc9981 +iris1 = (Sl=6.3, Sw=2.7, Pl=4.9, Pw=1.8) + +# ╔═╡ bd2f0804-f7cd-4253-9b47-8eca6a04dcfd +p_D1_setosa = exp(logprior(iris_setosa(), iris1)) + +# ╔═╡ 98f80d23-90dc-4206-bb97-9fd052dab8eb +p_D1_virginica = exp(logprior(iris_virginica(), iris1)) + +# ╔═╡ f964b986-d5bc-4efd-a437-a1e8adf7d93e +p_D2_versicolor = exp(logprior(iris_versicolor(), iris1)) + +# ╔═╡ 1fa08d98-1486-4b1b-a532-7dbe2cb78538 +p_versicolor_D1 = 1/3*p_D2_versicolor / (1/3*p_D1_setosa + 1/3*p_D1_virginica + 1/4*p_D2_versicolor) + +# ╔═╡ cd07dda5-6729-4ade-8a40-593cccc679e7 +md"Prior psetosa=0.1, pversicolor=.7, pvirginica=0.2" + +# ╔═╡ a1dde58c-561b-4f07-9fba-72d96cc77771 +p_versicolor_D1_unequalprior = 0.7p_D2_versicolor / (0.1p_D1_setosa + 0.2p_D1_virginica + 0.7p_D2_versicolor) + +# ╔═╡ 21608c4e-a58f-47d3-b8cb-b854d63c134d +iris2 = (;Sl=5.5, Sw=3.3) + +# ╔═╡ fd9fefc0-a97f-43c5-b57d-b6461d94b0fa +exp(logprior(iris_setosa() | (;Pw=1, Pl=2.0), iris2)) + +# ╔═╡ c54c8f74-e4ac-41f9-a6e9-1bbd15dfbff6 +exp(logprior(iris_virginica() | (;Pw=1, Pl=2.0), iris2)) + +# ╔═╡ 128a10b2-0e80-4e17-aac6-a0023f42ca95 +exp(logprior(iris_versicolor() | (;Pw=1, Pl=2.0), iris2)) + +# ╔═╡ 3a6e862a-1896-4418-8ad4-ef1802e77ad6 +chain = sample(iris_setosa() | iris2, NUTS(), 1000) + +# ╔═╡ d6924c52-8fa5-4745-a8e0-afafb4a9e720 +bayesfactor_setosa(Pl) = logprior(iris_setosa() | (;Pw=2.0), (;Sl=5.6, Sw=3.3, Pl)) - logprior(iris_versicolor() | (;Pw=2.0), (;Sl=5.6, Sw=3.3, Pl)) + +# ╔═╡ 62080edf-98c2-4dbd-ba21-6302c84e6b83 +plot(bayesfactor_setosa, 1, 2) + +# ╔═╡ 6e8c6716-8abf-4674-bbc4-2fb2af38b92a +summarize(chain) + +# ╔═╡ f50a68aa-aae8-4370-9b51-c93111dc2ef9 +iris[rand(1:150),:] + +# ╔═╡ a9f035c5-485e-456d-850e-ac0d0ffa90db + + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" + +[compat] +CSV = "~0.10.15" +DataFrames = "~1.7.0" +Plots = "~1.40.9" +PlutoUI = "~0.7.60" +Turing = "~0.35.3" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.3" +manifest_format = "2.0" +project_hash = "22225b836147842b02e8a2efda6df74a0b52460f" + +[[deps.ADTypes]] +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" +uuid = 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["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" +uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" +version = "1.1.1+0" + +[[deps.Xorg_libSM_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" +uuid = "c834827a-8449-5923-a945-d239c165b7dd" +version = "1.2.4+0" + +[[deps.Xorg_libX11_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" +uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" +version = "1.8.6+1" + +[[deps.Xorg_libXau_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a" +uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" +version = "1.0.11+1" + +[[deps.Xorg_libXcursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = 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+version = "1.7.10+4" + +[[deps.Xorg_libXinerama_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] +git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" +uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" +version = "1.1.4+4" + +[[deps.Xorg_libXrandr_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" +uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" +version = "1.5.2+4" + +[[deps.Xorg_libXrender_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" +uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" +version = "0.9.11+0" + +[[deps.Xorg_libpthread_stubs_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a" +uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" +version = "0.1.1+1" + +[[deps.Xorg_libxcb_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" +uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" +version = "1.17.0+1" + +[[deps.Xorg_libxkbfile_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" +uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" +version = "1.1.2+0" + +[[deps.Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.4+0" + +[[deps.Xorg_xcb_util_image_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] +git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_keysyms_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_renderutil_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" +version = "0.3.9+1" + +[[deps.Xorg_xcb_util_wm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" +version = "0.4.1+1" + +[[deps.Xorg_xkbcomp_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" +uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" +version = "1.4.6+0" + +[[deps.Xorg_xkeyboard_config_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" +uuid = "33bec58e-1273-512f-9401-5d533626f822" +version = "2.39.0+0" + +[[deps.Xorg_xtrans_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e" +uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +version = "1.5.0+1" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" + +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.6+1" + +[[deps.ZygoteRules]] +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.5" + +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.56.3+0" + +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+1" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.9.0+0" + +[[deps.libass_jll]] +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" +uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" +version = "0.15.2+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+1" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[deps.libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" +uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" +version = "2.0.3+0" + +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + +[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.44+0" + +[[deps.libvorbis_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" +uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +version = "1.3.7+2" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" + +[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+1" +""" + +# ╔═╡ Cell order: +# ╠═8ff3f3a2-b954-11ef-36c3-b7ee53f18169 +# ╠═442ba9c0-8889-4042-b762-12e712a39454 +# ╠═511b6a4e-9f71-4f5c-a339-7180ed5a49d6 +# ╠═73e46529-bee5-4441-9032-21875fed3205 +# ╠═faa90341-f1c9-4ba2-9402-2bd90beb1582 +# ╠═e3b62465-67b8-437b-a2f1-c6d25d35be7c +# ╠═cc4db3e7-53f6-4a5c-b02c-fc614dd863ae +# ╠═186cd276-e053-46b8-b78a-cb11527665ba +# ╠═a2071b91-7731-4892-9c5c-f42def71be78 +# ╠═1be97aba-fbd0-4e33-af34-277a25258e09 +# ╠═f9c475fb-6290-41a3-8adc-74b7978c3794 +# ╠═03050492-060c-4d96-8f13-928471c14661 +# ╠═f356378e-a3ee-40b0-b552-f3895aca3115 +# ╠═4a42186e-5047-4dac-9bb7-7e06c7998fd9 +# ╠═76b747a8-a35a-492c-9054-dc03ad847eef +# ╠═5b0e3a81-efb2-4678-abd3-a98dde3ce19c +# ╠═f7cba63e-ea70-4f56-a33f-4fb50d026d87 +# ╠═a679613f-c714-4722-ba8f-7f82109a2230 +# ╠═999da0e9-f80c-4da9-82a7-6449f22dfc90 +# ╠═09b1610a-bf64-4db5-a95c-57f952b586d4 +# ╠═1034df52-a8cf-4a96-904a-b3c5844bd587 +# ╠═43c431de-cb55-4f3e-89c4-123bceb81ba2 +# ╠═a93ae961-5eea-4dbe-b16a-f3f54aa18f20 +# ╠═475f7447-c1d7-40e7-a523-1f981ccc9981 +# ╠═bd2f0804-f7cd-4253-9b47-8eca6a04dcfd +# ╠═98f80d23-90dc-4206-bb97-9fd052dab8eb +# ╠═f964b986-d5bc-4efd-a437-a1e8adf7d93e +# ╠═1fa08d98-1486-4b1b-a532-7dbe2cb78538 +# ╠═cd07dda5-6729-4ade-8a40-593cccc679e7 +# ╠═a1dde58c-561b-4f07-9fba-72d96cc77771 +# ╠═21608c4e-a58f-47d3-b8cb-b854d63c134d +# ╠═fd9fefc0-a97f-43c5-b57d-b6461d94b0fa +# ╠═c54c8f74-e4ac-41f9-a6e9-1bbd15dfbff6 +# ╠═128a10b2-0e80-4e17-aac6-a0023f42ca95 +# ╠═3a6e862a-1896-4418-8ad4-ef1802e77ad6 +# ╠═d6924c52-8fa5-4745-a8e0-afafb4a9e720 +# ╠═62080edf-98c2-4dbd-ba21-6302c84e6b83 +# ╠═6e8c6716-8abf-4674-bbc4-2fb2af38b92a +# ╠═f50a68aa-aae8-4370-9b51-c93111dc2ef9 +# ╠═a9f035c5-485e-456d-850e-ac0d0ffa90db +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/examples/lotka_volterra.jl b/examples/lotka_volterra.jl new file mode 100644 index 00000000..a57f5e92 --- /dev/null +++ b/examples/lotka_volterra.jl @@ -0,0 +1,2964 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). +macro bind(def, element) + #! format: off + quote + local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local el = $(esc(element)) + global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) + el + end + #! format: on +end + +# ╔═╡ ac1e6158-d41f-11ef-07a3-bbf7014dbbcd +using Catalyst, DifferentialEquations, Plots + +# ╔═╡ b29ecd80-0e11-4501-a3bd-fbb778630072 +using PlutoUI + +# ╔═╡ 4dd925bf-d490-4b0a-8363-db376cbad00b +lotka_volterra = @reaction_network begin + α, 🐰 --> 2🐰 + β, 🦊 --> ∅ + γ, 🐰 + 🦊 --> 🦊 + 0.1🦊 +end + +# ╔═╡ f1d5bd29-2142-415a-84e2-2ab4e21cd0db +osys = convert(ODESystem, lotka_volterra, combinatoric_ratelaws=false) + +# ╔═╡ 9bfd05e1-6a66-40e9-ad2d-0b2911095647 +sol = solve(oprob, RK4()) + +# ╔═╡ 79212598-3858-43e5-af34-4059fea38246 +plot(sol) + +# ╔═╡ b051487d-12fc-4a38-b580-3379ddb1521d +plot(sol, idxs=(:🐰,:🦊), xlab="rabbits", ylab="foxes", arrow=true) + +# ╔═╡ 10880546-4f88-430c-8453-8a18fec6b611 +md"Can you adapt the model to include a carrying capacity of 20 for the rabbits?" + +# ╔═╡ 5449da57-bd43-4fa4-8519-ff0c91cf8001 +@bind showsol CheckBox() + +# ╔═╡ f4e99c48-acfc-4acc-a70f-c4d4d33c2d72 +showsol && md""" +``` +lotka_volterra = @reaction_network begin + α * (1 - 🐰/20), 🐰 --> 2🐰 + β, 🦊 --> ∅ + γ, 🐰 + 🦊 --> 🦊 + 0.1🦊 +end +``` +""" + +# ╔═╡ df247423-a290-440e-a87b-020584db645e +# ╠═╡ disabled = true +#=╠═╡ +oprob = ODEProblem(lotka_volterra, [:🐰=>10.0, :🦊 => 1.0], + (0.0, 50.0), [:α=>0.8, :β=>0.2, :γ=>0.6], combinatoric_ratelaws=false) + ╠═╡ =# + +# ╔═╡ a5acd96a-b759-4177-8097-a5f73ddda483 +oprob = ODEProblem(complete(osys), [:🐰=>10.0, :🦊 => 1.0], + (0.0, 50.0), [:α=>0.8, :β=>0.2, :γ=>0.6]) + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" +DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" + +[compat] +Catalyst = "~14.4.1" +DifferentialEquations = "~7.15.0" +Plots = "~1.40.9" +PlutoUI = "~0.7.23" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated 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+ +# ╔═╡ Cell order: +# ╠═ac1e6158-d41f-11ef-07a3-bbf7014dbbcd +# ╠═b29ecd80-0e11-4501-a3bd-fbb778630072 +# ╠═4dd925bf-d490-4b0a-8363-db376cbad00b +# ╠═f1d5bd29-2142-415a-84e2-2ab4e21cd0db +# ╠═df247423-a290-440e-a87b-020584db645e +# ╠═a5acd96a-b759-4177-8097-a5f73ddda483 +# ╠═9bfd05e1-6a66-40e9-ad2d-0b2911095647 +# ╠═79212598-3858-43e5-af34-4059fea38246 +# ╠═b051487d-12fc-4a38-b580-3379ddb1521d +# ╟─10880546-4f88-430c-8453-8a18fec6b611 +# ╟─5449da57-bd43-4fa4-8519-ff0c91cf8001 +# ╟─f4e99c48-acfc-4acc-a70f-c4d4d33c2d72 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/examples/phosphorous.jl b/examples/phosphorous.jl new file mode 100644 index 00000000..d04755e8 --- /dev/null +++ b/examples/phosphorous.jl @@ -0,0 +1,3072 @@ +### A Pluto.jl notebook ### +# v0.19.43 + +using Markdown +using InteractiveUtils + +# ╔═╡ 331bb76c-984f-11ef-1770-fbcc0b6a2078 +using Plots, ForwardDiff, Measurements + +# ╔═╡ f51e8425-6dc4-46b8-b71b-1646928b2a39 +using Turing + +# ╔═╡ e72b1480-460c-4ae0-9b66-96b2b006a460 +using StatsPlots + +# ╔═╡ 3ff5a0ef-72b3-4b45-b74f-b2e7830d60b2 +using GlobalSensitivity + +# ╔═╡ 26e86a44-44fc-45a6-8dc4-746f6f52169c +md""" + +# Phosphorous + +The Vollenweider formula is a simple empirical model of water quality: + +$$P = \frac{L/q}{1+\sqrt{z/q}}$$ + +with +- $P [mg/m^3]$ the phosphorous concentration; +- $L [mg/m^2 a]$ annual phosphorous loading rate; +- $z [m]$ mean water depth; +- $q [m/a]$ annual hydraulic loading. + + +As parameter values, you can take $L=680$ mg/m$^3a$, $q=10.6$ m/a and $z=84$ m. As possible ranges, assume $L$ in [500, 900], $q$ in [8, 13.5] and $z$ in [81, 87]. + +1. Compute the effect of measurement errors. Assume a standard error of 10% of the measurement value for each parameter. Compute the standard error on $P$ when only one of the parameters has uncertainty and when all the parameters together are uncertain. Which parameter has the largest contribution to the error? +2. Compute the (normalized) local sensitivity index for each parameter. +3. Using a simple Turing.jl model, perform a MC analysis where each parameter is drawn from a symmetric triangular distribution with the given ranges. Make a histogram of the outcomes of $P$. Next, fix each parameter seprately and draw the histogram where the other parameters are uncertain. +4. Perform a Sobol sensitivity analysis. +""" + +# ╔═╡ adccba9f-c21c-4bdc-9f94-7e41b19905b9 +P(L, q, z) = (L/q) / (1 + √(z/q)) + +# ╔═╡ 2111abf0-1686-4f91-b584-faf7edd66764 +L = 680 + +# ╔═╡ e166d062-79d0-443d-9204-f8954865089b +q = 10.6 + +# ╔═╡ 864c170e-6651-4897-a2e5-c303fd026b95 +z = 84 + +# ╔═╡ 06bc367b-8791-430d-8f3a-1627f9a2293d +P(L, q, z) + +# ╔═╡ 27173d9d-f8cf-49a2-9e75-7e53d4fd69b3 +md"## Error" + +# ╔═╡ 56400fdf-4030-4de1-a602-7fea1337f56a +P(L ± 0.1L, q, z) + +# ╔═╡ 2641bf6d-d51d-4b95-99c4-0bb62887d126 +P(L, q ± 0.1q, z) + +# ╔═╡ 0777722d-1518-488f-8d1e-a88723b7e80f +P(L, q, z ± 0.1z) + +# ╔═╡ 530af759-e315-4bd6-a721-0596923684be +P(L ± 0.1L, q ± 0.1q, z ± 0.1z) + +# ╔═╡ 74667497-6366-434e-b222-e0c3e9b9382c +md"## Local sensitivity" + +# ╔═╡ fcd25d5f-b699-4358-9ea9-cdaf61dbd0d3 +s_L = ForwardDiff.derivative(L->P(L, q, z), L) * L / P(L, q, z) + +# ╔═╡ 1ec8563f-6591-4856-b6d2-8144539ecb5d +s_q = ForwardDiff.derivative(q->P(L, q, z), q) * q / P(L, q, z) + +# ╔═╡ 287d6180-d703-4093-bea6-5c3c9e279c3b +s_z = ForwardDiff.derivative(z->P(L, q, z), z) * z / P(L, q, z) + +# ╔═╡ 4cb30337-135f-4f85-b592-fe9b36f61adc +# in one go +ForwardDiff.gradient(((L, q, z),) -> P(L, q, z), [L, q, z]) ./ P(L, q, z) .* [L, q, z] + +# ╔═╡ 6423c5d2-c911-439a-bdf6-7a2aa2cff4a8 +md" ## Sampling" + +# ╔═╡ faac3047-1207-404f-8191-b4cca62546af +@model function vollenweider(;L=missing, q=missing, z=missing) + L ~ TriangularDist(500.0, 900.0) + q ~ TriangularDist(8, 13.5) + z ~ TriangularDist(81.0, 87.0) + return P(L, q, z) +end + +# ╔═╡ de55f46a-e756-4f0d-81f1-f3aff3767110 +sampler_all = vollenweider() + +# ╔═╡ 66da0499-6af4-44b0-90ef-e408624bc8e3 +sampler_L_fixed = vollenweider(L=L) + +# ╔═╡ 335cfab5-ed1f-49c3-97bd-f2e7bb853b88 +sampler_q_fixed = vollenweider(q=q) + +# ╔═╡ c5ab8899-8799-41e4-b053-023a6f85d327 +sampler_z_fixed = vollenweider(z=z) + +# ╔═╡ 81728cba-1bbf-432e-bef4-47ef34317d7c +all_free = [sampler_all() for i in 1:10000] + +# ╔═╡ c5703b40-7947-4ff3-b44f-ba7621cdfa29 +L_fixed = [sampler_L_fixed() for i in 1:10000] + +# ╔═╡ 5c5bc74e-f756-44a4-8419-db5660d1c3d9 +z_fixed = [sampler_z_fixed() for i in 1:10000] + +# ╔═╡ d73f02fb-1592-497f-bcbc-6553756be05d +q_fixed = [sampler_q_fixed() for i in 1:10000] + +# ╔═╡ 0009ac3d-fa1a-4820-a47f-742ad225c16f +histogram(L_fixed, xlab="P", title="P uncertain") + +# ╔═╡ 6acfc674-2280-4389-a973-c62a97437415 +histogram(z_fixed, xlab="P", title="L fixed") + +# ╔═╡ 3c7c0bb2-a954-46f4-ad77-9e833b9a3ba9 +histogram(q_fixed, xlab="P", title="z fixed") + +# ╔═╡ 3eaf0b53-1178-4544-a23d-80782958192d +histogram(q_fixed, xlab="P", title="q fixed") + +# ╔═╡ d49f1e99-e000-4775-ac36-7c79be76b5d1 +boxplot([all_free, L_fixed, q_fixed, z_fixed], ylab="P", label=["free" "L fixed" "q fixed" "z fixed"]) + +# ╔═╡ 1007658c-c505-456e-a14e-86bb32798789 +md"## Sobol" + +# ╔═╡ 60c82bad-5807-45b0-9d57-c6b0826127ce +p_range = [[500.0, 900.0], [8, 13.5], [81.0, 87.0]] + +# ╔═╡ 4392f6dd-8e61-45e4-a724-26a0f8e3c5c3 +sobol = gsa(((L, q, z),) -> P(L, q, z), Sobol(), p_range, samples=10_000) + +# ╔═╡ 690cefe7-46d2-4e14-a4a8-014c88d84d94 +sobol.S1 + +# ╔═╡ 6bd7ebaf-bc76-4c2c-bdf5-0fbc1a8d4859 +sobol.ST + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" +GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f" +Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" + +[compat] +ForwardDiff = "~0.10.36" +GlobalSensitivity = "~2.7.0" +Measurements = "~2.11.0" +Plots = "~1.40.8" +StatsPlots = "~0.15.7" +Turing = "~0.34.1" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.3" +manifest_format = "2.0" 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"1.4.6+0" + +[[deps.Xorg_xkeyboard_config_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" +uuid = "33bec58e-1273-512f-9401-5d533626f822" +version = "2.39.0+0" + +[[deps.Xorg_xtrans_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +version = "1.5.0+0" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" + +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.6+1" + +[[deps.ZygoteRules]] +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.5" + +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.53.0+0" + +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.9.0+0" + +[[deps.libass_jll]] +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" +uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" 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"ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + +[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.44+0" + +[[deps.libvorbis_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" +uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +version = "1.3.7+2" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" + +[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+1" +""" + +# ╔═╡ Cell order: +# ╠═331bb76c-984f-11ef-1770-fbcc0b6a2078 +# ╟─26e86a44-44fc-45a6-8dc4-746f6f52169c +# ╠═adccba9f-c21c-4bdc-9f94-7e41b19905b9 +# ╠═2111abf0-1686-4f91-b584-faf7edd66764 +# ╠═e166d062-79d0-443d-9204-f8954865089b +# ╠═864c170e-6651-4897-a2e5-c303fd026b95 +# ╠═06bc367b-8791-430d-8f3a-1627f9a2293d +# ╠═27173d9d-f8cf-49a2-9e75-7e53d4fd69b3 +# ╠═56400fdf-4030-4de1-a602-7fea1337f56a +# ╠═2641bf6d-d51d-4b95-99c4-0bb62887d126 +# ╠═0777722d-1518-488f-8d1e-a88723b7e80f +# ╠═530af759-e315-4bd6-a721-0596923684be +# ╠═74667497-6366-434e-b222-e0c3e9b9382c +# ╠═fcd25d5f-b699-4358-9ea9-cdaf61dbd0d3 +# ╠═1ec8563f-6591-4856-b6d2-8144539ecb5d +# ╠═287d6180-d703-4093-bea6-5c3c9e279c3b +# ╠═4cb30337-135f-4f85-b592-fe9b36f61adc +# ╠═6423c5d2-c911-439a-bdf6-7a2aa2cff4a8 +# ╠═f51e8425-6dc4-46b8-b71b-1646928b2a39 +# ╠═faac3047-1207-404f-8191-b4cca62546af +# ╠═de55f46a-e756-4f0d-81f1-f3aff3767110 +# ╠═66da0499-6af4-44b0-90ef-e408624bc8e3 +# ╠═335cfab5-ed1f-49c3-97bd-f2e7bb853b88 +# ╠═c5ab8899-8799-41e4-b053-023a6f85d327 +# ╠═81728cba-1bbf-432e-bef4-47ef34317d7c +# ╠═c5703b40-7947-4ff3-b44f-ba7621cdfa29 +# ╠═5c5bc74e-f756-44a4-8419-db5660d1c3d9 +# ╠═d73f02fb-1592-497f-bcbc-6553756be05d +# ╠═0009ac3d-fa1a-4820-a47f-742ad225c16f +# ╠═6acfc674-2280-4389-a973-c62a97437415 +# ╠═3c7c0bb2-a954-46f4-ad77-9e833b9a3ba9 +# ╠═3eaf0b53-1178-4544-a23d-80782958192d +# ╠═e72b1480-460c-4ae0-9b66-96b2b006a460 +# ╠═d49f1e99-e000-4775-ac36-7c79be76b5d1 +# ╠═1007658c-c505-456e-a14e-86bb32798789 +# ╠═3ff5a0ef-72b3-4b45-b74f-b2e7830d60b2 +# ╠═60c82bad-5807-45b0-9d57-c6b0826127ce +# ╠═4392f6dd-8e61-45e4-a724-26a0f8e3c5c3 +# ╠═690cefe7-46d2-4e14-a4a8-014c88d84d94 +# ╠═6bd7ebaf-bc76-4c2c-bdf5-0fbc1a8d4859 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/examples/poppies.jl b/examples/poppies.jl new file mode 100644 index 00000000..cfdea560 --- /dev/null +++ b/examples/poppies.jl @@ -0,0 +1,116 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# ╔═╡ 57420478-d744-11ef-2ec5-735d47866238 +import Pkg; Pkg.activate("..") + +# ╔═╡ 6261bb1a-5f73-4c9d-8ca9-a52f51bd9c2e +using Plots, Turing, PlutoUI, StatsPlots + +# ╔═╡ dc1fe99a-c3fc-4c3c-b149-5283dd581f6e +md""" +# Poppy inference 🌺 + +A farmer has a long field of 1 km. He knows that at some point, the soil type switches from sandy soil to clay-dominated soil. To estimate the point where the soil type switches, the farmer looks at the vegetation. Poppies are known to prefer sand-rich soils over clay. The farmer takes a look over the transect and notes the x-coordinate of where he found poppies sprouting. +""" + +# ╔═╡ ed7a6888-f104-4513-91c0-6ab0f7c5ba65 +poppy_locations = [ +8.39358, +80.4798, +118.559, +177.407, +274.531, +309.858, +384.819, +388.152, +447.347, +544.646, +604.76, +641.367, +] + +# ╔═╡ ec80dad4-20a7-4d29-a4d6-3ea4da8c7f43 +scatter(poppy_locations, zeros(length(poppy_locations)), color="red", xlab="x [m]", xlims=[0,1000], yaxis=false, label="poppy location") + +# ╔═╡ f0c2a3f9-f03c-482d-9df0-8f780e192557 +md""" +1. Can you infer the location where the soil switches type using Bayesian reasoning? Logically, this point should be between after the last poppy and before 1000 m. Give the 95% credibility interval! +""" + +# ╔═╡ 7c871370-5266-4b50-8971-c7e865990580 +@model function poppies(locations) + # sample boundary + x_boundary ~ missing + + # number of poppies + n = missing + + for i in 1:n + # sample location + locations[i] ~ missing + end +end + +# ╔═╡ d2843d5a-97d9-4b49-b55d-07a3ee3a432f +md""" + +Additional questions (you need to modify the model): +2. The farmer is quite sure the transition spot is between 600 and 1000 meter, with its most likely value at 700 meter. Can you incorportate this information? +3. Can you estimate $\lambda$, the expected number of poppies per meter? Using a Bayesian approach, you can take TriangularDist(0, 0.1) as a prior. Hint: you need to treat the number of poppy locations `n` as a variable to condition on. + +""" + +# ╔═╡ 33d0742e-5bdb-4fa6-8fd5-01b7eee2b0ee +md"**Solution**" + +# ╔═╡ 3a48a515-4040-43ab-a18c-376312061eeb +@model function poppies_sol(locations, n) + # sample boundary + + #x_boundary ~ Uniform(maximum(locations), 1000) + x_boundary ~ TriangularDist(600, 1000, 700) + + λ ~ TriangularDist(0, 0.1) + + n ~ Poisson(λ * x_boundary) + + for i in 1:n + locations[i] ~ Uniform(0, x_boundary) + end +end + +# ╔═╡ aae1502f-f253-4891-8209-6583c5abe7ef +chain = sample(poppies_sol(poppy_locations, length(locations)), NUTS(), 10000) + +# ╔═╡ d7affc89-0d96-411e-a890-c0c45374053b +quantile(chain) + +# ╔═╡ a050822f-e2d1-4966-aec7-d3e95d5b9e37 +plot(chain) + +# ╔═╡ 621b0c2b-acbb-4a7d-bce7-aa37baf47fde +summarize(chain) + +# ╔═╡ eb1a46dd-a68e-476a-a33d-20036d1cbbce +23/674 + +# ╔═╡ Cell order: +# ╠═6261bb1a-5f73-4c9d-8ca9-a52f51bd9c2e +# ╠═57420478-d744-11ef-2ec5-735d47866238 +# ╠═dc1fe99a-c3fc-4c3c-b149-5283dd581f6e +# ╠═ed7a6888-f104-4513-91c0-6ab0f7c5ba65 +# ╠═ec80dad4-20a7-4d29-a4d6-3ea4da8c7f43 +# ╠═f0c2a3f9-f03c-482d-9df0-8f780e192557 +# ╠═7c871370-5266-4b50-8971-c7e865990580 +# ╠═d2843d5a-97d9-4b49-b55d-07a3ee3a432f +# ╠═33d0742e-5bdb-4fa6-8fd5-01b7eee2b0ee +# ╠═3a48a515-4040-43ab-a18c-376312061eeb +# ╠═aae1502f-f253-4891-8209-6583c5abe7ef +# ╠═d7affc89-0d96-411e-a890-c0c45374053b +# ╠═a050822f-e2d1-4966-aec7-d3e95d5b9e37 +# ╠═621b0c2b-acbb-4a7d-bce7-aa37baf47fde +# ╠═eb1a46dd-a68e-476a-a33d-20036d1cbbce diff --git a/makefigs.jl b/makefigs.jl index b2a243f7..180cd14c 100644 --- a/makefigs.jl +++ b/makefigs.jl @@ -6,19 +6,20 @@ fontscale = 1.5 notebooks = Dict( #"modelling_distributions.jl" => "probmod", - #"MCMC.jl" => "MCMC", + # "MCMC.jl" => "MCMC", #"simulation_tools.jl" => "simulation_tools", #"modelling_ODEs.jl" => "ODEs", #"optimization.jl" => "optimization", #"calibration.jl" => "calibration", # LV very unstable, might need to rerun several times "uncertainty.jl" => "uncertainty", - "hiptobesquare.jl" => "model_selection", + #"hiptobesquare.jl" => "model_selection", ) for (nb, dir) in notebooks # run notebook and generate a plots dict let + println("$dir : $nb") include(joinpath("scripts", nb)) for (name, pl) in plots Plots.scalefontsizes(fontscale) diff --git a/project/project_antibiotics.jl b/project/project_antibiotics.jl index 6ac2c042..4b38765d 100644 --- a/project/project_antibiotics.jl +++ b/project/project_antibiotics.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 1e078c8b-2df9-4646-b629-bac7f151e937 @@ -20,6 +22,9 @@ using Catalyst, DifferentialEquations # ╔═╡ 158c4ad8-a38b-4828-812f-1abce60695dc using SciMLSensitivity +# ╔═╡ 6785c1af-28e5-46b4-ba34-a8ab65be7ff8 +using ForwardDiff + # ╔═╡ 21357c48-f35d-11ee-23f8-2534bb1d82f4 begin @@ -93,8 +98,8 @@ md"### One dose of antibiotics" # ╔═╡ a2164307-6d18-4983-9aaa-25c8f5828655 md"We set some sensible parameter values:" -# ╔═╡ dea41d07-dedc-47a0-867b-ea5e503c2a50 -pars = [:r=>2.7, :K=>1e3, :θ=>0.2, :a=>0.2, :g=>log(2), :v=>5.3, :Ks=>4] +# ╔═╡ eab8adc0-e3c7-4693-990b-cb47e3d9c2cf +pars = [:r=>2.7, :K=>1e3, :θ=>0.2, :a=>0.2, :g=>log(2), :v=>5.3, :Ks=>4.] # ╔═╡ 556243a1-c387-4606-94d9-2dc06dfdc5f0 md"We can simulate the system. Let us assume an initial concentration of antibiotics $C_0$ at $t=0$ and see what the effect is." @@ -109,7 +114,7 @@ tspan = (0.0, 50.0) oprob = ODEProblem(antibiotics, [:C=>C0], tspan, pars); # ╔═╡ aa32c5e2-0f67-4910-a612-d958fa13169c -plot(solve(oprob, Rosenbrock23())) +plot(solve(oprob, RK4())) # ╔═╡ 4679507b-e6e4-4d39-8610-77141f7b82e0 md""" @@ -158,27 +163,44 @@ md"### Sensitivity analysis" # ╔═╡ a0bff583-53ee-4a76-8dea-93711b93ec4c md"We can explore the system further by performing a local sensitivity analysis. Let us explore two parameters: the effectivity of the antibiotics (given by parameter $K_s$, the concentration where it at half its maximal effectivty) and $a$, the fitness cost of the resistant bacteria. We only consider a single initial dose of antibiotics." -# ╔═╡ ae0e6fd3-c410-4c04-bf90-dcf1b8194441 +# ╔═╡ 1dc98bcc-c991-43f2-884e-ec6c20ee4554 begin - par_vector = [Dict(pars)[Symbol(p)] for p in parameters(antibiotics)] - - sensprob = ODEForwardSensitivityProblem(oprob.f, [500.0, 500.0, 50.0], tspan, par_vector) - senssol = solve(sensprob, saveat=0.2) - x, dp = extract_local_sensitivities(senssol) - -end; + tsteps = 0:0.1:30 + + S((Ks, a)) = solve(remake(oprob, p=[:Ks=>Ks, :a=>a]), RK4(), saveat=tsteps)[:S] + R((Ks, a)) = solve(remake(oprob, p=[:Ks=>Ks, :a=>a]), RK4(), saveat=tsteps)[:R] + + sens_S((Ks, a)) = ForwardDiff.jacobian(S, [Ks, a]) # sensitivity for susceptible bacteria + sens_R((Ks, a)) = ForwardDiff.jacobian(R, [Ks, a]) # sensitivity for resistant bacteria + +end + +# ╔═╡ c321d1b8-e22b-4e28-adfc-dc2b20d28083 +@bind Ks Slider(1.0:1.0:20, show_value=true, default=4) + +# ╔═╡ 9f856137-5a46-4a6d-be12-aa38f9e20642 +@bind a Slider(0:0.1:0.9, show_value=true, default=0.1) + +# ╔═╡ 5600d0fa-80ef-40c2-ae12-570c348d1f14 +md"Below is a simulation with the given parameters:" + +# ╔═╡ 7c18a27d-a738-4d04-b712-d87fd91828af +plot(tsteps, [S([Ks, a]) R([Ks, a])], label=["S" "R"], xlab="t", title="Bacterial load with Ks=$Ks and a=$a") -# ╔═╡ f460412b-e17b-46fb-ae62-748dd55e475e -plot(senssol.t, dp[end]', label=["S(t)" "R(t)" "C(t)"], xlab="t", title="Local sensitivity analysis of Ks", lw=2, ylab="sensitivity") +# ╔═╡ 3e1c9cd4-aa4e-4f29-8788-45708b94406f +md"Next, we perform a sensitivity analysis for Ks and a, respectively." + +# ╔═╡ 752a90ee-3e92-4426-b33c-9d65b8c465dc +plot(tsteps, [sens_S((Ks, a))[:,1] sens_R((Ks, a))[:,1]], label=["S" "R"], xlab="t", title="Sensitivity for Ks") # ╔═╡ d45219d2-183e-4ca1-89bc-34d0eae1419b md"We see here that $K_s$ greatly positively impacts both types of bacteria shortly after the the antibiotics has been removed. The greater $K_s$, the higher the antibiotics concentration needs to be to substantionally effect the bacterial density. The effect is the greatest for resistant bacteria. At longer time intervals, a small increase in $K_s$ give a positive effect on the susceptible bacteria and a negative effect on the resistant ones. Due to competition, this is a zero-sum game and if the susceptible bacteria are less harmed, they can easier take back a large share of the system." -# ╔═╡ 7c7608c3-1ec7-493e-ae31-6d02fe3531c7 -plot(senssol.t, dp[3]', label=["S(t)" "R(t)" "C(t)"], xlab="t", title="Local sensitivity analysis of fitness cost a", lw=2, ylab="sensitivity") +# ╔═╡ d5287aba-93ab-440a-9cb5-97d879f5af9b +plot(tsteps, [sens_S((Ks, a))[:,2] sens_R((Ks, a))[:,2]], label=["S" "R"], xlab="t", title="Sensitivity for a") # ╔═╡ c93ed717-dcfd-46f5-83c1-91d8eb7fa943 -md"Above, we see the effect of the fitness cost $a$, the decrease in growth rate the resistant bacteria show. Though the fitness cost only directly impacts the resistant bacteria, both are impacted due to competition. Just after the initial boom when the antibiotics have dissipated, there is a large negative local minimun for the resistant bacteria. After that, we see a strong negative effect for the resistant bacteria and, conversely, a positive effect for the susceptible ones." +md"Above, we see the effect of the fitness cost $a$, the decrease in growth rate the resistant bacteria show. Though the fitness cost only directly impacts the resistant bacteria, both are impacted due to competition. Just after the initial boom when the antibiotics have dissipated, there is a large negative local minimum for the resistant bacteria. After that, we see a strong negative effect for the resistant bacteria and, conversely, a positive effect for the susceptible ones." # ╔═╡ 60c63f1b-5a27-4539-a486-78c083457b0e md""" @@ -197,29 +219,38 @@ PLUTO_PROJECT_TOML_CONTENTS = """ [deps] Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" +ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" + +[compat] +Catalyst = "~14.4.1" +DifferentialEquations = "~7.15.0" +ForwardDiff = "~0.10.38" +Plots = "~1.40.9" +PlutoUI = "~0.7.60" +SciMLSensitivity = "~7.72.0" """ # ╔═╡ 00000000-0000-0000-0000-000000000002 PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.0" +julia_version = "1.10.3" manifest_format = "2.0" -project_hash = "dcfef334ea005c5012a604db9cc8aa6cc9f3e763" +project_hash = "a694337c1cd8ff504cbdc6890daf6a9ff22e851a" [[deps.ADTypes]] -git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.7" +version = "1.11.0" +weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] -[[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "d7832de8cf7af26abac741f10372080ac6cb73df" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.34.7" + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" + ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -243,11 +274,38 @@ git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "MacroTools"] +git-tree-sha1 = "e93c42e833e6d4bd28be7b3b56d8deb99fd51f25" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.40" + + [deps.Accessors.extensions] + AxisKeysExt = "AxisKeys" + DatesExt = "Dates" + IntervalSetsExt = "IntervalSets" + LinearAlgebraExt = "LinearAlgebra" + StaticArraysExt = "StaticArrays" + StructArraysExt = "StructArrays" + TestExt = "Test" + UnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -270,16 +328,21 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.18.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -287,15 +350,20 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "33207a8be6267bc389d0701e97a9bce6a4de68eb" +git-tree-sha1 = "2bf6e01f453284cb61c312836b4680331ddfc44b" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.9.2" +version = "1.11.0" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -306,15 +374,25 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "0.1.0" +version = "1.0.1" + + [deps.Atomix.extensions] + AtomixCUDAExt = "CUDA" + AtomixMetalExt = "Metal" + AtomixoneAPIExt = "oneAPI" + + [deps.Atomix.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "30b7ea34abc4fe816eb1a5f434a43da804836163" +git-tree-sha1 = "fc8d8197de6c69ad6fd01c255b6b386ca8199331" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.7.0" +version = "1.9.0" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -324,40 +402,72 @@ weakdeps = ["SparseArrays"] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.Bijections]] -git-tree-sha1 = "c9b163bd832e023571e86d0b90d9de92a9879088" +git-tree-sha1 = "d8b0439d2be438a5f2cd68ec158fe08a7b2595b7" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" -version = "0.1.6" +version = "0.1.9" [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" 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"BandedMatrices", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "98da8bd76b89a4ae1b8dde9fc6dcd75dcd6b5282" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.6.3" +version = "5.12.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" - BoundaryValueDiffEqOrdinaryDiffEqExt = "OrdinaryDiffEq" [deps.BoundaryValueDiffEq.weakdeps] ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" - OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" + +[[deps.BoundaryValueDiffEqCore]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "34c7d203f7a5002a7c27e69ae4f70f940cd22890" +uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" +version = "1.2.0" + +[[deps.BoundaryValueDiffEqFIRK]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "6305d58ba2f53faec7bf44dfba5b591b524254b0" +uuid = "85d9eb09-370e-4000-bb32-543851f73618" +version = "1.2.0" + +[[deps.BoundaryValueDiffEqMIRK]] +deps = ["ADTypes", "Adapt", 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"Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" - -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" +version = "1.18.2+1" [[deps.Cassette]] -git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" +git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" uuid = "7057c7e9-c182-5462-911a-8362d720325c" -version = "0.3.13" +version = "0.3.14" [[deps.Catalyst]] -deps = ["DataStructures", "DiffEqBase", "DocStringExtensions", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] -git-tree-sha1 = "8e7e57c2ed4ecfb798f5a8cb230a9dd84765e7b1" +deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] +git-tree-sha1 = "dafd059c1d80ba02006978cd05ea7264ff1f362e" uuid = "479239e8-5488-4da2-87a7-35f2df7eef83" -version = "13.5.1" +version = "14.4.1" [deps.Catalyst.extensions] + CatalystBifurcationKitExtension = "BifurcationKit" + CatalystCairoMakieExtension = "CairoMakie" + CatalystGraphMakieExtension = "GraphMakie" CatalystHomotopyContinuationExtension = "HomotopyContinuation" + CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability" [deps.Catalyst.weakdeps] + BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" + CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" + GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2" HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "291821c1251486504f6bae435227907d734e94d2" +git-tree-sha1 = "4312d7869590fab4a4f789e97bd82f0a04eaaa05" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.66.0" +version = "1.72.2" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" +git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.23.0" +version = "1.25.1" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -423,21 +535,21 @@ weakdeps = ["SparseArrays"] [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" +version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.25.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -457,9 +569,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.11" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -467,10 +579,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] -git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" +deps = ["Crayons", "PrecompileTools"] +git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.12" +version = "0.8.15" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -478,16 +590,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.15.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -496,13 +613,22 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.1.1+0" [[deps.CompositeTypes]] git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" version = "0.1.4" +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + [[deps.ConcreteStructs]] git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" uuid = "2569d6c7-a4a2-43d3-a901-331e8e4be471" @@ -510,19 +636,19 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.1" +version = "2.4.3" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] @@ -561,11 +687,17 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DelayDiffEq]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "dd3dfeca90deb4b38be9598d7c51cd558816e596" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] +git-tree-sha1 = "7123a01ba4ec2d4058bd14478afd5318c49ea6c1" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.45.1" +version = "5.52.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -574,12 +706,13 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "044648af911974c3928058c1f8c83f159dece274" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "b1e23a7fe7371934d9d538114a7e7166c1d09e05" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.145.6" +version = "6.161.0" [deps.DiffEqBase.extensions] + DiffEqBaseCUDAExt = "CUDA" DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] @@ -588,10 +721,12 @@ version = "6.145.6" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" [deps.DiffEqBase.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" @@ -600,21 +735,21 @@ version = "6.145.6" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "cf334da651a6e42c50e1477d6ab978f1b8be3057" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "f6bc598f21c7bf2f7885cff9b3c9078e606ab075" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.36.1" -weakdeps = ["OrdinaryDiffEq", "Sundials"] +version = "4.2.2" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "880d1fcf95e6492a4e7d65c2866dbdbf6580d4f8" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.21.0" +version = "5.24.0" weakdeps = ["ReverseDiff"] [deps.DiffEqNoiseProcess.extensions] @@ -634,15 +769,70 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "81042254a307980b8ab5b67033aca26c2e157ebb" +git-tree-sha1 = 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["ReverseDiff", "DiffResults"] + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.DispatchDoctor]] +deps = ["MacroTools", "Preferences"] +git-tree-sha1 = "f311fe66bfe4e38b2f1c8d1081f06920092b57aa" +uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" +version = "0.4.19" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.DispatchDoctor.extensions] + DispatchDoctorChainRulesCoreExt = "ChainRulesCore" + DispatchDoctorEnzymeCoreExt = "EnzymeCore" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -655,9 +845,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "22c595ca4146c07b16bcf9c8bea86f731f7109d2" +git-tree-sha1 = "7901a6117656e29fa2c74a58adb682f380922c47" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.108" +version = "0.25.116" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -676,33 +866,45 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "490392af2c7d63183bfa2c8aaa6ab981c5ba7561" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.6.7" +version = "0.7.14" + + [deps.DomainSets.extensions] + DomainSetsMakieExt = "Makie" + + [deps.DomainSets.weakdeps] + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.DynamicPolynomials]] -deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "30a1848c4f4fc35d1d4bbbd125650f6a11b5bc6c" +deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"] +git-tree-sha1 = "9a3ae38b460449cc9e7dd0cfb059c76028724627" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.5.7" +version = "0.6.1" -[[deps.EllipsisNotation]] -deps = ["StaticArrayInterface"] -git-tree-sha1 = "3507300d4343e8e4ad080ad24e335274c2e297a9" -uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.8.0" +[[deps.DynamicQuantities]] +deps = ["DispatchDoctor", "TestItems", "Tricks"] +git-tree-sha1 = "4923007a8e500f13be4c0119554776993c055ece" +uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" +version = "1.4.0" + + [deps.DynamicQuantities.extensions] + DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" + DynamicQuantitiesMeasurementsExt = "Measurements" + DynamicQuantitiesScientificTypesExt = "ScientificTypes" + DynamicQuantitiesUnitfulExt = "Unitful" + + [deps.DynamicQuantities.weakdeps] + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" @@ -710,19 +912,31 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] -git-tree-sha1 = "3fb48f9c18de1993c477457265b85130756746ae" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] +git-tree-sha1 = "f39747b06eb299ca32c237d8423f092a8391e60f" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.20" -weakdeps = ["SpecialFunctions"] +version = "0.13.28" [deps.Enzyme.extensions] + EnzymeBFloat16sExt = "BFloat16s" + EnzymeChainRulesCoreExt = "ChainRulesCore" + EnzymeGPUArraysCoreExt = "GPUArraysCore" + EnzymeLogExpFunctionsExt = "LogExpFunctions" EnzymeSpecialFunctionsExt = "SpecialFunctions" + EnzymeStaticArraysExt = "StaticArrays" + + [deps.Enzyme.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.EnzymeCore]] -git-tree-sha1 = "1bc328eec34ffd80357f84a84bb30e4374e9bd60" +git-tree-sha1 = "0cdb7af5c39e92d78a0ee8d0a447d32f7593137e" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.6" +version = "0.8.8" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -730,44 +944,54 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "32d418c804279c60dd38ac7868126696f3205a4f" +git-tree-sha1 = "b81b0143399acd84a2ed2a1fa0b4ab55e25ee625" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.102+0" +version = "0.0.172+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" +git-tree-sha1 = "8a4be429317c42cfae6a7fc03c31bad1970c310d" uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" -version = "0.0.20230411+0" +version = "0.0.20230411+1" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.2+0" +version = 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"53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -777,35 +1001,62 @@ version = "4.4.4+1" [[deps.FastAlmostBandedMatrices]] deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] -git-tree-sha1 = "9dc913faf8552fd09b92a0d7fcc25f1d5609d795" +git-tree-sha1 = "3f03d94c71126b6cfe20d3cbcc41c5cd27e1c419" uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" -version = "0.1.1" +version = "0.1.4" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.8" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" uuid = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a" version = "0.3.2" +[[deps.FastGaussQuadrature]] +deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "fd923962364b645f3719855c88f7074413a6ad92" +uuid = "442a2c76-b920-505d-bb47-c5924d526838" +version = "1.0.2" + [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f4102aab9c7df8691ed09f9c42e34f5ab5458ab9" +git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "2.0.3" +version = "2.0.4" + +[[deps.FastPower]] +git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" +uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" +version = "1.1.1" + + [deps.FastPower.extensions] + FastPowerEnzymeExt = "Enzyme" + FastPowerForwardDiffExt = "ForwardDiff" + FastPowerMeasurementsExt = "Measurements" + FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" + FastPowerReverseDiffExt = "ReverseDiff" + FastPowerTrackerExt = "Tracker" + + [deps.FastPower.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.11.0" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -813,20 +1064,27 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" +[[deps.FindFirstFunctions]] +git-tree-sha1 = "670e1d9ceaa4a3161d32fe2d2fb2177f8d78b330" +uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224" +version = "1.4.1" + [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "73d1214fec245096717847c62d389a5d2ac86504" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.22.0" +version = "2.26.2" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -837,9 +1095,9 @@ version = "0.8.5" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" +git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.96+0" +version = "2.15.0+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -848,9 +1106,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -858,21 +1116,21 @@ weakdeps = ["StaticArrays"] [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" +git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.1+0" +version = "2.13.3+1" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" +git-tree-sha1 = "846f7026a9decf3679419122b49f8a1fdb48d2d5" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.14+0" +version = "1.0.16+0" [[deps.FunctionProperties]] deps = ["Cassette", "DiffRules"] -git-tree-sha1 = "7b3faeaa8c624f2ad08221d3c3838c6b9af6bfc2" +git-tree-sha1 = "bf7c740307eb0ee80e05d8aafbd0c5a901578398" uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc" -version = "0.1.1" +version = "0.1.2" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -886,50 +1144,50 @@ uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" version = "0.1.3" [[deps.Functors]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d3e63d9fa13f8eaa2f06f64949e2afc593ff52c2" +deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"] +git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.10" +version = "0.5.2" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "fcb0584ff34e25155876418979d4c8971243bb89" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.9+0" +version = "3.4.0+2" [[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" +deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "Statistics"] +git-tree-sha1 = "86a185085bffbafb11c046f676ee876597b76b66" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "11.2.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.2.0" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "a846f297ce9d09ccba02ead0cae70690e072a119" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "8e30cd0b1934f03dd925416970061c1014c6686f" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.25.0" +version = "1.1.0" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "ddda044ca260ee324c5fc07edb6d7cf3f0b9c350" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "424c8f76017e39fdfcdbb5935a8e6742244959e8" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.5" +version = "0.73.10" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "278e5e0f820178e8a26df3184fcb2280717c79b1" +git-tree-sha1 = "b90934c8cb33920a8dc66736471dc3961b42ec9f" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.5+0" +version = "0.73.10+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -945,9 +1203,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.82.4+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -956,56 +1214,49 @@ version = "1.3.1" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" +version = "1.3.14+1" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "4f2b57488ac7ee16124396de4f2bbdd51b2602ad" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.0" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.Groebner]] -deps = ["AbstractAlgebra", "Combinatorics", "ExprTools", "Logging", "MultivariatePolynomials", "PrecompileTools", "PrettyTables", "Primes", "Printf", "Random", "SIMD", "TimerOutputs"] -git-tree-sha1 = "6b505ef15e55bdc5bb3ddbcfebdff1c9e67081e8" -uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.5.1" - -[[deps.GroupsCore]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "6df9cd6ee79fc59feab33f63a1b3c9e95e2461d5" -uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" -version = "0.4.2" - [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "c67b33b085f6e2faf8bf79a61962e7339a81129c" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.15" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.5.0+0" + +[[deps.HashArrayMappedTries]] +git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" +uuid = "076d061b-32b6-4027-95e0-9a2c6f6d7e74" +version = "0.2.0" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.25" [[deps.Hyperscript]] deps = ["Test"] @@ -1021,9 +1272,9 @@ version = "0.9.5" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" +git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.4" +version = "0.2.5" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1037,9 +1288,9 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[deps.Inflate]] -git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.4" +version = "0.1.5" [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" @@ -1047,10 +1298,10 @@ uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" version = "0.1.2" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.1.0+0" +version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1067,6 +1318,16 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsRecipesBaseExt = "RecipesBase" IntervalSetsStatisticsExt = "Statistics" +[[deps.InverseFunctions]] +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.17" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" @@ -1079,15 +1340,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.9" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.7.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1097,47 +1358,46 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.1.1+0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "1c4880cb70a5c6c87ea36deccc3d7f9e7969c18c" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"] +git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.56" +version = "1.0.62" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] -git-tree-sha1 = "c451feb97251965a9fe40bacd62551a72cc5902c" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "ed3b5f80be8fc7d1b0185edb862f2273e02cbec2" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.10.1" +version = "9.14.1" weakdeps = ["FastBroadcast"] - [deps.JumpProcesses.extensions] - JumpProcessFastBroadcastExt = "FastBroadcast" - [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" +git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.1" +version = "0.6.0" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "ed7167240f40e62d97c1f5f7735dea6de3cc5c49" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] +git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.18" -weakdeps = ["EnzymeCore"] +version = "0.9.31" +weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" + LinearAlgebraExt = "LinearAlgebra" + SparseArraysExt = "SparseArrays" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.6" +version = "0.9.8" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1146,16 +1406,16 @@ uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "aaafe88dccbd957a8d82f7d05be9b69172e0cee3" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.1+0" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.3" +version = "9.1.3" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1165,74 +1425,67 @@ version = "6.6.3" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" +git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +version = "0.0.34+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "18.1.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.2+3" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LabelledArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "d1f981fba6eb3ec393eede4821bca3f2b7592cd4" -uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.15.1" - -[[deps.LambertW]] -git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" -uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" -version = "0.4.6" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "e0b5cd21dc1b44ec6e64f351976f961e6f31d6c4" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.3" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.15" - -[[deps.Lazy]] -deps = ["MacroTools"] -git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" -uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" -version = "0.15.1" +version = "0.1.17" [[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "f289bee714e11708df257c57514585863aa02b33" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.10.0" -weakdeps = ["StaticArrays"] +version = "2.3.1" [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" LazyArraysStaticArraysExt = "StaticArrays" + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1246,95 +1499,111 @@ version = "1.0.0" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" +git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+1" +version = "3.2.2+2" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] +git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.6.0+0" +version = "1.7.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "df37206100d39f79b3376afb6b9cee4970041c61" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.51.1+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" +git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.1+0" +version = "2.40.2+2" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "4ab7581296671007fc33f07a721631b8855f4b1d" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" +git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.1+0" +version = "2.40.2+2" + +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "6f8e084deabe3189416c4e505b1c53e1b590cae8" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "9d5872d134bd33dd3e120767004f760770958863" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.22.1" +version = "2.38.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -1347,7 +1616,7 @@ version = "2.22.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -1360,9 +1629,9 @@ version = "2.22.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1379,15 +1648,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "8f6786d8b2b3248d79db3ad359ce95382d5a6df8" +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.170" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1401,9 +1670,9 @@ version = "0.1.4" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.1.0+0" +version = "2024.2.0+0" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1411,10 +1680,9 @@ uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" [[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.13" +version = "0.5.15" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1427,15 +1695,23 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MatrixFactorizations]] deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" +git-tree-sha1 = "16a726dba99685d9e94c8d0a8f655383121fc608" uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.2.0" +version = "3.0.1" +weakdeps = ["BandedMatrices"] + + [deps.MatrixFactorizations.extensions] + MatrixFactorizationsBandedMatricesExt = "BandedMatrices" [[deps.MaybeInplace]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "b1f2f92feb0bc201e91c155ef575bcc7d9cc3526" +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" -version = "0.1.2" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1446,7 +1722,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1463,22 +1739,30 @@ version = "1.2.0" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "11f35f9619c625c18454a94a9013e7d047501fbf" +deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "EnumX", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SCCNonlinearSolve", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "c497ca1ba15722a5009cd6571a7a618c60b98dc3" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.75.0" +version = "9.59.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" + MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" + MTKHomotopyContinuationExt = "HomotopyContinuation" + MTKInfiniteOptExt = "InfiniteOpt" + MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57" + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1487,15 +1771,15 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "dad7be0c92b688bf8f24af170825ccedc104b116" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.5" +version = "0.5.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "a3589efe0005fc4718775d8641b2de9060d23f73" +git-tree-sha1 = "a2710df6b0931f987530f59427441b21245d8f5e" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.4" +version = "1.6.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1510,38 +1794,42 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" [[deps.NNlib]] -deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "e0cea7ec219ada9ac80ec2e82e374ab2f154ae05" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "bdc9d30f151590aca0af22690f5ab7dc18a551cb" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.16" +version = "0.9.27" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] NNlibCUDAExt = "CUDA" NNlibEnzymeCoreExt = "EnzymeCore" + NNlibFFTWExt = "FFTW" + NNlibForwardDiffExt = "ForwardDiff" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.2" +version = "1.0.3" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "72b036b728461272ae1b1c3f7096cb4c319d8793" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.4.0" +version = "3.15.1" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -1549,11 +1837,10 @@ version = "3.4.0" NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" NonlinearSolveMINPACKExt = "MINPACK" + NonlinearSolveNLSolversExt = "NLSolvers" NonlinearSolveNLsolveExt = "NLsolve" NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" [deps.NonlinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" @@ -1561,22 +1848,43 @@ version = "3.4.0" FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" SIAMFANLEquations = 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NonlinearSolveBaseForwardDiffExt = "ForwardDiff" + NonlinearSolveBaseLineSearchExt = "LineSearch" + NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseSparseArraysExt = "SparseArrays" + NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + +[[deps.NonlinearSolveFirstOrder]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "a1ea35ab0bcc99753e26d574ba1e339f19d100fa" +uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" +version = "1.2.0" [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "195e0a19842f678dd3473ceafbe9d82dfacc583c" +git-tree-sha1 = "dfcc26739b1ffa3ab51fb16f01ba7eb144f7bc50" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.1" +version = "0.4.3" [[deps.OffsetArrays]] -git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e" +git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.0" +version = "1.15.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1591,12 +1899,12 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" +version = "0.8.1+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -1606,21 +1914,21 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = 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"UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "442e1e7ac27dd5ff8825c3fa62fbd1e86397974b" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.4" +version = "1.40.9" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1730,9 +2233,9 @@ version = "1.40.4" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] -git-tree-sha1 = "ab55ee1510ad2af0ff674dbcced5e94921f867a9" +git-tree-sha1 = "eba4810d5e6a01f612b948c9fa94f905b49087b0" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.59" +version = "0.7.60" [[deps.PoissonRandom]] deps = ["Random"] @@ -1741,16 +2244,16 @@ uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.4" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "b3e2bae88cf07baf0a051fe09666b8ef97aefe93" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = 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= "21216c6a-2e73-6563-6e65-726566657250" version = "1.4.3" -[[deps.PrettyTables]] -deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" -uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.1" - [[deps.Primes]] deps = ["IntegerMathUtils"] git-tree-sha1 = "cb420f77dc474d23ee47ca8d14c90810cafe69e7" @@ -1797,28 +2294,50 @@ deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[deps.PtrArrays]] -git-tree-sha1 = "077664975d750757f30e739c870fbbdc01db7913" +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.1.0" +version = "1.2.1" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", 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"729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.11.1" +weakdeps = ["Enzyme"] + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] @@ -1827,17 +2346,11 @@ git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7" uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" -[[deps.RandomExtensions]] -deps = ["Random", "SparseArrays"] -git-tree-sha1 = "b8a399e95663485820000f26b6a43c794e166a49" -uuid = "fb686558-2515-59ef-acaa-46db3789a887" -version = "0.4.4" - [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -1858,30 +2371,38 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "27ee1c03e732c488ecce1a25f0d7da9b5d936574" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.3.3" +version = "3.27.4" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] + RecursiveArrayToolsStructArraysExt = "StructArrays" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "c04dacfc546591d43c39dc529c922d6a06a5a694" +git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.22" +version = "0.2.23" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1914,32 +2435,32 @@ version = "1.15.3" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.5.1+0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" + +[[deps.SCCNonlinearSolve]] +deps = ["CommonSolve", "PrecompileTools", "Reexport", "SciMLBase", "SymbolicIndexingInterface"] +git-tree-sha1 = "0caf35e2204c9045ca203b147b5dac4fa8e1cf20" +uuid = "9dfe8606-65a1-4bb3-9748-cb89d1561431" +version = "1.0.0" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.5.0" - [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1947,18 +2468,19 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.42" +version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "09324a0ae70c52a45b91b236c62065f78b099c37" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "3e5a9c5d6432b77a271646b4ada2573f239ac5c4" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.15.2" +version = "2.70.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" SciMLBasePartialFunctionsExt = "PartialFunctions" SciMLBasePyCallExt = "PyCall" SciMLBasePythonCallExt = "PythonCall" @@ -1968,23 +2490,53 @@ version = "2.15.2" [deps.SciMLBase.weakdeps] ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" + [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.7" +version = "0.3.12" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLSensitivity]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote"] -git-tree-sha1 = "3b0fde1944502bd736bcdc3d0df577dddb54d189" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] +git-tree-sha1 = "9eff93778a5c61244027bfe9c4f016153bbbf156" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.51.0" +version = "7.72.0" + + [deps.SciMLSensitivity.extensions] + SciMLSensitivityMooncakeExt = "Mooncake" + + [deps.SciMLSensitivity.weakdeps] + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + +[[deps.SciMLStructures]] +deps = ["ArrayInterface"] +git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.6.1" + +[[deps.ScopedValues]] +deps = ["HashArrayMappedTries", "Logging"] +git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" +uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" +version = "1.3.0" [[deps.Scratch]] deps = ["Dates"] @@ -2012,25 +2564,22 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "df8266e0d4960d61325db8c54fad3fa95712b57e" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.4.0" +version = "1.12.3" +weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker", "Zygote"] [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" - SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" - SimpleNonlinearSolveStaticArraysExt = "StaticArrays" - - [deps.SimpleNonlinearSolve.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" + SimpleNonlinearSolveTrackerExt = "Tracker" + SimpleNonlinearSolveZygoteExt = "Zygote" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2055,12 +2604,33 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" + +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "010b3c44301805d1ede9159f449a351d61172aa6" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.9" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "cce98ad7c896e52bb0eded174f02fc2a29c38477" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "d79802152d958607f414f5447cb25e314db979c0" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.18.0" +version = "2.23.1" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2082,6 +2652,16 @@ git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" +[[deps.SparseMatrixColorings]] +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9" +uuid = "0a514795-09f3-496d-8182-132a7b665d35" +version = "0.4.10" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -2090,25 +2670,31 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" +git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.4.0" +version = "2.5.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "b366eb1eb68075745777d80861c6706c33f588ae" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.9" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.5.0" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -2117,9 +2703,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2" +git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.3" +version = "1.9.10" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2127,14 +2713,14 @@ weakdeps = ["ChainRulesCore", "Statistics"] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2143,110 +2729,126 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.7.0" [[deps.StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" +deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" +weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.SteadyStateDiffEq]] deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "a735fd5053724cf4de31c81b4e2cc429db844be5" +git-tree-sha1 = 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"SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "b0a5dce397b3bc5478ee1de3127878daa061db28" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.65.1" +version = "6.72.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "25349bf8f63aa36acbff5e3550a86e9f5b0ef682" +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.6" - -[[deps.StringManipulation]] -deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" -uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.5.7" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10" uuid = 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["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "e15f5a73f0d14b9079b807a9d1dac13e4302e997" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.24.0" +version = "4.26.1" [[deps.Sundials_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] -git-tree-sha1 = "04777432d74ec5bc91ca047c9e0e0fd7f81acdb6" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] +git-tree-sha1 = "ba4d38faeb62de7ef47155ed321dce40a549c305" uuid = 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"6cd993ab9bc5998272dd85ea57a6a5c75b373f76" +deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper", "WeakValueDicts"] +git-tree-sha1 = "bca944105ac43be732e3bdc38e39a4ce17391137" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "1.7.0" +version = "3.8.1" + + [deps.SymbolicUtils.extensions] + SymbolicUtilsLabelledArraysExt = "LabelledArrays" + SymbolicUtilsReverseDiffExt = "ReverseDiff" + + [deps.SymbolicUtils.weakdeps] + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils"] -git-tree-sha1 = "8d28ebc206dec9e250e21b9502a2662265897650" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "493c70c2a94a96dff97523afd2fb4ea7fd346b93" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.14.1" +version = "6.22.1" [deps.Symbolics.extensions] + SymbolicsForwardDiffExt = "ForwardDiff" + SymbolicsGroebnerExt = "Groebner" + SymbolicsLuxExt = "Lux" + SymbolicsNemoExt = "Nemo" + SymbolicsPreallocationToolsExt = ["PreallocationTools", "ForwardDiff"] SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" + Lux = "b2108857-7c20-44ae-9111-449ecde12c47" + Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a" + PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" [[deps.TOML]] @@ -2261,10 +2863,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2277,10 +2879,20 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" +[[deps.TermInterface]] +git-tree-sha1 = "d673e0aca9e46a2f63720201f55cc7b3e7169b16" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "2.0.0" + [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TestItems]] +git-tree-sha1 = "42fd9023fef18b9b78c8343a4e2f3813ffbcefcb" +uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe" +version = "1.0.0" + [[deps.ThreadingUtilities]] deps = ["ManualMemory"] git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" @@ -2289,9 +2901,9 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.26" [[deps.Tokenize]] git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" @@ -2300,33 +2912,29 @@ version = "0.5.29" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "5158100ed55411867674576788e710a815a0af02" +git-tree-sha1 = "c266e49953dadd0923caa17b3ea464ab6b97b3f2" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.34" +version = "0.2.37" weakdeps = ["PDMats"] [deps.Tracker.extensions] TrackerPDMatsExt = "PDMats" [[deps.TranscodingStreams]] -git-tree-sha1 = "5d54d076465da49d6746c647022f3b3674e64156" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.8" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.20" +version = "0.2.1" [[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +version = "0.1.9" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -2359,23 +2967,20 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "352edac1ad17e018186881b051960bfca78a075a" +git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.19.1" +version = "1.22.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.Unityper]] deps = ["ConstructionBase"] @@ -2384,15 +2989,13 @@ uuid = "a7c27f48-0311-42f6-a7f8-2c11e75eb415" version = "0.1.6" [[deps.UnsafeAtomics]] -git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" -version = "0.2.1" +version = "0.3.0" +weakdeps = ["LLVM"] -[[deps.UnsafeAtomicsLLVM]] -deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" -uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.3" + [deps.UnsafeAtomics.extensions] + UnsafeAtomicsLLVM = ["LLVM"] [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -2401,9 +3004,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "6129a4faf6242e7c3581116fbe3270f3ab17c90d" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.67" +version = "0.21.71" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -2419,33 +3022,38 @@ version = "1.3.243+0" [[deps.Wayland_jll]] deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "7558e29847e99bc3f04d6569e82d0f5c54460703" +git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.21.0+1" +version = "1.21.0+2" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" +git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.31.0+0" +version = "1.36.0+0" + +[[deps.WeakValueDicts]] +git-tree-sha1 = "98528c2610a5479f091d470967a25becfd83edd0" +uuid = "897b6980-f191-5a31-bcb0-bf3c4585e0c1" +version = "0.1.0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488" +git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.6+0" +version = "2.13.5+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.6.4+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2461,81 +3069,81 @@ version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" +git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+0" +version = "1.8.6+3" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" +git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+0" +version = "1.0.11+3" [[deps.Xorg_libXcursor_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "807c226eaf3651e7b2c468f687ac788291f9a89b" uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" -version = "1.2.0+4" +version = "1.2.3+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" +git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+0" +version = "1.1.4+3" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" +git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.6+0" +version = "1.3.6+3" [[deps.Xorg_libXfixes_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "6fcc21d5aea1a0b7cce6cab3e62246abd1949b86" uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" -version = "5.0.3+4" +version = "6.0.0+0" [[deps.Xorg_libXi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] -git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] +git-tree-sha1 = "984b313b049c89739075b8e2a94407076de17449" uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" -version = "1.7.10+4" +version = "1.8.2+0" [[deps.Xorg_libXinerama_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] -git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll"] +git-tree-sha1 = "a1a7eaf6c3b5b05cb903e35e8372049b107ac729" uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" -version = "1.1.4+4" +version = "1.1.5+0" [[deps.Xorg_libXrandr_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "b6f664b7b2f6a39689d822a6300b14df4668f0f4" uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" -version = "1.5.2+4" +version = "1.5.4+0" [[deps.Xorg_libXrender_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" +git-tree-sha1 = "a490c6212a0e90d2d55111ac956f7c4fa9c277a6" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.11+0" +version = "0.9.11+1" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" +git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+0" +version = "0.1.1+3" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+3" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" +git-tree-sha1 = "dbc53e4cf7701c6c7047c51e17d6e64df55dca94" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.2+0" +version = "1.1.2+1" [[deps.Xorg_xcb_util_cursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] @@ -2575,9 +3183,9 @@ version = "0.4.1+1" [[deps.Xorg_xkbcomp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" +git-tree-sha1 = "ab2221d309eda71020cdda67a973aa582aa85d69" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.6+0" +version = "1.4.6+1" [[deps.Xorg_xkeyboard_config_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] @@ -2587,26 +3195,26 @@ version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +version = "1.5.0+3" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "622cf78670d067c738667aaa96c553430b65e269" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.7+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" +git-tree-sha1 = "0b3c944f5d2d8b466c5d20a84c229c17c528f49e" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.70" +version = "0.6.75" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] @@ -2628,32 +3236,38 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.56.3+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d" uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" -version = "3.1.1+0" +version = "3.1.1+1" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.9.0+0" +version = "3.11.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.7.0+0" +version = "5.8.0+1" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2662,10 +3276,10 @@ uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" version = "1.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libinput_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] @@ -2675,15 +3289,15 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.45+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2694,7 +3308,7 @@ version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2705,7 +3319,7 @@ version = "2021.12.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2721,9 +3335,9 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" +git-tree-sha1 = "63406453ed9b33a0df95d570816d5366c92b7809" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" +version = "1.4.1+2" """ # ╔═╡ Cell order: @@ -2738,7 +3352,7 @@ version = "1.4.1+1" # ╟─f284fda5-aaf7-4121-a8f0-b996d501bec5 # ╟─aaf3d52e-7e6b-4742-b9df-5440b148e7ee # ╟─a2164307-6d18-4983-9aaa-25c8f5828655 -# ╠═dea41d07-dedc-47a0-867b-ea5e503c2a50 +# ╠═eab8adc0-e3c7-4693-990b-cb47e3d9c2cf # ╟─556243a1-c387-4606-94d9-2dc06dfdc5f0 # ╠═98451eb8-8755-47fe-b8c6-ce2959256dd8 # ╠═b62c37ac-8d33-49ac-8aa6-18d959bc6933 @@ -2755,11 +3369,17 @@ version = "1.4.1+1" # ╟─0bfc00dd-cb88-4166-8cb0-2583882975f4 # ╟─89798b17-a1f0-43ff-9b3f-42cae0d6020a # ╠═158c4ad8-a38b-4828-812f-1abce60695dc +# ╠═6785c1af-28e5-46b4-ba34-a8ab65be7ff8 # ╟─a0bff583-53ee-4a76-8dea-93711b93ec4c -# ╟─ae0e6fd3-c410-4c04-bf90-dcf1b8194441 -# ╠═f460412b-e17b-46fb-ae62-748dd55e475e +# ╟─1dc98bcc-c991-43f2-884e-ec6c20ee4554 +# ╠═c321d1b8-e22b-4e28-adfc-dc2b20d28083 +# ╠═9f856137-5a46-4a6d-be12-aa38f9e20642 +# ╟─5600d0fa-80ef-40c2-ae12-570c348d1f14 +# ╟─7c18a27d-a738-4d04-b712-d87fd91828af +# ╟─3e1c9cd4-aa4e-4f29-8788-45708b94406f +# ╟─752a90ee-3e92-4426-b33c-9d65b8c465dc # ╟─d45219d2-183e-4ca1-89bc-34d0eae1419b -# ╟─7c7608c3-1ec7-493e-ae31-6d02fe3531c7 +# ╟─d5287aba-93ab-440a-9cb5-97d879f5af9b # ╟─c93ed717-dcfd-46f5-83c1-91d8eb7fa943 # ╟─60c63f1b-5a27-4539-a486-78c083457b0e # ╟─890afefc-f42b-4d74-b775-6dee5e5f0c2b diff --git a/project/project_cocktails backup 1.jl b/project/project_cocktails backup 1.jl new file mode 100644 index 00000000..686b43c5 --- /dev/null +++ b/project/project_cocktails backup 1.jl @@ -0,0 +1,2492 @@ +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# ╔═╡ 1c4709fc-58a6-4a2c-857c-49a5442a180f +using DifferentialEquations, ModelingToolkit, Unitful + +# ╔═╡ 21357c48-f35d-11ee-23f8-2534bb1d82f4 +begin + + # make this cell invisible when you are finished + title = "Cocktail shaking model" + names = ["Michiel"] + + academic_year = "2023_20224" + + email_main_person = "mail@domain.be" + + using PlutoUI # interactivity + using Plots # plotting + TableOfContents() +end; + +# ╔═╡ 14c7e803-c0ff-4211-8b60-2c9c246934dd +md""" +# $title + +**$(join(names, ", ", " and "))** +""" + +# ╔═╡ 6948149f-854e-4b3c-b51c-099dd221ab83 +md""" +## Abstract + +About 250 words about your project: +- (1-2 sentence) basic introduction to your topic, accessible to every bioengineering student +- (1-2 sentences) bit more specialized introduction +- (1-2 sentences) general goal of the project +- (2-3 sentences) short overview of how you built the model and what analysis you did +""" + +# ╔═╡ 89551690-500d-4e37-ae20-5beb71cc87ac +md""" +## Model + +general outline of the model + variables + parameters + +For example, the metabolic rate $y$ as a function of the mass $m$ of an organism follows a power law. +""" + +# ╔═╡ 7b1a87c5-0856-4968-ba2b-36da650cd0c8 +begin + @variables t #[unit = u"s"] # mixing time in seconds + @variables I(t)=200 #[unit = u"g"] # amount of ice + @variables L(t)=100 #[unit = u"L"] # amount of liquid + @variables T(t)=20 #[unit = u"°C"] # cocktail temperature + @variables S(t)=203 #[unit = u"g/L"] # sugar concentration + @variables Z(t) +end; + +# ╔═╡ 08b40947-7218-4885-b25c-982821ca0361 +begin + @constants Cmelt = 3.34e5 #[unit = u"J/kg"] + @constants Cₚ = 4.187e3 #[unit = u"J/kg * K"] +end; + +# ╔═╡ b1073c63-cb31-4160-98e1-ec1a0ca22d9c +10u"J/kg/K" * (10u"°C"-5u"°C") + +# ╔═╡ 7110e56a-dfc1-4885-9eee-c59eeb37010f +Dₜ = Differential(t) + +# ╔═╡ d560e96d-c6dc-4127-9616-1c186914cef5 +melting = Dₜ(I) ~ -0.001 #* T #*I^0.66 + +# ╔═╡ 75b7ed6d-f27f-4f73-9c78-014b659323b8 +#water_balance = Dₜ(I) + Dₜ(L) ~ 0 +water_balance = I+L ~ 100 + +# ╔═╡ 3da54360-1f31-48a0-87cf-0d47132862bc +heat_balance = Cmelt * Dₜ(I) ~ Cₚ * L * Dₜ(T) + +# ╔═╡ 3ccb5e2b-9ed3-486c-ac18-de62d2297e07 +sugar_balance = expand_derivatives(Dₜ(S*L)) ~ 0 +#sugar_balance = S*L ~ 10 + +# ╔═╡ aed58771-86c1-4928-a1ba-b7d2f503b188 +md"Finally, the perceived sweetness depends on the sugar concentration and the temperature. Setting up such a relation is done in the field of psychophysics (e.g. [Steven's law](https://en.wikipedia.org/wiki/Stevens%27s_power_law)). Based on [this article](https://pubmed.ncbi.nlm.nih.gov/7100291/), we obtain a fairly simple emperical relation." + +# ╔═╡ 98451eb8-8755-47fe-b8c6-ce2959256dd8 +sweetness = Z ~ 14.0 * (S / 342.30)^(1.422 - 0.0146T) + +# ╔═╡ aa32c5e2-0f67-4910-a612-d958fa13169c +@named sys_or = ODESystem([melting, water_balance,heat_balance,sugar_balance,sweetness]) + +# ╔═╡ 7f9c8c7d-90ef-496c-b907-300feba5edfc +simpsys = structural_simplify(sys, simplify=true) + +# ╔═╡ 4595b9f6-3e9b-4160-8def-456b0c6c0caf +@mtkbuild sys = ODESystem([melting, water_balance,heat_balance,sugar_balance,sweetness]) + +# ╔═╡ 58d13e42-4edc-412c-a1e0-30e11fb2585e +states(simpsys) + +# ╔═╡ 8cf34815-4ff7-4930-bc91-11081e1ab3f3 +ODEProblem(simpsys, [S=>10, L=>0.3, S=>0.2, T=>21, I=>200], (0, 50)) + +# ╔═╡ f284fda5-aaf7-4121-a8f0-b996d501bec5 +md"## Simulation and analysis" + +# ╔═╡ 2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 +md""" +Explore your model +""" + +# ╔═╡ 67380c07-a07c-4a0e-8654-80f27b951461 +plot(y, 0.01, 1000, label="metabolic rate", xlab="mass (kg)") + +# ╔═╡ 86307aaa-1349-444b-bc9b-e5c115727671 + + +# ╔═╡ ef1b3843-a963-4a18-85c4-ca5a6e791d00 + + +# ╔═╡ aa4ebdb8-27a1-493b-b95e-d2ac4c3e6d54 + + +# ╔═╡ 60c63f1b-5a27-4539-a486-78c083457b0e +md""" +## Conclusion + +A short conclusion of your analysis with a relection on how you would improve this model. +""" + +# ╔═╡ 890afefc-f42b-4d74-b775-6dee5e5f0c2b +md"## Appendix" + +# ╔═╡ 1f4b988a-6632-4589-8913-5de0574d94b3 +perceived_sweetness(S, T) = 14.9 * (S / 342.30)^(1.42224 - 0.0146071T) + +# ╔═╡ 797ce7d7-c49d-4a00-a8e3-058b6de4d3a9 +heatmap(1:200, 4:40, perceived_sweetness, xlabel="Sugar concentration (g/L)", ylabel="temperature (°C)", title="perceived sweetness") + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" +ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +PlutoUI = 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+version = "3.2.9+0" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.43.0+0" + +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.4.0+0" + +[[deps.libass_jll]] +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" +version = "0.15.1+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.7.0+0" + +[[deps.libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" +version = "2.0.2+0" + +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + +[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.43+1" + +[[deps.libvorbis_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +version = "1.3.7+1" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" + +[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+1" +""" + +# ╔═╡ Cell order: +# ╟─14c7e803-c0ff-4211-8b60-2c9c246934dd +# ╠═6948149f-854e-4b3c-b51c-099dd221ab83 +# ╠═1c4709fc-58a6-4a2c-857c-49a5442a180f +# ╠═89551690-500d-4e37-ae20-5beb71cc87ac +# ╠═7b1a87c5-0856-4968-ba2b-36da650cd0c8 +# ╠═08b40947-7218-4885-b25c-982821ca0361 +# ╠═b1073c63-cb31-4160-98e1-ec1a0ca22d9c +# ╠═7110e56a-dfc1-4885-9eee-c59eeb37010f +# ╠═d560e96d-c6dc-4127-9616-1c186914cef5 +# ╠═75b7ed6d-f27f-4f73-9c78-014b659323b8 +# ╠═3da54360-1f31-48a0-87cf-0d47132862bc +# ╠═3ccb5e2b-9ed3-486c-ac18-de62d2297e07 +# ╠═aed58771-86c1-4928-a1ba-b7d2f503b188 +# ╠═98451eb8-8755-47fe-b8c6-ce2959256dd8 +# ╟─797ce7d7-c49d-4a00-a8e3-058b6de4d3a9 +# ╠═aa32c5e2-0f67-4910-a612-d958fa13169c +# ╠═7f9c8c7d-90ef-496c-b907-300feba5edfc +# ╠═4595b9f6-3e9b-4160-8def-456b0c6c0caf +# ╠═58d13e42-4edc-412c-a1e0-30e11fb2585e +# ╠═8cf34815-4ff7-4930-bc91-11081e1ab3f3 +# ╟─f284fda5-aaf7-4121-a8f0-b996d501bec5 +# ╠═2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 +# ╠═67380c07-a07c-4a0e-8654-80f27b951461 +# ╠═86307aaa-1349-444b-bc9b-e5c115727671 +# ╠═ef1b3843-a963-4a18-85c4-ca5a6e791d00 +# ╠═aa4ebdb8-27a1-493b-b95e-d2ac4c3e6d54 +# ╠═60c63f1b-5a27-4539-a486-78c083457b0e +# ╟─890afefc-f42b-4d74-b775-6dee5e5f0c2b +# ╠═21357c48-f35d-11ee-23f8-2534bb1d82f4 +# ╟─1f4b988a-6632-4589-8913-5de0574d94b3 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/project/project_cocktails.jl b/project/project_cocktails.jl index 36232f26..04530a7e 100644 --- a/project/project_cocktails.jl +++ b/project/project_cocktails.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils @@ -95,12 +95,12 @@ sweetness = Z ~ 14.0 * (S / 342.30)^(1.422 - 0.0146T) # ╔═╡ aa32c5e2-0f67-4910-a612-d958fa13169c @named sys_or = ODESystem([melting, water_balance,heat_balance,sugar_balance,sweetness]) -# ╔═╡ 4595b9f6-3e9b-4160-8def-456b0c6c0caf -@mtkbuild sys = ODESystem([melting, water_balance,heat_balance,sugar_balance,sweetness]) - # ╔═╡ 7f9c8c7d-90ef-496c-b907-300feba5edfc simpsys = structural_simplify(sys, simplify=true) +# ╔═╡ 4595b9f6-3e9b-4160-8def-456b0c6c0caf +@mtkbuild sys = ODESystem([melting, water_balance,heat_balance,sugar_balance,sweetness]) + # ╔═╡ 58d13e42-4edc-412c-a1e0-30e11fb2585e states(simpsys) @@ -143,2320 +143,6 @@ perceived_sweetness(S, T) = 14.9 * (S / 342.30)^(1.42224 - 0.0146071T) # ╔═╡ 797ce7d7-c49d-4a00-a8e3-058b6de4d3a9 heatmap(1:200, 4:40, perceived_sweetness, xlabel="Sugar concentration (g/L)", ylabel="temperature (°C)", title="perceived sweetness") -# ╔═╡ 00000000-0000-0000-0000-000000000001 -PLUTO_PROJECT_TOML_CONTENTS = """ -[deps] -DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" -Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - -[compat] -DifferentialEquations = "~7.13.0" -ModelingToolkit = "~8.75.0" -Plots = "~1.39.0" -PlutoUI = "~0.7.58" -Unitful = "~1.19.0" -""" - -# ╔═╡ 00000000-0000-0000-0000-000000000002 -PLUTO_MANIFEST_TOML_CONTENTS = """ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.9.0" -manifest_format = "2.0" -project_hash = "a7255f58d02bc974b024509e272a27584fdf4bd4" - -[[deps.ADTypes]] -git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.7" - 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- # ╔═╡ Cell order: # ╟─14c7e803-c0ff-4211-8b60-2c9c246934dd # ╠═6948149f-854e-4b3c-b51c-099dd221ab83 @@ -2488,5 +174,3 @@ version = "1.4.1+1" # ╟─890afefc-f42b-4d74-b775-6dee5e5f0c2b # ╠═21357c48-f35d-11ee-23f8-2534bb1d82f4 # ╟─1f4b988a-6632-4589-8913-5de0574d94b3 -# ╟─00000000-0000-0000-0000-000000000001 -# ╟─00000000-0000-0000-0000-000000000002 diff --git a/project/project_ladybugs.jl b/project/project_ladybugs.jl index 60162eec..c9fd9cf6 100644 --- a/project/project_ladybugs.jl +++ b/project/project_ladybugs.jl @@ -1,2833 +1,2831 @@ -### A Pluto.jl notebook ### -# v0.19.45 - -using Markdown -using InteractiveUtils - -# ╔═╡ 21357c48-f35d-11ee-23f8-2534bb1d82f4 -begin - # make this cell invisible when you are finished - title = "APHID ANNIHILATION 🤘🔥🔥" - names = ["Vo Orbeeld", "Pro Ject"] - - x = 4 - academic_year = "202$(x)_202$(x+1)" - - email_main_person = "mail@domain.be" - - using PlutoUI # interactivity - using Random # set seed - using Catalyst, JumpProcesses, OrdinaryDiffEq # modeling - using Optim - using StatsPlots # plots - TableOfContents() -end; - -# ╔═╡ 14c7e803-c0ff-4211-8b60-2c9c246934dd -md""" -# $title - -**$(join(names, ", ", " and "))** -""" - -# ╔═╡ 6948149f-854e-4b3c-b51c-099dd221ab83 -md""" -## Abstract - -Belgium's native ladybugs, or lady beetles, have had it rough the last few decades. In 1995, the Asian lady beetle _Harmonia axyridis_ was introduced in Belgium as a biological pest-control agent, and quickly established itself as the new kingpin (R.L. Koch, 2003). While useful for controlling agricultural pests such as aphids, the beetle has been found to have a negative effect on biodiversity by outcompeting native ladybugs, essentially bullying the poor things (Brown et al., 2008). - -The goal of this project is to create a simple model for the dynamics of a ladybug population living off aphids and subsequently to use it to investigate what feeding strategy is optimal for the ladybugs. We then intend to help the native ladybugs by passing this information on to them. - -Since we are dealing with relatively small population sizes that can go to 0, we have chosen to model this system as a discrete stochastic jump process. We optimized the ladybug's aphid predation rate for an ideal deterministic case and then investigated whether how this optimal feeding rate performed in a stochastic environment. -""" - -# ╔═╡ 89551690-500d-4e37-ae20-5beb71cc87ac -md""" -## Model -""" - -# ╔═╡ aed58771-86c1-4928-a1ba-b7d2f503b188 -md""" -First we introduce our notations for the different components of the model. - -Variables: -- 🦗: The aphid population size -- 🐞: The ladybug population size - -Parameters: -- 🚩🦗: The environment's carrying capacity for aphids. -- 🍼🦗: The aphid's birth rate. -- 👌🦗: The aphid's target population level as designated by the ladybugs. -- 🍴🐞: The ladybug's aphid predation rate. This is the rate at which native ladybugs eat aphids. -- 💀🐞: The ladybug's mortality rate. - - -We'll now introduce the model step by step in the following section. Let's start by defining the time span over which we'll simulate our model: six months, equating about one growing season -""" - -# ╔═╡ eaac6193-f4b6-4901-bd7b-1ff6025c739b -tspan = (0.0, 6*30.0) - -# ╔═╡ 98451eb8-8755-47fe-b8c6-ce2959256dd8 -md""" -### Aphids -""" - -# ╔═╡ ccfd3dbc-a9f0-4dfb-9a04-bdc69c95796b -md""" -We start with the aphids, which will serve as the ladybugs' food source. We will use a simple Gompertz model for their growth, as aphids are known for their explosive (exponential) population growth, yet their maximum population size is limited by how many aphids their host plant can feed. In reality aphids are of course able to switch host plants, but for simplicity's sake we will consider an aphid population with one single host plant (which does not deteriorate). -""" - -# ╔═╡ d5b50429-b4d7-4d1a-aa24-d7aa6dabba4e -aphid_rn = @reaction_network begin - @parameters 🚩🦗 = 10_000 🍼🦗 = 0.1 - @species 🦗(t) = 1000 - - 🍼🦗*(🚩🦗-🦗)/🚩🦗, 🦗 --> 2🦗 -end - -# ╔═╡ ec92e20d-bd34-4d2e-a828-281cdfff5184 -sol_aph = JumpInputs(aphid_rn, [], tspan, []) |> JumpProblem |> solve; - -# ╔═╡ 4273bd12-3df5-452d-a439-b2a612f8a138 -plot(sol_aph, label = "Aphids", palette = :okabe_ito, title = "Evolution of an unbothered aphid population", size = (700, 400), margin = 3Plots.mm) - -# ╔═╡ aa32c5e2-0f67-4910-a612-d958fa13169c -md""" -### Get eaten by ladybugs -""" - -# ╔═╡ 9dcdbf69-0750-4cab-b174-0399095dc819 -md""" -Next we add the ladybugs. They eat aphids to make more ladybugs, and then die of old age after living a fulfilling ladybug life. - -We assume two ladybugs need to eat 30 aphids to produce a child. Additionally, the rate at which aphids get eaten scales linearly with the amount of ladybugs, but not the amount of aphids. This is because we assume the number of ladybugs will be the limiting factor: 20 ladybugs will eat twice as many aphids as 10 ladybugs, but it does not matter whether 1000 or 2000 aphids are present (we thus also assume the ladybugs have no difficulty finding the aphids). Finally, we also assume ladybugs will always leave a certain number of aphids alive lest their food source goes extinct. - -To model ladybug mortality, we also assume a first-order process. The more ladybugs are present, the more ladybugs will die on any given day by reaching old age, or perhaps getting eaten by a bird. -""" - -# ╔═╡ 7806ad6b-3a18-417c-98e0-a3657b9e8dd1 -ladybug_rn = @reaction_network begin - @parameters 🚩🦗 = 10_000 🍼🦗 = 0.1 👌🦗 = 300 🍴🐞 = 0.3 💀🐞 = 0.1 - @species 🦗(t) = 1000 🐞(t) = 10 - - 🍼🦗*(🚩🦗-🦗)/🚩🦗, 🦗 --> 2🦗 - 🍴🐞*🐞*(🦗 - 👌🦗)/🦗, 2🐞 + 30🦗 => 3🐞 - 💀🐞, 🐞 --> 0 -end - -# ╔═╡ d14a7e77-eb62-44dd-bc70-0853ccd41f08 -md""" -Let's double check everything is in order: -""" - -# ╔═╡ 8959ff62-c0fd-42b8-b03a-f58439470fb1 -convert(ODESystem, ladybug_rn) - -# ╔═╡ 0bd9835b-cfcc-440b-829e-666fd4899411 -sol_bugged = JumpInputs(ladybug_rn, [], tspan, []) |> JumpProblem |> solve; - -# ╔═╡ 5f78a353-90d2-451e-ad9d-c55b9124f3ae -# ╠═╡ show_logs = false -plot(sol_bugged, label = ["Aphids" "Ladybugs"], palette = :okabe_ito, yaxis = :log, ylims = (1, 1e4), title = "Evolution of a very much bothered aphid population (& ladybugs)", size = (800, 500), margin = 3Plots.mm) - -# ╔═╡ 61667718-20fc-40b3-87b8-a7546e2713fb -md""" -And that's it for the structure of our ladybug model! -""" - -# ╔═╡ f284fda5-aaf7-4121-a8f0-b996d501bec5 -md"## Simulation and analysis" - -# ╔═╡ 2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 -md""" -### Optimisation of ladybug behaviour -""" - -# ╔═╡ eacb84c4-94dc-48d0-95c4-05636650057a -md""" -Given our simple ladybug model, we'd like to find the optimal ladybug behaviour so that they have the largest possible population size at the end of the growing season. - -To this end we'll optimize a loss function: -- that returns the negative ladybug population size at the end of the growing season: maximize population size => minimize the inverse -- in function of the aphid predation rate $🍴🐞$ and the desired minimal aphid population level $👌🦗$: the other 3 parameters are outside of the ladybugs' control -""" - -# ╔═╡ 797a59c5-d120-4008-901d-14db799ab558 -md""" -For the callibration process, we'll assume a perfectly deterministic system by modeling it as an ODE problem rather than a jump problem. This is because trying to optimize a strongly stochastic process is a pain and we'd rather not deal with that. -""" - -# ╔═╡ eaa2c110-9ba9-4b28-bf41-13943f54a8e6 -ladyprob = ODEProblem(ladybug_rn, [], tspan, []); - -# ╔═╡ ace97b1f-04ef-401a-93d8-4e6bffdb8985 -function ladybug_loss(params) - sol = remake(ladyprob, p = [:🍴🐞 => params[1], :👌🦗 => params[2]]) |> - x -> solve(x, reltol = 1e-9, abstol = 1e-9) # set tolerance of the solver very low or the optimizer finds the right parameters to break it and make the aphid population go below 0 for even more ladybugs - - return -sol[:🐞][end] -end - -# ╔═╡ 698811dd-81b0-4a17-98f4-29109912d85f -md""" -We use constrained optimisation since both parameters must be positive. In addition, we set a minimum value of 100 for the aphids' target aphid population level. This is an estimation for how many aphids are needed to start a new population the next growing season. -""" - -# ╔═╡ 88e28b17-7ed5-4da5-8310-860f1d1e8cff -res = optimize(ladybug_loss, [0, 100], [1, Inf], [0.3, 300], Fminbox(NelderMead())); - -# ╔═╡ 00d095f7-e90f-4924-b6f1-9703ff26987f -params_opt = [:🍴🐞 => res.minimizer[1], :👌🦗 => res.minimizer[2]] - -# ╔═╡ 3574468f-6996-4e6a-b86b-21f8ef1457a6 -# ╠═╡ show_logs = false -remake(ladyprob, p = params_opt) |> - x -> solve(x, reltol = 1e-9, abstol = 1e-9) |> - x -> plot(x, yaxis = :log, ylims = (1, 1e4), label = ["Aphids" "Ladybug"], palette = :okabe_ito, title = "Evolution of an optimally bothered aphid population (& ladybugs)", size = (800, 500), margin = 3Plots.mm) - -# ╔═╡ d85498b1-9180-4763-b79a-9fc5c326921e -md""" -We can see that a lower predation rate allows for the aphid population to flourish while the ladybug population steadily rises, until the ladybug population reaches a critical size near the end of the growing season. At this point there are so many ladybugs the aphid population starts collapsing ending with a strong crash just at the end of the growing season. Patience seems to be the key! -""" - -# ╔═╡ 6619d108-791d-4cea-8690-005d1bf2b3e6 -md""" -### Uncertainty assessment of ladybug behaviour -""" - -# ╔═╡ 79d65032-5b0e-412d-a69b-6aef7b1e51be -md""" -We've found a set of optimal parameters for ladybug behaviour, but that was for a deterministic case. We now want to get an idea of whether these parameters will truly result in high population sizes when considering a more realistic stochastic scenario. To achieve this, we perform a simple grid search over different values of the aphid predation rate $🍴🐞$ in the neighbourhood of the optimal value. We perform multiple runs per point to take into account the random nature of the outcome. We did not take the target aphid level $👌🦗$ into account as quickly playing around with different values showed very little change in the output (not shown for brevity). -""" - -# ╔═╡ 48439a0a-cda3-4995-b69c-4d0ac8072178 -function ladybug_performance(🍴🐞, jump_prob) - sol = remake(jump_prob, p = [:🍴🐞 => 🍴🐞, :👌🦗 => res.minimizer[2]]) |> - solve - return sol[:🐞][end] # we're interested in the ladybug population level at the end of the growing season -end - -# ╔═╡ 5f342652-3dc4-4560-a66d-1862be258e9b -begin - Random.seed!(1337) # for reproducability - num_repeats = 100 - jump_prob = DiscreteProblem(ladybug_rn, [], tspan, []) |> - x -> JumpProblem(ladybug_rn, x) - plot(title = "Final ladybug population sizes in function of aphid predation rate", xlabel = "Aphid predation rate", ylabel = "Ladybug population size", size = (800, 500), margin = 3Plots.mm) - - grid_points = 0.05:0.01:0.2 - for (grididx, 🍴🐞) in enumerate(grid_points) - performances = [ladybug_performance(🍴🐞, jump_prob) for _ in 1:num_repeats] # do a few simulations with the same value for 🍴🐞 - boxplot!([grididx], performances, label = false, outliers = false, color = :orange) - end - xticks!(1:length(grid_points), string.(grid_points)) # boxplots always have a width of 1, so we need to fidget with the x-axis a little - -end - -# ╔═╡ 6605f38c-76d8-4a73-8134-c758ccf13085 -md""" -From this figure we can see that ladybugs with a predation rate that is too low (<= 0.1) always go extinct by the end of the growing season, presumably because they die faster than they replenish the population. Around the optimal value we see a big peak in the expected and maximum final population sizes, steadily decreasing as the predation rate grows (with what seems another local optimum near 0.16). This confirms our previous finding that patient ladybugs will, on average, perform well with respect to their population size at the end of the growing season, though not quite as well as in a deterministic scenario. -""" - -# ╔═╡ 60c63f1b-5a27-4539-a486-78c083457b0e -md""" -## Conclusion - -In our project we made a simple model for the dynamics of a ladybug predating on aphids. We then optimized the predation strategy of the ladybugs in a deterministic scenario and found that a patient predation strategy can be very rewarding. We then checked whether this was also true in a stochastic scenario, and found that it was indeed the case. - -Some following steps for this model would be to: -- Validate whether it can approximate real aphid-ladybug dynamics by trying to calibrate it on real data and change the model if required -- Introduce invasive ladybugs to the model and investigate their impact on the native ladybugs w.r.t. some of the model parameters -""" - -# ╔═╡ 890afefc-f42b-4d74-b775-6dee5e5f0c2b -md"## Appendix" - -# ╔═╡ 946cf45a-329b-42ca-9f77-a3c7bdc5611a -md""" -### References -""" - -# ╔═╡ e59da868-a7f5-48f0-af1b-8a990f146f20 -md""" -- Koch, R. L. (2003). The multicolored Asian lady beetle, Harmonia axyridis: a review of its biology, uses in biological control, and non-target impacts. Journal of insect Science, 3(1), 32. -- Brown, P. M. J., Adriaens, T., Bathon, H., Cuppen, J., Goldarazena, A., Hägg, T., ... & Roy, D. B. (2008). Harmonia axyridis in Europe: spread and distribution of a non-native coccinellid. 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-# ╔═╡ Cell order: -# ╟─14c7e803-c0ff-4211-8b60-2c9c246934dd -# ╟─6948149f-854e-4b3c-b51c-099dd221ab83 -# ╟─89551690-500d-4e37-ae20-5beb71cc87ac -# ╟─aed58771-86c1-4928-a1ba-b7d2f503b188 -# ╟─eaac6193-f4b6-4901-bd7b-1ff6025c739b -# ╟─98451eb8-8755-47fe-b8c6-ce2959256dd8 -# ╟─ccfd3dbc-a9f0-4dfb-9a04-bdc69c95796b -# ╠═d5b50429-b4d7-4d1a-aa24-d7aa6dabba4e -# ╟─ec92e20d-bd34-4d2e-a828-281cdfff5184 -# ╟─4273bd12-3df5-452d-a439-b2a612f8a138 -# ╟─aa32c5e2-0f67-4910-a612-d958fa13169c -# ╟─9dcdbf69-0750-4cab-b174-0399095dc819 -# ╠═7806ad6b-3a18-417c-98e0-a3657b9e8dd1 -# ╟─d14a7e77-eb62-44dd-bc70-0853ccd41f08 -# ╟─8959ff62-c0fd-42b8-b03a-f58439470fb1 -# ╟─0bd9835b-cfcc-440b-829e-666fd4899411 -# ╟─5f78a353-90d2-451e-ad9d-c55b9124f3ae -# ╟─61667718-20fc-40b3-87b8-a7546e2713fb -# ╟─f284fda5-aaf7-4121-a8f0-b996d501bec5 -# ╟─2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 -# ╟─eacb84c4-94dc-48d0-95c4-05636650057a -# ╟─797a59c5-d120-4008-901d-14db799ab558 -# ╠═eaa2c110-9ba9-4b28-bf41-13943f54a8e6 -# ╠═ace97b1f-04ef-401a-93d8-4e6bffdb8985 -# ╟─698811dd-81b0-4a17-98f4-29109912d85f -# ╠═88e28b17-7ed5-4da5-8310-860f1d1e8cff -# ╠═00d095f7-e90f-4924-b6f1-9703ff26987f -# ╟─3574468f-6996-4e6a-b86b-21f8ef1457a6 -# ╟─d85498b1-9180-4763-b79a-9fc5c326921e -# ╟─6619d108-791d-4cea-8690-005d1bf2b3e6 -# ╟─79d65032-5b0e-412d-a69b-6aef7b1e51be -# ╠═48439a0a-cda3-4995-b69c-4d0ac8072178 -# ╟─5f342652-3dc4-4560-a66d-1862be258e9b -# ╟─6605f38c-76d8-4a73-8134-c758ccf13085 -# ╟─60c63f1b-5a27-4539-a486-78c083457b0e -# ╟─890afefc-f42b-4d74-b775-6dee5e5f0c2b -# ╟─21357c48-f35d-11ee-23f8-2534bb1d82f4 -# ╟─946cf45a-329b-42ca-9f77-a3c7bdc5611a -# ╟─e59da868-a7f5-48f0-af1b-8a990f146f20 -# ╟─00000000-0000-0000-0000-000000000001 -# ╟─00000000-0000-0000-0000-000000000002 +### A Pluto.jl notebook ### +# v0.20.3 + +using Markdown +using InteractiveUtils + +# ╔═╡ 21357c48-f35d-11ee-23f8-2534bb1d82f4 +begin + # make this cell invisible when you are finished + title = "APHID ANNIHILATION 🤘🔥🔥" + names = ["Vo Orbeeld", "Pro Ject"] + + x = 4 + academic_year = "202$(x)_202$(x+1)" + + email_main_person = "mail@domain.be" + + using PlutoUI # interactivity + using Random # set seed + using Catalyst, JumpProcesses, OrdinaryDiffEq # modeling + using Optim + using StatsPlots # plots + TableOfContents() +end; + +# ╔═╡ 14c7e803-c0ff-4211-8b60-2c9c246934dd +md""" +# $title + +**$(join(names, ", ", " and "))** +""" + +# ╔═╡ 6948149f-854e-4b3c-b51c-099dd221ab83 +md""" +## Abstract + +Belgium's native ladybugs, or lady beetles, have had it rough the last few decades. In 1995, the Asian lady beetle _Harmonia axyridis_ was introduced in Belgium as a biological pest-control agent, and quickly established itself as the new kingpin (R.L. Koch, 2003). While useful for controlling agricultural pests such as aphids, the beetle has been found to have a negative effect on biodiversity by outcompeting native ladybugs, essentially bullying the poor things (Brown et al., 2008). + +The goal of this project is to create a simple model for the dynamics of a ladybug population living off aphids and subsequently to use it to investigate what feeding strategy is optimal for the ladybugs. We then intend to help the native ladybugs by passing this information on to them. + +Since we are dealing with relatively small population sizes that can go to 0, we have chosen to model this system as a discrete stochastic jump process. We optimized the ladybug's aphid predation rate for an ideal deterministic case and then investigated whether how this optimal feeding rate performed in a stochastic environment. +""" + +# ╔═╡ 89551690-500d-4e37-ae20-5beb71cc87ac +md""" +## Model +""" + +# ╔═╡ aed58771-86c1-4928-a1ba-b7d2f503b188 +md""" +First we introduce our notations for the different components of the model. + +Variables: +- 🦗: The aphid population size +- 🐞: The ladybug population size + +Parameters: +- 🚩🦗: The environment's carrying capacity for aphids. +- 🍼🦗: The aphid's birth rate. +- 👌🦗: The aphid's target population level as designated by the ladybugs. +- 🍴🐞: The ladybug's aphid predation rate. This is the rate at which native ladybugs eat aphids. +- 💀🐞: The ladybug's mortality rate. + + +We'll now introduce the model step by step in the following section. Let's start by defining the time span over which we'll simulate our model: six months, equating about one growing season +""" + +# ╔═╡ eaac6193-f4b6-4901-bd7b-1ff6025c739b +tspan = (0.0, 6*30.0) + +# ╔═╡ 98451eb8-8755-47fe-b8c6-ce2959256dd8 +md""" +### Aphids +""" + +# ╔═╡ ccfd3dbc-a9f0-4dfb-9a04-bdc69c95796b +md""" +We start with the aphids, which will serve as the ladybugs' food source. We will use a simple Gompertz model for their growth, as aphids are known for their explosive (exponential) population growth, yet their maximum population size is limited by how many aphids their host plant can feed. In reality aphids are of course able to switch host plants, but for simplicity's sake we will consider an aphid population with one single host plant (which does not deteriorate). +""" + +# ╔═╡ d5b50429-b4d7-4d1a-aa24-d7aa6dabba4e +aphid_rn = @reaction_network begin + @parameters 🚩🦗 = 10_000 🍼🦗 = 0.1 + @species 🦗(t) = 1000 + + 🍼🦗*(🚩🦗-🦗)/🚩🦗, 🦗 --> 2🦗 +end + +# ╔═╡ ec92e20d-bd34-4d2e-a828-281cdfff5184 +sol_aph = JumpInputs(aphid_rn, [], tspan, []) |> JumpProblem |> solve; + +# ╔═╡ 4273bd12-3df5-452d-a439-b2a612f8a138 +plot(sol_aph, label = "Aphids", palette = :okabe_ito, title = "Evolution of an unbothered aphid population", size = (700, 400), margin = 3Plots.mm) + +# ╔═╡ aa32c5e2-0f67-4910-a612-d958fa13169c +md""" +### Get eaten by ladybugs +""" + +# ╔═╡ 9dcdbf69-0750-4cab-b174-0399095dc819 +md""" +Next we add the ladybugs. They eat aphids to make more ladybugs, and then die of old age after living a fulfilling ladybug life. + +We assume two ladybugs need to eat 30 aphids to produce a child. Additionally, the rate at which aphids get eaten scales linearly with the amount of ladybugs, but not the amount of aphids. This is because we assume the number of ladybugs will be the limiting factor: 20 ladybugs will eat twice as many aphids as 10 ladybugs, but it does not matter whether 1000 or 2000 aphids are present (we thus also assume the ladybugs have no difficulty finding the aphids). Finally, we also assume ladybugs will always leave a certain number of aphids alive lest their food source goes extinct. + +To model ladybug mortality, we also assume a first-order process. The more ladybugs are present, the more ladybugs will die on any given day by reaching old age, or perhaps getting eaten by a bird. +""" + +# ╔═╡ 7806ad6b-3a18-417c-98e0-a3657b9e8dd1 +ladybug_rn = @reaction_network begin + @parameters 🚩🦗 = 10_000 🍼🦗 = 0.1 👌🦗 = 300 🍴🐞 = 0.3 💀🐞 = 0.1 + @species 🦗(t) = 1000 🐞(t) = 10 + + 🍼🦗*(🚩🦗-🦗)/🚩🦗, 🦗 --> 2🦗 + 🍴🐞*🐞*(🦗 - 👌🦗)/🦗, 2🐞 + 30🦗 => 3🐞 + 💀🐞, 🐞 --> 0 +end + +# ╔═╡ d14a7e77-eb62-44dd-bc70-0853ccd41f08 +md""" +Let's double check everything is in order: +""" + +# ╔═╡ 8959ff62-c0fd-42b8-b03a-f58439470fb1 +convert(ODESystem, ladybug_rn) + +# ╔═╡ 0bd9835b-cfcc-440b-829e-666fd4899411 +sol_bugged = JumpInputs(ladybug_rn, [], tspan, []) |> JumpProblem |> solve; + +# ╔═╡ 5f78a353-90d2-451e-ad9d-c55b9124f3ae +# ╠═╡ show_logs = false +plot(sol_bugged, label = ["Aphids" "Ladybugs"], palette = :okabe_ito, yaxis = :log, ylims = (1, 1e4), title = "Evolution of a very much bothered aphid population (& ladybugs)", size = (800, 500), margin = 3Plots.mm) + +# ╔═╡ 61667718-20fc-40b3-87b8-a7546e2713fb +md""" +And that's it for the structure of our ladybug model! +""" + +# ╔═╡ f284fda5-aaf7-4121-a8f0-b996d501bec5 +md"## Simulation and analysis" + +# ╔═╡ 2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 +md""" +### Optimisation of ladybug behaviour +""" + +# ╔═╡ eacb84c4-94dc-48d0-95c4-05636650057a +md""" +Given our simple ladybug model, we'd like to find the optimal ladybug behaviour so that they have the largest possible population size at the end of the growing season. + +To this end we'll optimize a loss function: +- that returns the negative ladybug population size at the end of the growing season: maximize population size => minimize the inverse +- in function of the aphid predation rate $🍴🐞$ and the desired minimal aphid population level $👌🦗$: the other 3 parameters are outside of the ladybugs' control +""" + +# ╔═╡ 797a59c5-d120-4008-901d-14db799ab558 +md""" +For the callibration process, we'll assume a perfectly deterministic system by modeling it as an ODE problem rather than a jump problem. This is because trying to optimize a strongly stochastic process is a pain and we'd rather not deal with that. +""" + +# ╔═╡ eaa2c110-9ba9-4b28-bf41-13943f54a8e6 +ladyprob = ODEProblem(ladybug_rn, [], tspan, []); + +# ╔═╡ ace97b1f-04ef-401a-93d8-4e6bffdb8985 +function ladybug_loss(params) + sol = remake(ladyprob, p = [:🍴🐞 => params[1], :👌🦗 => params[2]]) |> + x -> solve(x, reltol = 1e-9, abstol = 1e-9) # set tolerance of the solver very low or the optimizer finds the right parameters to break it and make the aphid population go below 0 for even more ladybugs + + return -sol[:🐞][end] +end + +# ╔═╡ 698811dd-81b0-4a17-98f4-29109912d85f +md""" +We use constrained optimisation since both parameters must be positive. In addition, we set a minimum value of 100 for the aphids' target aphid population level. This is an estimation for how many aphids are needed to start a new population the next growing season. +""" + +# ╔═╡ 88e28b17-7ed5-4da5-8310-860f1d1e8cff +res = optimize(ladybug_loss, [0, 100], [1, Inf], [0.3, 300], Fminbox(NelderMead())); + +# ╔═╡ 00d095f7-e90f-4924-b6f1-9703ff26987f +params_opt = [:🍴🐞 => res.minimizer[1], :👌🦗 => res.minimizer[2]] + +# ╔═╡ 3574468f-6996-4e6a-b86b-21f8ef1457a6 +# ╠═╡ show_logs = false +remake(ladyprob, p = params_opt) |> + x -> solve(x, reltol = 1e-9, abstol = 1e-9) |> + x -> plot(x, yaxis = :log, ylims = (1, 1e4), label = ["Aphids" "Ladybug"], palette = :okabe_ito, title = "Evolution of an optimally bothered aphid population (& ladybugs)", size = (800, 500), margin = 3Plots.mm) + +# ╔═╡ d85498b1-9180-4763-b79a-9fc5c326921e +md""" +We can see that a lower predation rate allows for the aphid population to flourish while the ladybug population steadily rises, until the ladybug population reaches a critical size near the end of the growing season. At this point there are so many ladybugs the aphid population starts collapsing ending with a strong crash just at the end of the growing season. Patience seems to be the key! +""" + +# ╔═╡ 6619d108-791d-4cea-8690-005d1bf2b3e6 +md""" +### Uncertainty assessment of ladybug behaviour +""" + +# ╔═╡ 79d65032-5b0e-412d-a69b-6aef7b1e51be +md""" +We've found a set of optimal parameters for ladybug behaviour, but that was for a deterministic case. We now want to get an idea of whether these parameters will truly result in high population sizes when considering a more realistic stochastic scenario. To achieve this, we perform a simple grid search over different values of the aphid predation rate $🍴🐞$ in the neighbourhood of the optimal value. We perform multiple runs per point to take into account the random nature of the outcome. We did not take the target aphid level $👌🦗$ into account as quickly playing around with different values showed very little change in the output (not shown for brevity). +""" + +# ╔═╡ 48439a0a-cda3-4995-b69c-4d0ac8072178 +function ladybug_performance(🍴🐞, jump_prob) + sol = remake(jump_prob, p = [:🍴🐞 => 🍴🐞, :👌🦗 => res.minimizer[2]]) |> + solve + return sol[:🐞][end] # we're interested in the ladybug population level at the end of the growing season +end + +# ╔═╡ 5f342652-3dc4-4560-a66d-1862be258e9b +begin + Random.seed!(1337) # for reproducability + num_repeats = 100 + jump_prob = DiscreteProblem(ladybug_rn, [], tspan, []) |> + x -> JumpProblem(ladybug_rn, x) + plot(title = "Final ladybug population sizes in function of aphid predation rate", xlabel = "Aphid predation rate", ylabel = "Ladybug population size", size = (800, 500), margin = 3Plots.mm) + + grid_points = 0.05:0.01:0.2 + for (grididx, 🍴🐞) in enumerate(grid_points) + performances = [ladybug_performance(🍴🐞, jump_prob) for _ in 1:num_repeats] # do a few simulations with the same value for 🍴🐞 + boxplot!([grididx], performances, label = false, outliers = false, color = :orange) + end + xticks!(1:length(grid_points), string.(grid_points)) # boxplots always have a width of 1, so we need to fidget with the x-axis a little + +end + +# ╔═╡ 6605f38c-76d8-4a73-8134-c758ccf13085 +md""" +From this figure we can see that ladybugs with a predation rate that is too low (<= 0.1) always go extinct by the end of the growing season, presumably because they die faster than they replenish the population. Around the optimal value we see a big peak in the expected and maximum final population sizes, steadily decreasing as the predation rate grows (with what seems another local optimum near 0.16). This confirms our previous finding that patient ladybugs will, on average, perform well with respect to their population size at the end of the growing season, though not quite as well as in a deterministic scenario. +""" + +# ╔═╡ 60c63f1b-5a27-4539-a486-78c083457b0e +md""" +## Conclusion + +In our project we made a simple model for the dynamics of a ladybug predating on aphids. We then optimized the predation strategy of the ladybugs in a deterministic scenario and found that a patient predation strategy can be very rewarding. We then checked whether this was also true in a stochastic scenario, and found that it was indeed the case. + +Some following steps for this model would be to: +- Validate whether it can approximate real aphid-ladybug dynamics by trying to calibrate it on real data and change the model if required +- Introduce invasive ladybugs to the model and investigate their impact on the native ladybugs w.r.t. some of the model parameters +""" + +# ╔═╡ 890afefc-f42b-4d74-b775-6dee5e5f0c2b +md"## Appendix" + +# ╔═╡ 946cf45a-329b-42ca-9f77-a3c7bdc5611a +md""" +### References +""" + +# ╔═╡ e59da868-a7f5-48f0-af1b-8a990f146f20 +md""" +- Koch, R. L. (2003). The multicolored Asian lady beetle, Harmonia axyridis: a review of its biology, uses in biological control, and non-target impacts. Journal of insect Science, 3(1), 32. +- Brown, P. M. J., Adriaens, T., Bathon, H., Cuppen, J., Goldarazena, A., Hägg, T., ... & Roy, D. B. (2008). Harmonia axyridis in Europe: spread and distribution of a non-native coccinellid. 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+version = "1.3.6+0" + +[[deps.Xorg_libXfixes_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" +uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" +version = "5.0.3+4" + +[[deps.Xorg_libXi_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] +git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" +uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" +version = "1.7.10+4" + +[[deps.Xorg_libXinerama_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] +git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" +uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" +version = "1.1.4+4" + +[[deps.Xorg_libXrandr_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" +uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" +version = "1.5.2+4" + +[[deps.Xorg_libXrender_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" +uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" +version = "0.9.11+0" + +[[deps.Xorg_libpthread_stubs_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" +uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" +version = "0.1.1+0" + +[[deps.Xorg_libxcb_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" +uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" +version = "1.17.0+0" + +[[deps.Xorg_libxkbfile_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" +uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" +version = "1.1.2+0" + +[[deps.Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.4+0" + +[[deps.Xorg_xcb_util_image_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] +git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_keysyms_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_renderutil_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" +version = "0.3.9+1" + +[[deps.Xorg_xcb_util_wm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" +version = "0.4.1+1" + +[[deps.Xorg_xkbcomp_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" +uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" +version = "1.4.6+0" + +[[deps.Xorg_xkeyboard_config_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" +uuid = "33bec58e-1273-512f-9401-5d533626f822" +version = "2.39.0+0" + +[[deps.Xorg_xtrans_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +version = "1.5.0+0" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" + +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.6+0" + +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.43.0+0" + +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.9.0+0" + +[[deps.libass_jll]] +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" +version = "0.15.1+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+1" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[deps.libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" +version = "2.0.2+0" + +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + +[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.43+1" + +[[deps.libvorbis_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" +uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +version = "1.3.7+2" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" + +[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+1" +""" + +# ╔═╡ Cell order: +# ╟─14c7e803-c0ff-4211-8b60-2c9c246934dd +# ╟─6948149f-854e-4b3c-b51c-099dd221ab83 +# ╟─89551690-500d-4e37-ae20-5beb71cc87ac +# ╟─aed58771-86c1-4928-a1ba-b7d2f503b188 +# ╟─eaac6193-f4b6-4901-bd7b-1ff6025c739b +# ╟─98451eb8-8755-47fe-b8c6-ce2959256dd8 +# ╟─ccfd3dbc-a9f0-4dfb-9a04-bdc69c95796b +# ╠═d5b50429-b4d7-4d1a-aa24-d7aa6dabba4e +# ╟─ec92e20d-bd34-4d2e-a828-281cdfff5184 +# ╟─4273bd12-3df5-452d-a439-b2a612f8a138 +# ╟─aa32c5e2-0f67-4910-a612-d958fa13169c +# ╟─9dcdbf69-0750-4cab-b174-0399095dc819 +# ╠═7806ad6b-3a18-417c-98e0-a3657b9e8dd1 +# ╟─d14a7e77-eb62-44dd-bc70-0853ccd41f08 +# ╟─8959ff62-c0fd-42b8-b03a-f58439470fb1 +# ╟─0bd9835b-cfcc-440b-829e-666fd4899411 +# ╟─5f78a353-90d2-451e-ad9d-c55b9124f3ae +# ╟─61667718-20fc-40b3-87b8-a7546e2713fb +# ╟─f284fda5-aaf7-4121-a8f0-b996d501bec5 +# ╟─2a0b0c1f-9510-4f71-9d65-b4fb7c854a98 +# ╟─eacb84c4-94dc-48d0-95c4-05636650057a +# ╟─797a59c5-d120-4008-901d-14db799ab558 +# ╠═eaa2c110-9ba9-4b28-bf41-13943f54a8e6 +# ╠═ace97b1f-04ef-401a-93d8-4e6bffdb8985 +# ╟─698811dd-81b0-4a17-98f4-29109912d85f +# ╠═88e28b17-7ed5-4da5-8310-860f1d1e8cff +# ╠═00d095f7-e90f-4924-b6f1-9703ff26987f +# ╟─3574468f-6996-4e6a-b86b-21f8ef1457a6 +# ╟─d85498b1-9180-4763-b79a-9fc5c326921e +# ╟─6619d108-791d-4cea-8690-005d1bf2b3e6 +# ╟─79d65032-5b0e-412d-a69b-6aef7b1e51be +# ╠═48439a0a-cda3-4995-b69c-4d0ac8072178 +# ╟─5f342652-3dc4-4560-a66d-1862be258e9b +# ╟─6605f38c-76d8-4a73-8134-c758ccf13085 +# ╟─60c63f1b-5a27-4539-a486-78c083457b0e +# ╟─890afefc-f42b-4d74-b775-6dee5e5f0c2b +# ╟─21357c48-f35d-11ee-23f8-2534bb1d82f4 +# ╟─946cf45a-329b-42ca-9f77-a3c7bdc5611a +# ╟─e59da868-a7f5-48f0-af1b-8a990f146f20 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/scripts/MCMC.jl b/scripts/MCMC.jl index 492b1f49..c4d129f1 100644 --- a/scripts/MCMC.jl +++ b/scripts/MCMC.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 103e5ba0-cfdc-11ee-13b1-cf53dfdd9a3b diff --git a/scripts/autodiff.jl b/scripts/autodiff.jl index 28e1c5dd..b198a482 100644 --- a/scripts/autodiff.jl +++ b/scripts/autodiff.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.40 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 47f98a52-f2b2-11ea-0ac6-9b4b74b7b15d @@ -931,31 +933,35 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -ForwardDiff = "~0.10.36" -Plots = "~1.39.0" -PlutoUI = "~0.7.58" -Symbolics = "~5.14.1" -Zygote = "~0.6.69" +ForwardDiff = "~0.10.38" +Plots = "~1.40.9" +PlutoUI = "~0.7.60" +Symbolics = "~6.22.0" +Zygote = "~0.6.73" """ # ╔═╡ 00000000-0000-0000-0000-000000000002 PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.0" +julia_version = "1.10.3" manifest_format = "2.0" -project_hash = "e209e8e05c069e5b2b28053138a2dc0c41198d32" +project_hash = "29d55badf1f136800f39c64b6df5aaf1ad1aa178" [[deps.ADTypes]] -git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.7" +version = "1.11.0" -[[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "d7832de8cf7af26abac741f10372080ac6cb73df" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.34.7" + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" + ADTypesEnzymeCoreExt = "EnzymeCore" + + [deps.ADTypes.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -970,40 +976,76 @@ weakdeps = ["ChainRulesCore", "Test"] [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] -git-tree-sha1 = "0f748c81756f2e5e6854298f11ad8b2dfae6911a" +git-tree-sha1 = "6e1d2a35f2f90a4bc7c2ed98079b2ba09c35b83a" uuid = "6e696c72-6542-2067-7265-42206c756150" -version = "1.3.0" +version = "1.3.2" [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.39" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" + AccessorsUnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "d5140b60b87473df18cf4fe66382b7c3596df047" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.17.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -1011,31 +1053,52 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "1.0.1" + + [deps.Atomix.extensions] + AtomixCUDAExt = "CUDA" + AtomixMetalExt = "Metal" + AtomixoneAPIExt = "oneAPI" + + [deps.Atomix.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" + [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.Bijections]] -git-tree-sha1 = "c9b163bd832e023571e86d0b90d9de92a9879088" +git-tree-sha1 = "d8b0439d2be438a5f2cd68ec158fe08a7b2595b7" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" -version = "0.1.6" +version = "0.1.9" [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -1044,27 +1107,21 @@ version = "0.5.0" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+1" - -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" +version = "1.18.2+1" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "4e42872be98fa3343c4f8458cbda8c5c6a6fa97c" +git-tree-sha1 = "bcffdcaed50d3453673b852f3522404a94b50fad" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.63.0" +version = "1.72.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.23.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -1072,21 +1129,21 @@ weakdeps = ["SparseArrays"] [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" +version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.24.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.11.5" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] @@ -1100,9 +1157,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.12.11" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -1115,16 +1172,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.14.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -1133,39 +1195,43 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.1.1+0" [[deps.CompositeTypes]] -git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" +git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.3" +version = "0.1.4" + +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.1" +version = "2.4.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" - -[[deps.Crayons]] -git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" -uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.1.1" +version = "0.6.3" [[deps.DataAPI]] git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" @@ -1174,9 +1240,9 @@ version = "1.16.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "0f4b5d62a88d8f59003e43c25a8a90de9eb76317" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.18" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -1187,6 +1253,12 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DelimitedFiles]] deps = ["Mmap"] git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" @@ -1210,10 +1282,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.107" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -1232,27 +1304,27 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "490392af2c7d63183bfa2c8aaa6ab981c5ba7561" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.6.7" +version = "0.7.14" + + [deps.DomainSets.extensions] + DomainSetsMakieExt = "Makie" + + [deps.DomainSets.weakdeps] + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.DynamicPolynomials]] -deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "0bb0a6f812213ecc8fbbcf472f4a993036858971" +deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"] +git-tree-sha1 = "9a3ae38b460449cc9e7dd0cfb059c76028724627" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.5.5" +version = "0.6.1" [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" @@ -1261,32 +1333,38 @@ version = "1.0.4" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" +git-tree-sha1 = "8a4be429317c42cfae6a7fc03c31bad1970c310d" uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" -version = "0.0.20230411+0" +version = "0.0.20230411+1" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" +git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.5.0+0" +version = "2.6.4+1" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.Expronicon]] +deps = ["MLStyle", "Pkg", "TOML"] +git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" +uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" +version = "0.8.5" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -1298,10 +1376,10 @@ version = "4.4.4+1" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" +deps = ["LinearAlgebra"] +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.9.3" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -1311,15 +1389,15 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FixedPointNumbers]] deps = ["Statistics"] -git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[deps.Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.93+0" +version = "2.15.0+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -1328,9 +1406,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -1338,15 +1416,15 @@ weakdeps = ["StaticArrays"] [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" +git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.1+0" +version = "2.13.3+1" [[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.10+0" +version = "1.0.14+0" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -1364,34 +1442,34 @@ deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.9+0" +version = "3.4.0+1" [[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" +deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] +git-tree-sha1 = "4ec797b1b2ee964de0db96f10cce05b81f23e108" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "11.1.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.2.0" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "27442171f28c952804dede8ff72828a96f2bfc1f" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "52adc6828958ea8a0cf923d53aa10773dbca7d5f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.10" +version = "0.73.9" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "025d171a2847f616becc0f84c8dc62fe18f0f6dd" +git-tree-sha1 = "4e9e2966af45b06f24fd952285841428f1d6e858" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.10+0" +version = "0.73.9+0" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -1401,50 +1479,38 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff" +git-tree-sha1 = "48b5d4c75b2c9078ead62e345966fa51a25c05ad" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.0+0" +version = "2.82.2+1" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" +version = "1.3.14+1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.Groebner]] -deps = ["AbstractAlgebra", "Combinatorics", "ExprTools", "Logging", "MultivariatePolynomials", "PrecompileTools", "PrettyTables", "Primes", "Printf", "Random", "SIMD", "TimerOutputs"] -git-tree-sha1 = "6b505ef15e55bdc5bb3ddbcfebdff1c9e67081e8" -uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.5.1" - -[[deps.GroupsCore]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "6df9cd6ee79fc59feab33f63a1b3c9e95e2461d5" -uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" -version = "0.4.2" - [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "8e59b47b9dc525b70550ca082ce85bcd7f5477cd" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "627fcacdb7cb51dc67f557e1598cdffe4dda386d" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.5" +version = "1.10.14" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.5.0+0" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.25" [[deps.Hyperscript]] deps = ["Test"] @@ -1460,15 +1526,15 @@ version = "0.9.5" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" +git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.4" +version = "0.2.5" [[deps.IRTools]] -deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "5d8c5713f38f7bc029e26627b687710ba406d0dd" +deps = ["InteractiveUtils", "MacroTools"] +git-tree-sha1 = "950c3717af761bc3ff906c2e8e52bd83390b6ec2" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.12" +version = "0.4.14" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -1495,6 +1561,16 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsRecipesBaseExt = "RecipesBase" IntervalSetsStatisticsExt = "Statistics" +[[deps.InverseFunctions]] +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.17" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" @@ -1507,15 +1583,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.9" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1525,27 +1601,43 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3336abae9a713d2210bb57ab484b1e065edd7d23" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.2+0" +version = "3.0.4+0" + +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] +git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.31" + + [deps.KernelAbstractions.extensions] + EnzymeExt = "EnzymeCore" + LinearAlgebraExt = "LinearAlgebra" + SparseArraysExt = "SparseArrays" + + [deps.KernelAbstractions.weakdeps] + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "ab01dde107f21aa76144d0771dccc08f152ccac7" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.2" +version = "9.1.3" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1555,58 +1647,43 @@ version = "6.6.2" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" +git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +version = "0.0.34+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "18.1.7+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LabelledArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "d1f981fba6eb3ec393eede4821bca3f2b7592cd4" -uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.15.1" - -[[deps.LambertW]] -git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" -uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" -version = "0.4.6" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "cad560042a7cc108f5a4c24ea1431a9221f22c1b" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.2" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" -[[deps.Lazy]] -deps = ["MacroTools"] -git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" -uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" -version = "0.15.1" - [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1614,21 +1691,26 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -1640,46 +1722,46 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] +git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.6.0+0" +version = "1.7.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dae976433497a2f841baadea93d27e68f1a12a97" +git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.39.3+0" +version = "2.40.2+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0a04a1318df1bf510beb2562cf90fb0c386f58c4" +git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.39.3+1" +version = "2.40.2+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1687,9 +1769,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1706,15 +1788,20 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" version = "0.1.4" +[[deps.MLStyle]] +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" +uuid = "d8e11817-5142-5d16-987a-aa16d5891078" +version = "0.4.17" + [[deps.MacroTools]] deps = ["Markdown", "Random"] git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" @@ -1734,7 +1821,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1743,28 +1830,28 @@ version = "0.3.2" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "769c9175942d91ed9b83fa929eee4fe6a1d128ad" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.4" +version = "0.5.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "302fd161eb1c439e4115b51ae456da4e9984f130" +git-tree-sha1 = "a2710df6b0931f987530f59427441b21245d8f5e" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.1" +version = "1.6.0" [[deps.NaNMath]] deps = ["OpenLibm_jll"] @@ -1785,24 +1872,24 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" +version = "0.8.1+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "af81a32750ebc831ee28bdaaba6e1067decef51e" +git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.2" +version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "60e3045590bd104a16fefb12836c00c0ef8c7f8c" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.13+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1811,20 +1898,20 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.2+0" +version = "1.3.3+0" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" +version = "1.7.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+0" +version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1832,6 +1919,12 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.31" +[[deps.Pango_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +uuid = "36c8627f-9965-5494-a995-c6b170f724f3" +version = "1.54.1+0" + [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" @@ -1845,32 +1938,32 @@ version = "1.3.0" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" +git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.42.2+0" +version = "0.43.4+0" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.0" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.1.0" +version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.3" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.39.0" +version = "1.40.9" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1888,21 +1981,9 @@ version = "1.39.0" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] -git-tree-sha1 = "71a22244e352aa8c5f0f2adde4150f62368a3f2e" +git-tree-sha1 = "eba4810d5e6a01f612b948c9fa94f905b49087b0" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.58" - -[[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] -git-tree-sha1 = "01ac95fca7daabe77a9cb705862bd87016af9ddb" -uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.13" - - [deps.PreallocationTools.extensions] - PreallocationToolsReverseDiffExt = "ReverseDiff" - - [deps.PreallocationTools.weakdeps] - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" +version = "0.7.60" [[deps.PrecompileTools]] deps = ["Preferences"] @@ -1916,12 +1997,6 @@ git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.4.3" -[[deps.PrettyTables]] -deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" -uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.1" - [[deps.Primes]] deps = ["IntegerMathUtils"] git-tree-sha1 = "cb420f77dc474d23ee47ca8d14c90810cafe69e7" @@ -1932,32 +2007,55 @@ version = "0.5.6" deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +[[deps.PtrArrays]] +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" +version = "1.2.1" + [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] -git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b" +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.5.3+1" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.11.1" + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" + + [deps.QuadGK.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -[[deps.RandomExtensions]] -deps = ["Random", "SparseArrays"] -git-tree-sha1 = "b8a399e95663485820000f26b6a43c794e166a49" -uuid = "fb686558-2515-59ef-acaa-46db3789a887" -version = "0.4.4" - [[deps.RealDot]] deps = ["LinearAlgebra"] git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9" @@ -1977,22 +2075,30 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "27ee1c03e732c488ecce1a25f0d7da9b5d936574" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.3.3" +version = "3.27.4" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] + RecursiveArrayToolsStructArraysExt = "StructArrays" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -2015,40 +2121,35 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.5.1+0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "d8911cc125da009051fb35322415641d02d9e37f" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.6" - [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "09324a0ae70c52a45b91b236c62065f78b099c37" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "87e054302a94a2d087f918ad50b0290977db67e6" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.15.2" +version = "2.67.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" SciMLBasePartialFunctionsExt = "PartialFunctions" SciMLBasePyCallExt = "PyCall" SciMLBasePythonCallExt = "PythonCall" @@ -2058,6 +2159,7 @@ version = "2.15.2" [deps.SciMLBase.weakdeps] ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" @@ -2065,10 +2167,21 @@ version = "2.15.2" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.7" +version = "0.3.12" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" + +[[deps.SciMLStructures]] +deps = ["ArrayInterface"] +git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.6.1" [[deps.Scratch]] deps = ["Dates"] @@ -2092,9 +2205,9 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -2108,6 +2221,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -2117,19 +2231,25 @@ version = "0.1.2" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.5.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.3" +version = "1.9.8" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2137,14 +2257,14 @@ weakdeps = ["ChainRulesCore", "Statistics"] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2153,41 +2273,33 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.7.0" [[deps.StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf" +deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.2" +version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" +weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - -[[deps.StringManipulation]] -deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" -uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" - [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.18" -weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] +version = "0.6.21" +weakdeps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "SparseArrays", "StaticArrays"] [deps.StructArrays.extensions] StructArraysAdaptExt = "Adapt" - StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"] + StructArraysLinearAlgebraExt = "LinearAlgebra" StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" @@ -2196,31 +2308,56 @@ deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] -deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] -git-tree-sha1 = "be414bfd80c2c91197823890c66ef4b74f5bf5fe" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "8db233b54917e474165d582bef2244fa040e0a56" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.1" +version = "0.3.36" + +[[deps.SymbolicLimits]] +deps = ["SymbolicUtils"] +git-tree-sha1 = "fabf4650afe966a2ba646cabd924c3fd43577fc3" +uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3" +version = "0.2.2" [[deps.SymbolicUtils]] -deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TimerOutputs", "Unityper"] -git-tree-sha1 = "669e43e90df46fcee4aa859b587da7a7948272ac" +deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "1.5.1" +version = "3.7.2" + + [deps.SymbolicUtils.extensions] + SymbolicUtilsLabelledArraysExt = "LabelledArrays" + SymbolicUtilsReverseDiffExt = "ReverseDiff" + + [deps.SymbolicUtils.weakdeps] + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils"] -git-tree-sha1 = "8d28ebc206dec9e250e21b9502a2662265897650" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "ce9c95fc859007747a4faf10166201e0b10d4313" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.14.1" +version = "6.22.0" [deps.Symbolics.extensions] + SymbolicsForwardDiffExt = "ForwardDiff" + SymbolicsGroebnerExt = "Groebner" + SymbolicsLuxExt = "Lux" + SymbolicsNemoExt = "Nemo" + SymbolicsPreallocationToolsExt = ["PreallocationTools", "ForwardDiff"] SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" + Lux = "b2108857-7c20-44ae-9111-449ecde12c47" + Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a" + PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" [[deps.TOML]] @@ -2235,10 +2372,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2251,35 +2388,30 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" +[[deps.TermInterface]] +git-tree-sha1 = "d673e0aca9e46a2f63720201f55cc7b3e7169b16" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "2.0.0" + [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.26" [[deps.TranscodingStreams]] -git-tree-sha1 = "14389d51751169994b2e1317d5c72f7dc4f21045" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.6" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.3" [[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" - -[[deps.TruncatedStacktraces]] -deps = ["InteractiveUtils", "MacroTools", "Preferences"] -git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" -uuid = "781d530d-4396-4725-bb49-402e4bee1e77" -version = "1.4.0" +version = "0.1.9" [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" @@ -2301,23 +2433,20 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" +git-tree-sha1 = "01915bfcd62be15329c9a07235447a89d588327c" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.19.0" +version = "1.21.1" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.Unityper]] deps = ["ConstructionBase"] @@ -2325,6 +2454,15 @@ git-tree-sha1 = "25008b734a03736c41e2a7dc314ecb95bd6bbdb0" uuid = "a7c27f48-0311-42f6-a7f8-2c11e75eb415" version = "0.1.6" +[[deps.UnsafeAtomics]] +git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.3.0" +weakdeps = ["LLVM"] + + [deps.UnsafeAtomics.extensions] + UnsafeAtomicsLLVM = ["LLVM"] + [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" @@ -2350,45 +2488,45 @@ version = "1.31.0+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "07e470dabc5a6a4254ffebc29a1b3fc01464e105" +git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.5+0" +version = "2.13.5+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "31c421e5516a6248dfb22c194519e37effbf1f30" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.1+0" +version = "5.6.3+0" [[deps.Xorg_libICE_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "e5becd4411063bdcac16be8b66fc2f9f6f1e8fe5" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.0.10+1" +version = "1.1.1+0" [[deps.Xorg_libSM_jll]] -deps = ["Libdl", "Pkg", "Xorg_libICE_jll"] -git-tree-sha1 = "4a9d9e4c180e1e8119b5ffc224a7b59d3a7f7e18" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.3+0" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" +git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+0" +version = "1.8.6+1" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" +git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+0" +version = "1.0.11+1" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -2398,15 +2536,15 @@ version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" +git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+0" +version = "1.1.4+1" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+1" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -2433,22 +2571,22 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" +git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+0" +version = "0.1.1+1" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+1" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -2506,26 +2644,26 @@ version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +version = "1.5.0+1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+1" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" +git-tree-sha1 = "c7dc3148a64d1cd3768c29b3db5972d1c302661b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.69" +version = "0.6.73" [deps.Zygote.extensions] ZygoteColorsExt = "Colors" @@ -2551,32 +2689,38 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.56.3+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d" uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" -version = "3.1.1+0" +version = "3.1.1+1" [[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" +version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.7.0+0" +version = "5.8.0+1" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2585,10 +2729,10 @@ uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" version = "1.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libinput_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] @@ -2598,15 +2742,15 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2617,12 +2761,12 @@ version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/scripts/calibration.jl b/scripts/calibration.jl index 12d70bab..7e339678 100644 --- a/scripts/calibration.jl +++ b/scripts/calibration.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.43 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 3e70b82a-e4d3-4747-9679-aa5ab41d5b06 @@ -127,7 +129,7 @@ md"[mm?](https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplement MM?" # ╔═╡ 03373997-a9eb-4d5a-9ef5-8822c3f95285 -md"## Poisson" +md"## Poisson via Laplace approximation" # ╔═╡ 70f8de3c-5c5f-4ff0-92eb-e6d2a06451e1 @bind λ_pois Slider(0:0.2:50, show_value=true, default=26) @@ -141,21 +143,42 @@ xs_tiny = [2, 4, 3, 4] # ╔═╡ d733961a-094a-4724-9b16-ee669a559945 ll_pois2(λ) = sum(x->loglikelihood(Poisson(λ), x), xs_tiny) +# ╔═╡ de91d6d5-8115-4c79-9420-6f85873975b4 +plot(ll_pois2, 0.1, 10) + # ╔═╡ 46551486-d8a3-4aca-a92d-8c7f1c4439c0 pois_map(λ) = ll_pois2(λ) - log(λ) +# ╔═╡ 580a4e54-5675-45f5-a3b8-241c2d5b470d +pois_map(λ::AbstractVecOrMat) = pois_map(λ[1]) + +# ╔═╡ 87e09095-3a14-4cef-b8a3-705b9cb243d5 +plot(pois_map, 0.1, 10) + # ╔═╡ 0d6cc24c-6008-4bb7-8fb9-45223febc05b λ_star = optimize(x->-pois_map(x[1]), [mean(xs_tiny)], Newton()).minimizer[1] +# ╔═╡ 439bcebe-7607-441b-bae7-834482dd6059 +mean(xs_tiny) + # ╔═╡ 1e634f77-286b-44ce-b768-72b060ee898b md"Fisher information using the second-order derivative:" # ╔═╡ 0082f110-22df-49d5-8958-29e9516e9ca8 fi = -ForwardDiff.derivative(l->ForwardDiff.derivative(pois_map, l), λ_star) +# ╔═╡ 697e8128-40d1-4c77-acfc-b948c88c394e +ForwardDiff.hessian(pois_map, [λ_star]) + +# ╔═╡ ba822f9b-0b29-451e-9349-e08e3e5697fa +pois_map(9) + # ╔═╡ 362fe960-f247-4d7b-ab9d-01b67d1e647e σ_λ = inv(√(fi)) +# ╔═╡ f041b223-efec-4a29-a753-d6563a7f9a10 +sqrt(mean(xs_tiny)) / sqrt(length(xs_tiny)) # classical estimator voor sde + # ╔═╡ 8feddb40-5cf8-4d76-a959-dd3071c20e27 post_Laplace = Normal(λ_star, σ_λ) @@ -218,7 +241,7 @@ p = (alpha, beta, gamma, delta) lv_prob = ODEProblem(lotka_volterra!, [1.0, 1.0], (0.0, 10.0), p) # ╔═╡ b3c31cca-b472-4dec-b700-11cbff9465a9 -plot(solve(lv_prob, Tsit5()), lw=2) +plot(solve(lv_prob, Tsit5()), lw=2, ylab="population size") # ╔═╡ 14810fe9-e6fe-46c7-b6cf-9705b5974113 begin @@ -226,7 +249,7 @@ begin odedata = Array(sol) + 0.8 * randn(size(Array(sol))) # Plot simulation and noisy observations. - plot(sol; alpha=0.3) + plot(sol; alpha=0.3, ylab="population size") scatter!(sol.t, odedata'; color=[1 2], label="", marker=[:o :^]) end @@ -572,7 +595,7 @@ optimize(yeast_mod, MLE(), LBFGS()) |> coeftable ╠═╡ =# # ╔═╡ dd285391-6df6-47f7-a568-8786d2000f24 -optimize(yeast_mod, MAP(), LBFGS()) |> coeftable +optimize(yeast_mod, MAP(), NelderMead()) |> coeftable # ╔═╡ 16089b87-a760-4309-86b9-8300bb5a23cf chain_yeast = sample(yeast_mod, NUTS(), MCMCSerial(), 5000, 5); @@ -679,7 +702,7 @@ plots = Dict() # ╔═╡ 6edf2f34-1e9e-4775-bd6a-624d003b6688 let - plots["poly_data"] = scatter(xpoly, ypoly) + plots["poly_data"] = scatter(xpoly, ypoly, ylab=L"y",xlab=L"x") end # ╔═╡ 181a4886-a515-4f06-9434-64b7387ee0d3 @@ -793,7 +816,7 @@ plots["LV_diagnostic"] = plot(lv_chain) # ╔═╡ 60022e21-b74a-41b7-a43d-6b14ed482112 let - p = plot(; legend=false) + p = plot(; legend=false, ylab="population size") posterior_samples = sample(lv_chain[[:α, :β, :γ, :δ]], 300; replace=false) for p in eachrow(Array(posterior_samples)) sol_p = solve(lv_prob, Tsit5(); p=p, saveat=0.1) @@ -809,7 +832,7 @@ end # ╔═╡ 94cbbbd8-00f7-47fa-b814-0cbca085b886 let - p = plot(; legend=false) + p = plot(; legend=false, ylab="population size") posterior_samples = sample(chain2[[:α, :β, :γ, :δ]], 300; replace=false) for p in eachrow(Array(posterior_samples)) sol_p = solve(lv_prob, Tsit5(); p=p, saveat=0.1) @@ -829,7 +852,7 @@ plots["LV_counts_diag"] = plot(lv_chain3) # ╔═╡ f845114c-b612-43c1-8a49-c3da8f52e278 let - p = plot(; legend=false) + p = plot(; legend=false, ylab="population size") posterior_samples = sample(lv_chain3[[:α, :β, :γ, :δ]], 300; replace=false) for p in eachrow(Array(posterior_samples)) sol_p = solve(lv_prob, Tsit5(); p=p, saveat=0.1) @@ -852,7 +875,7 @@ plots # ╠═a10a9f8e-4088-49e2-a497-b1d253d83ecc # ╠═4b38ba22-8c3f-4c90-b42a-79063489641e # ╠═3e70b82a-e4d3-4747-9679-aa5ab41d5b06 -# ╠═0b6b3b7f-98e7-4922-82de-6a98453a627c +# ╟─0b6b3b7f-98e7-4922-82de-6a98453a627c # ╠═1b055cac-6192-438f-8f3f-9891f5f06f49 # ╠═ecceb6b5-74f4-4b5a-9c73-4ae1477b2c47 # ╠═4ca12cc9-3bae-4535-a5c9-11cac5b2c89f @@ -906,14 +929,21 @@ plots # ╠═cd3746d4-518d-476e-abf4-2ac92a2c1387 # ╠═19221533-56dd-4d87-a00f-1b8f47160b00 # ╠═37aac79a-ec46-4b6f-a9b8-abf16a5fe7b7 -# ╠═d864db4d-e240-4b90-a8f7-0327eb9e18b0 +# ╟─d864db4d-e240-4b90-a8f7-0327eb9e18b0 # ╠═6dc06148-79bf-44bf-8a5c-b6221b55bce0 # ╠═d733961a-094a-4724-9b16-ee669a559945 +# ╠═de91d6d5-8115-4c79-9420-6f85873975b4 +# ╠═87e09095-3a14-4cef-b8a3-705b9cb243d5 # ╠═46551486-d8a3-4aca-a92d-8c7f1c4439c0 +# ╠═580a4e54-5675-45f5-a3b8-241c2d5b470d # ╠═0d6cc24c-6008-4bb7-8fb9-45223febc05b +# ╠═439bcebe-7607-441b-bae7-834482dd6059 # ╟─1e634f77-286b-44ce-b768-72b060ee898b # ╠═0082f110-22df-49d5-8958-29e9516e9ca8 +# ╠═697e8128-40d1-4c77-acfc-b948c88c394e +# ╠═ba822f9b-0b29-451e-9349-e08e3e5697fa # ╠═362fe960-f247-4d7b-ab9d-01b67d1e647e +# ╠═f041b223-efec-4a29-a753-d6563a7f9a10 # ╠═8feddb40-5cf8-4d76-a959-dd3071c20e27 # ╠═8b71bd3c-60b6-425c-87cf-64652d04c8b7 # ╠═6ed728a8-80a8-457a-8908-3c840b88efae diff --git a/scripts/hiptobesquare.jl b/scripts/hiptobesquare.jl index 5f37a8e6..729c124c 100644 --- a/scripts/hiptobesquare.jl +++ b/scripts/hiptobesquare.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.43 +# v0.20.3 using Markdown using InteractiveUtils @@ -15,42 +15,6 @@ Given four points on the plane, can we determine wether they form a general quad """ -# ╔═╡ 41e1e987-1c8b-4f5b-aaa1-c6d9221dd718 -md"Look at some samples from each model." - -# ╔═╡ 865c0b8c-8154-412f-a5ce-828767e3fe4c -# likelihood function -function ll(model, ((x1, y1), (x2, y2), (x3, y3), (x4, y4))) - return logprior(model, (;x1, y1, x2, y2, x3, y3, x4, y4)) -end - -# ╔═╡ 6a884693-6a8b-423e-889e-4fb72823dd52 -examples = Dict( - 'A' => [(17.84717547196566, 19.760715118486512), (34.6061398162441, -33.38433191621974), (-1.693375136201844, -31.987940353049794), (-30.695701527005323, 6.7824003353973605)], - 'B' => [(0.06879125492495752, 23.66395708167892), (15.48365977053534, -9.183291910824748), (-12.008630133706683, -9.549131031542046), (-13.5065409760042, 23.765726315750936)], - 'C' => [(21.51869365548042, 8.158751439337376), (8.088970745018122, -21.19041987275375), (-21.269534643997858, -8.25944315605066), (-8.530202167842445, 21.010662780051337)], - 'D' => [(17.30454621153156, 11.780046713473705), (17.647126164256964, -11.935772579978874), (-17.446512799022273, -11.444824263465748), (-17.356604119938453, 12.115750066824315)] -) - -# ╔═╡ 60d39b99-826b-4d25-a589-0939218b9dda -md"Look at four figures, what type of four-sided figure fits best?" - -# ╔═╡ 1f9e8740-5f69-465c-9428-010959ad6e54 -md"What if we only know the first 3 points? (open question)" - -# ╔═╡ 72f991f2-d65a-4197-bbe4-218457ca126e -# likelihood function -function ll3(model, ((x1, y1), (x2, y2), (x3, y3), (x4, y4))) - modcond = model | (x4=0, y4=0) - return logprior(modcond, (;x1, y1, x2, y2, x3, y3)) -end - -# ╔═╡ a09ab912-9591-4c98-b68c-18a158cee8bb -md"For C, let us only use the first three points." - -# ╔═╡ 93c6a456-4c2a-4de8-b0d0-ba8ab5f84568 -((x1, y1), (x2, y2), (x3, y3), (x4, y4)) = examples['C'] - # ╔═╡ 1f6a1199-b68e-4306-a0b6-68eeb0ab0c35 @model function quadrangle(;a=40, σ=0) x1 ~ Uniform(0, a) @@ -129,6 +93,26 @@ end return [(x1, y1), (x2, y2), (x3, y3), (x4, y4)] end +# ╔═╡ 41e1e987-1c8b-4f5b-aaa1-c6d9221dd718 +md"Look at some samples from each model." + +# ╔═╡ 865c0b8c-8154-412f-a5ce-828767e3fe4c +# likelihood function +function ll(model, ((x1, y1), (x2, y2), (x3, y3), (x4, y4))) + return logprior(model, (;x1, y1, x2, y2, x3, y3, x4, y4)) +end + +# ╔═╡ 6a884693-6a8b-423e-889e-4fb72823dd52 +examples = Dict( + 'A' => [(17.84717547196566, 19.760715118486512), (34.6061398162441, -33.38433191621974), (-1.693375136201844, -31.987940353049794), (-30.695701527005323, 6.7824003353973605)], + 'B' => [(0.06879125492495752, 23.66395708167892), (15.48365977053534, -9.183291910824748), (-12.008630133706683, -9.549131031542046), (-13.5065409760042, 23.765726315750936)], + 'C' => [(21.51869365548042, 8.158751439337376), (8.088970745018122, -21.19041987275375), (-21.269534643997858, -8.25944315605066), (-8.530202167842445, 21.010662780051337)], + 'D' => [(17.30454621153156, 11.780046713473705), (17.647126164256964, -11.935772579978874), (-17.446512799022273, -11.444824263465748), (-17.356604119938453, 12.115750066824315)] +) + +# ╔═╡ 60d39b99-826b-4d25-a589-0939218b9dda +md"Look at four figures, what type of four-sided figure fits best?" + # ╔═╡ a3c06ab2-4107-4ecf-903b-71ad1d4e2749 for k in "ABCD" a = 40 @@ -147,6 +131,16 @@ for k in "ABCD" println() end +# ╔═╡ 1f9e8740-5f69-465c-9428-010959ad6e54 +md"What if we only know the first 3 points? (open question)" + +# ╔═╡ 72f991f2-d65a-4197-bbe4-218457ca126e +# likelihood function +function ll3(model, ((x1, y1), (x2, y2), (x3, y3), (x4, y4))) + modcond = model | (x4=0, y4=0) + return logprior(modcond, (;x1, y1, x2, y2, x3, y3)) +end + # ╔═╡ d7375d2b-5b9b-4729-bd99-24ca5e5696e5 for k in "ABCD" a = 40 @@ -165,6 +159,12 @@ for k in "ABCD" println() end +# ╔═╡ a09ab912-9591-4c98-b68c-18a158cee8bb +md"For C, let us only use the first three points." + +# ╔═╡ 93c6a456-4c2a-4de8-b0d0-ba8ab5f84568 +((x1, y1), (x2, y2), (x3, y3), (x4, y4)) = examples['C'] + # ╔═╡ c97046d2-1086-4226-a805-b0daaeb69cec parall_C = parallelogram() | (;x1, y1, x2, y2, x3, y3) diff --git a/scripts/modelling_ODEs.jl b/scripts/modelling_ODEs.jl index d155a1fd..91496605 100644 --- a/scripts/modelling_ODEs.jl +++ b/scripts/modelling_ODEs.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 093b722d-28af-4219-8546-39a3262146b2 @@ -142,7 +144,7 @@ coffee_sol = solve(coffee_prob, saveat=0.1, tstops=1.9:0.001:3.3) # ╔═╡ f3737612-5458-4c6e-a634-246b2cb8cb05 begin - plot(qin, 0:0.01:8, ls=:dash, label="q", color=:red, lw=2, xlab="t", title="Debit of milk added") + plot(qin, 0:0.01:8, ls=:dash, label="q [L/min]", color=:red, lw=2, xlab="t", title="Inflow of milk added") vspan!([2, 3], alpha=0.4, color=:pink, label="") end @@ -193,9 +195,11 @@ function lma_illustration(n, m; ϵ=0.05, kwargs...) scatter!(x1, y1, label="A") scatter!(x2, y2, label="B", m=:^) D = (x1 .- x2').^2 .+ (y1 .- y2').^2 .|> sqrt - n_events = count(<(ϵ), D) ÷ 2 - title!(p, "[A] = $n, [B] = $m\n $(n_events) reaction events") d = minimum(D, dims=2) + n_events = count(<(ϵ), d) + + title!(p, "[A] = $n, [B] = $m\n $(n_events) reaction events") + θs = 0:0.1:2π for i in 1:n if d[i] < ϵ @@ -336,7 +340,7 @@ latexify(michaelis_menten_kinetics, form=:ode) |> clipboard eqmm = (k₁ + k₋₁) * ES ~ k₂ * (Eₜ - ES) * S # ╔═╡ b38ed246-abf9-4808-b9eb-0f003224d98d -Symbolics.solve_for([eqmm], [ES]) +Symbolics.symbolic_linear_solve([eqmm], [ES]) # ╔═╡ 03a01f2e-cf36-426f-9df2-b8d848be7526 DS = Differential(S) @@ -422,6 +426,46 @@ end # ╔═╡ 4888025a-986f-4d68-88fb-24872d08a465 convert(ODESystem, pharkin) +# ╔═╡ 8a4c283e-de4c-4ec4-9895-92b891269133 +md"## Cell compartment model" + +# ╔═╡ d99d3d04-a384-4486-8817-a0f5c603643c +# transcription and regulation +nuc = @network_component nuc begin + α, G --> G + M + (κ₊/V,κ₋), D + G <--> DG +end + +# ╔═╡ 22fc94fa-edbf-4852-bfad-f906f5de3d75 +# translation and dimerization +cyto = @network_component cyto begin + β, M --> M + P + (k₊/V,k₋), 2P <--> D + σ, P --> 0 + μ, M --> 0 +end + +# ╔═╡ 15887746-475d-437a-844c-890223b051af +begin +# export reactions, +# γ,δ=probability per time to be exported/imported +cell_model = @network_component model begin + γ, $(nuc.M) --> $(cyto.M) + δ, $(cyto.D) --> $(nuc.D) +end + +@named cell_model = compose(cell_model, [nuc, cyto]) +end + +# ╔═╡ 478a7d14-e01a-4216-9dc7-a87abc8efe77 +latexify(complete(cell_model)) |> clipboard + +# ╔═╡ e346bff6-e406-46a2-b8df-d7746b1c01da + + +# ╔═╡ f8e77802-db0a-42b4-9852-2be16186dc99 + + # ╔═╡ ff620b5c-8aa8-4b48-83bd-de533c53f52e md"### Reactor with dead zone" @@ -521,7 +565,7 @@ TableOfContents() plots = Dict() # ╔═╡ e2b7dd60-327c-45fd-a8d7-683b5d4f1274 -plots["tank"] = plot(t->q*A/r - q*A/r*exp(-t*r/A), 0, 50, lw=2, label=L"V(t)", title="Tank filling problem") +plots["tank"] = plot(t->q*A/r - q*A/r*exp(-t*r/A), 0, 50, lw=2, label=L"V(t)", title="Tank filling problem", xlab="t") # ╔═╡ 34906c24-e13c-422f-b330-bb905c356276 let @@ -532,7 +576,7 @@ end # ╔═╡ 0cb4e475-676b-4d9c-9a75-ea0a0659c5b0 let - p = plot(coffee_sol, idxs=2, label="T", title="Coffee temperature", color=:orange, lw=2) + p = plot(coffee_sol, idxs=2, label="T [°C]", title="Coffee temperature", color=:orange, lw=2) vspan!([2, 3], alpha=0.4, color=:pink, label="") plots["coffeetemp"] = p end @@ -548,6 +592,7 @@ let prob = ODEProblem(tanks!, [0., 0.], (0.0, 100.0), (V1, V2, r1, r2, q, cin)) sol = solve(prob, saveat=0.1) plot(cin, 0, 100, label=L"C_{in}(t)", lw=2, title="Tanks in series:\nexponential input") + ylabel!("concentration [g/L]") plots["tanks_exp"] = plot!(sol, ls=:auto, label=[L"C_1(t)" L"C_2(t)"], lw=2) end @@ -584,10 +629,10 @@ plots["LMA"] = plot(plots["LMA_50_50"], plots["LMA_10_10"], plots["LMA_100_100"] plots["NO_H2"] = plot(solve(reactsyst_prob, Rosenbrock23()), lw=2, ylabel="concentration [mol/L]", ls=:auto, idxs=[1,2,3,4]) # ╔═╡ ff4a8011-1d9d-4a5a-a89f-7f032f1619e1 -plots["exp_growth"] = plot(solve(ODEProblem(growth1, [], (0., 20.))), lw=2, title="Exponential growth") +plots["exp_growth"] = plot(solve(ODEProblem(growth1, [], (0., 20.))), lw=2, title="Exponential growth", ylab="population size") # ╔═╡ 8687a35e-5efd-45b7-b36e-acbe6d3932a3 -plots["log_growth"] = plot(solve(ODEProblem(growth2, [], (0., 20.))), lw=2, title="Logistic growth") +plots["log_growth"] = plot(solve(ODEProblem(growth2, [], (0., 20.))), lw=2, title="Logistic growth", ylab="population size") # ╔═╡ d5e019dc-c8b4-4296-a3c0-921f7dc4a388 let @@ -706,21 +751,21 @@ end # ╔═╡ 0e2b9af8-9701-4d1c-838d-c289669522d1 let β, γ = 0.03, 0.3 - prob_sir = ODEProblem(sir, [], (0.0, 30.0), (;β, γ)) + prob_sir = ODEProblem(sir, [], (0.0, 30.0), [:β=>β, :γ=>γ]) plots["sir_beta=$(β)_gamma=$γ"] = plot(solve(prob_sir), lw=2, title="SIR model\nβ=$β and γ=$γ", ls=:auto) end # ╔═╡ ac6c7513-3476-4968-9d6e-eec6d09e019d let β, γ = 0.3, 0.3 - prob_sir = ODEProblem(sir, [], (0.0, 30.0), (;β, γ)) + prob_sir = ODEProblem(sir, [], (0.0, 30.0), [:β=>β, :γ=>γ]) plots["sir_beta=$(β)_gamma=$γ"] = plot(solve(prob_sir), lw=2, title="SIR model\nβ=$β and γ=$γ", ls=:auto) end # ╔═╡ d408c7dc-4a57-400d-bad2-7ac02cc4fa14 let β, γ = 0.01, 0.3 - prob_sir = ODEProblem(sir, [], (0.0, 30.0), (;β, γ)) + prob_sir = ODEProblem(sir, [], (0.0, 30.0), [:β=>β, :γ=>γ]) plots["sir_beta=$(β)_gamma=$γ"] = plot(solve(prob_sir), lw=2, title="SIR model\nβ=$β and γ=$γ", ls=:auto) end @@ -736,7 +781,7 @@ length(plots) # ╠═a52da2c2-f7df-11ee-033f-8500edb3c03f # ╠═8cff27a7-fde1-4b49-8ad6-513302997a4e # ╠═34bec0a1-40e8-48a2-9109-94872aaff1b9 -# ╠═abebedae-b977-43ae-aaa0-6b00990a5de4 +# ╟─abebedae-b977-43ae-aaa0-6b00990a5de4 # ╠═0d09ba2e-3cac-4051-b98f-26b79736b225 # ╠═fdc534e1-e334-48c1-aac4-5a89c47484e0 # ╠═104ad25e-743b-4f47-8b10-0d3d6715f95c @@ -828,6 +873,13 @@ length(plots) # ╠═350eb38a-4345-460f-89ca-63982ceadcb1 # ╠═43140694-0a7d-4fe6-af17-54662c856073 # ╠═4888025a-986f-4d68-88fb-24872d08a465 +# ╠═8a4c283e-de4c-4ec4-9895-92b891269133 +# ╠═d99d3d04-a384-4486-8817-a0f5c603643c +# ╠═22fc94fa-edbf-4852-bfad-f906f5de3d75 +# ╠═15887746-475d-437a-844c-890223b051af +# ╠═478a7d14-e01a-4216-9dc7-a87abc8efe77 +# ╠═e346bff6-e406-46a2-b8df-d7746b1c01da +# ╠═f8e77802-db0a-42b4-9852-2be16186dc99 # ╠═ff620b5c-8aa8-4b48-83bd-de533c53f52e # ╠═17689a8f-6da2-470a-b015-c55098c8a723 # ╠═2f2398ed-355f-49ff-b5e0-1fa8215b51f6 diff --git a/scripts/optimization.jl b/scripts/optimization.jl index b7185ff5..ce424827 100644 --- a/scripts/optimization.jl +++ b/scripts/optimization.jl @@ -1,17 +1,19 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) + #! format: off quote local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el end + #! format: on end # ╔═╡ 99ff6d3d-0a9c-485c-87b0-d361080fd7ca @@ -208,7 +210,7 @@ plots = Dict() # ╔═╡ 90125dda-fa19-415c-a8d7-eb37bc1dbf14 begin - p_ros = contourf(-2:0.01:2, -1:0.01:3, log10 ∘ f_rosenbrock, color= cgrad(:speed), xlab=L"x_1", ylab=L"x_1", title="Rosenbrock function", xlims=[-2,2], ylims=[-1, 3]) + p_ros = contourf(-2:0.01:2, -1:0.01:3, log10 ∘ f_rosenbrock, color= cgrad(:speed), xlab=L"x_1", ylab=L"x_2", title="Rosenbrock function", xlims=[-2,2], ylims=[-1, 3]) plots["rosenbrock"] = scatter!([1], [1], label="", color="red") end @@ -358,7 +360,7 @@ end # ╔═╡ d8ca4713-5063-47f4-8763-ae72694dac0b let - p = plot(title="Convergence for the Rosenbrock function", xscale=:log10, yscale=:log10, xlab=L"k+1", ylab=L"f(x^{(k)})-f(x^\star)", ls=:auto) + p = plot(title="Convergence rates\nRosenbrock function", xscale=:log10, yscale=:log10, xlab=L"k+1", ylab=L"f(x^{(k)})-f(x^\star)", ls=:auto) f_gd = [p.value for p in sol_GD.trace] plot!(f_gd, label="gradient descent", lw=2, color=:blue, ls=:solid) f_newton = [p.value for p in sol_newton.trace] diff --git a/scripts/simulation_tools.jl b/scripts/simulation_tools.jl index cb297d00..70f483f9 100644 --- a/scripts/simulation_tools.jl +++ b/scripts/simulation_tools.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.42 +# v0.20.3 using Markdown using InteractiveUtils @@ -47,6 +47,9 @@ end # ╔═╡ 17683127-b550-4368-9e3e-3054bd5aa208 +# ╔═╡ 89d089b2-3220-4696-9ded-364c318b4a1e +md"### Dosed bioreactor" + # ╔═╡ 21e810e7-0879-4ffb-84f9-d67dafb900d6 bacterial_growth = @reaction_network begin @species X(t)=10 G(t)=8 @@ -62,7 +65,7 @@ dosetimes = 5:5:20 timed_feeding = [dosetimes] => [bacterial_growth.G ~ bacterial_growth.G + 10] # ╔═╡ 90a998c4-5fdd-42c3-9086-267a46fe3999 -@named reactor_dosed = ReactionSystem(equations(bacterial_growth); discrete_events=timed_feeding) +#@named reactor_dosed = ReactionSystem(equations(bacterial_growth); discrete_events=timed_feeding) # ╔═╡ 4c420cd0-975a-4d3b-a6cc-9eca35490c62 md"## Stiff ODEs" @@ -375,7 +378,32 @@ let plots["bouncing_ball"] = plot(sol, lw=2, label=[L"x(t)" L"v(t)"], title="Bouncing ball with callbacks") end +# ╔═╡ 5e7453ce-721b-4e4e-8f75-bb69aac8cf42 +let + @unpack G = bacterial_growth + dosing = [5, 10, 15, 20] => [G ~ G + 10] + + @named dosed_reactor = ReactionSystem(equations(bacterial_growth), + discrete_events=dosing) + + dosed_reactor = complete(dosed_reactor) + + oprob = ODEProblem(dosed_reactor, [], (0, 20)) + + sol = solve(oprob, Tsit5()) + + prob = ODEProblem(bacterial_growth, [], (0, 20)) + + plots["undosed bioreactor"] = plot(solve(prob, Tsit5()), lw=2, + title="Undosed bioreactor") + + plots["dosed_bioreactor"] = plot(sol, lw=2, title="Dosed bioreactor") + +end + # ╔═╡ 7b3ca635-5a3c-43f2-9690-5cdbd9074ed2 +# ╠═╡ disabled = true +#=╠═╡ let dosetimes = 5:5:20 affect!(integrator) = integrator.u[2] += 10 @@ -387,6 +415,7 @@ let title="Undosed bioreactor") plots["dosed_bioreactor"] = plot(sol, lw=2, title="Dosed bioreactor") end + ╠═╡ =# # ╔═╡ e22ed4e6-6420-490c-9d55-fee19069f534 let @@ -423,7 +452,7 @@ let W .-= X[[1], :] # start at 0 W .*= √(τ) p = plot(tsteps, W, lw=2, xlab=L"t", ylab=L"W(t)", - title="Five draws form a Wiener process", label="") + title="Five draws from a Wiener process", label="") plots["Wiener"] = p p end @@ -447,6 +476,39 @@ let p end +# ╔═╡ dc583986-3b76-44a7-ad5a-909aa392c38b +let + τ = 0.01 # stepsize + tsteps = 0:τ:15 + X = randn(length(tsteps), 10) + W = cumsum(X, dims=1) + W .-= X[[1], :] # start at 0 + W .*= √(τ) + p = plot(W[:,1:2:end], W[:,2:2:end], lw=2, xlab=L"x", ylab=L"y", + title="Five draws from a Wiener process (2D)", label="", alpha=0.8, aspect_ratio=:equal) + plots["Wiener_2D"] = p + p +end + +# ╔═╡ f3ec3c15-aa56-4b20-ad83-2acec0aad6b6 +let + τ = 0.02 # stepsize + tsteps = 0:τ:20 + n=5 + X = randn(length(tsteps), 15) + W = cumsum(X, dims=1) + W .-= X[[1], :] # start at 0 + W .*= √(τ) + + p = plot(lw=2, xlab=L"x", ylab=L"y", zlab=L"z", + title="Five draws from a Wiener process (3D)", label="", alpha=0.8, aspect_ratio=:equal) + for i in 1:3:15 + plot3d!(W[:,i], W[:,i+1], W[:,i+2], alpha=0.8, label="") + end + plots["Wiener_3D"] = p + p +end + # ╔═╡ 3d549763-2ba2-48b6-b486-2ddd462977dd let p = plot(solve(sprob_bm), lw=2) @@ -575,7 +637,9 @@ plots # ╠═992d2b4f-6521-4368-910d-3e7ef07fb6df # ╠═17683127-b550-4368-9e3e-3054bd5aa208 # ╠═0de4a715-89d6-403b-ac65-adaed6062371 +# ╟─89d089b2-3220-4696-9ded-364c318b4a1e # ╠═21e810e7-0879-4ffb-84f9-d67dafb900d6 +# ╠═5e7453ce-721b-4e4e-8f75-bb69aac8cf42 # ╠═7b3ca635-5a3c-43f2-9690-5cdbd9074ed2 # ╠═4c7feb9f-a039-48a8-a7d0-3633f1a635fe # ╠═5ae78d7c-fc07-45f3-a59b-eb032ff2974d @@ -595,6 +659,8 @@ plots # ╠═945febc8-2954-4d5c-a4b1-7f95c70ef4b6 # ╟─5099fd5b-735e-4de3-918a-685dd4a82c22 # ╟─18def41b-0827-4356-adfa-d3fc63e23cfa +# ╟─dc583986-3b76-44a7-ad5a-909aa392c38b +# ╠═f3ec3c15-aa56-4b20-ad83-2acec0aad6b6 # ╠═6501070e-9093-4928-89b9-b9dd34128810 # ╠═6c5f1ee1-ece0-4a44-8e92-c375f2bd40a7 # ╠═7d0a5294-6fc2-45d5-b04f-2824649f5d81 @@ -664,10 +730,10 @@ plots # ╠═0b52aede-1a71-4034-9921-2ffc9120c0ae # ╠═9d84b996-a3e2-48c1-ae51-2bfc343bff0f # ╠═4aa42d80-81b5-4144-8b4a-6c3ebf29d84b -# ╠═ae5be024-863d-46f1-b5d9-fc691b10e63b +# ╟─ae5be024-863d-46f1-b5d9-fc691b10e63b # ╠═52082e32-8c8f-4699-a44a-2fbe99b96319 # ╠═5bbf9db9-4537-416d-9edc-6487961b1690 -# ╠═6f6ba9c5-bc87-4b71-82a0-a4c64750a2ab +# ╟─6f6ba9c5-bc87-4b71-82a0-a4c64750a2ab # ╠═2bf198cd-4463-4f97-975e-f805a37fa780 # ╠═13036978-3008-4d7e-9661-a967381f4db6 # ╠═23c38172-8916-42e3-a186-5cdd16939b5b diff --git a/scripts/uncertainty.jl b/scripts/uncertainty.jl index b544beba..c3a74464 100644 --- a/scripts/uncertainty.jl +++ b/scripts/uncertainty.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.43 +# v0.20.3 using Markdown using InteractiveUtils @@ -101,13 +101,13 @@ generated_quantities(sir_mc(), throw) md"[Using the Beer-Lambert Law to Calculate the Concentration of a Solution | Chemistry | Study.com](https://study.com/skill/learn/using-the-beer-lambert-law-to-calculate-the-concentration-of-a-solution-explanation.html)" # ╔═╡ e6bfb7d1-e594-41c9-9ee2-9668cae70e71 -I = 0.2 ± 0.03; +Iobs = 0.2 ± 0.03; # ╔═╡ ccf61cf5-33b2-4349-a422-16a7c883038d I0 = 1.29 ± 0.06; # ╔═╡ 5a9da0cd-9809-445e-aeb3-b91875064106 -A = log10(I0 / I) +A = log10(I0 / Iobs) # ╔═╡ ae807e33-3e05-4a3d-a591-2b0e04c9d6d8 ϵ = 8850 ± 50; @@ -116,7 +116,7 @@ A = log10(I0 / I) l = 3 ± 5e-4; # ╔═╡ 8cf4e046-c979-4633-b922-43a46c914f3c -c = log10(I0 / I) / (l * ϵ) +c = log10(I0 / Iobs) / (l * ϵ) # ╔═╡ a3f82cf6-b25d-4de1-b264-93d6e047ec6d md"Radius of a circle" @@ -343,7 +343,7 @@ plots["mm_sens_vmax"] = plot(sens_mm_mumax, 0, 100, lw=2, title="Michaelis-Mente plots["mm_sens_vmax_rel"] = plot(sens_mm_mumax_rel, 0, 100, lw=2, title="Michaelis-Menten sensitivity (relative)", label="local sensititivity w.r.t. vmax", xlab="S [mol/L]", ylab="Sensitivity", ylims=(0, 2)) # ╔═╡ 7e7956b5-43fc-48fb-92ff-67d0fdb875b1 -plots["mm_sens"] = plot(plots["mm_sens_Ks"], plots["mm_sens_Ks_rel"], plots["mm_sens_vmax_rel"], plots["mm_sens_vmax"], size=(1000, 800)) +plots["mm_sens"] = plot(plots["mm_sens_Ks"], plots["mm_sens_vmax"], plots["mm_sens_Ks_rel"], plots["mm_sens_vmax_rel"], size=(1000, 800)) # ╔═╡ 71e3de0e-03d6-491b-9a1d-071e03f1f6ef plots["cuminf"] = contourf(β_vals, γ_vals, (g, l)->sir_summary((g, l))[1], color=:speed,