From 5876c678a4cc6fafa24fd70905adaeca25be9ab8 Mon Sep 17 00:00:00 2001 From: Torkel Date: Thu, 30 May 2024 17:05:24 -0400 Subject: [PATCH] update pages.jl --- docs/old_files/petab_ode_param_fitting.md | 2 +- docs/pages.jl | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/old_files/petab_ode_param_fitting.md b/docs/old_files/petab_ode_param_fitting.md index 4a1a87d87f..9e503d7411 100644 --- a/docs/old_files/petab_ode_param_fitting.md +++ b/docs/old_files/petab_ode_param_fitting.md @@ -41,7 +41,7 @@ Generally, PEtab takes five different inputs to define an optimisation problem ( 4. **Experimental (or simulation) conditions**: The simulations (each corresponding to a potential experiment) carried out during each step of the optimisation process (a `Dict{String,Dict{Symbol,Float64}}`). 5. **Measurements**: The measurements to which the model is fitted (a `DataFrame`). -### [Observables](@id petab_parameter_fitting_intro_observables) +### Observables The observables define the quantities that we may measure in our experiments. Typically, each corresponds to a single species, however, [more complicated observables are possible](@ref petab_observables_observables). For each observable, we also need a noise formula, defining the uncertainty in its measurements. By default, PEtab assumes normally distributed noise, with a mean equal to the true value and a standard deviation which we have to define. It is also possible to use [more advanced noise formulas](@ref petab_observables_noise_formula). In our example, we only have a single possible observable, the `P` species. We will assume that the noise is normally distributed with a standard deviation `0.5` (in our case this is not true, however, typically the noise distribution is unknown and a guess must be made). We combine this information in a `PEtabObservable` struct (to access the `P` species we must use [`@unpack`](@ref simulation_structure_interfacing_symbolic_representation)). Finally, we store all our observables in a dictionary, giving each an id tag (which is later used in the measurements input). diff --git a/docs/pages.jl b/docs/pages.jl index 96e6587bf3..96961289f1 100644 --- a/docs/pages.jl +++ b/docs/pages.jl @@ -2,8 +2,8 @@ pages = Any[ "Home" => "home.md", "Introduction to Catalyst" => Any[ "introduction_to_catalyst/catalyst_for_new_julia_users.md", - "introduction_to_catalyst/introduction_to_catalyst.md" - # Advanced introduction. + "introduction_to_catalyst/introduction_to_catalyst.md", + "introduction_to_catalyst/advanced_intro_to_catalyst.md" ], "Model Creation and Properties" => Any[ "model_creation/dsl_basics.md",