diff --git a/README.md b/README.md index d13c0ac..234233c 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ ps = [1e-4, 1e-2] # Model: non-Markovian part (delay reactions) τ = 20.0 delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) # add a delay time τ to the first delay channel + append!(integrator.de_chan[1], τ) # add a delay time τ to the first delay channel end delay_trigger = Dict(1 => delay_trigger_affect!) # the first reaction S+I -> E+I will trigger a delay reaction: E --> I after τ time. delay_complete = Dict(1 => [2 => 1, 3 => -1]) # E --> I after τ time: transfer from E (minus 1) to I (plus 1) after the completed delay reaction @@ -111,7 +111,7 @@ ps = [0.0282, 3.46] delay_trigger_affect! = [] for i in 1:burst_sup push!(delay_trigger_affect!, function (integrator, rng) - return append!(integrator.de_chan[1], fill(τ, i)) + append!(integrator.de_chan[1], fill(τ, i)) end) end delay_trigger = Dict([Pair(i, delay_trigger_affect![i]) for i in 1:burst_sup]) diff --git a/docs/src/tutorials/bursty.md b/docs/src/tutorials/bursty.md index 34511e0..88510a1 100644 --- a/docs/src/tutorials/bursty.md +++ b/docs/src/tutorials/bursty.md @@ -44,7 +44,7 @@ Next, we define the non-Markovian part. Here we mainly need to consider the dela delay_trigger_affect! = [] for n in 1:burst_sup push!(delay_trigger_affect!, function (integrator, rng) - return append!(integrator.de_chan[1], fill(τ, n)) + append!(integrator.de_chan[1], fill(τ, n)) end) end delay_trigger = Dict([Pair(i, delay_trigger_affect![i]) for i in 1:burst_sup]) diff --git a/docs/src/tutorials/delay_degradation.md b/docs/src/tutorials/delay_degradation.md index 1e171aa..33decf5 100644 --- a/docs/src/tutorials/delay_degradation.md +++ b/docs/src/tutorials/delay_degradation.md @@ -58,7 +58,7 @@ Then we turn to the definition of delay reactions ```julia τ = 15.0 delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(3 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => -1]) @@ -177,7 +177,7 @@ dprob = DiscreteProblem(u0, tspan, p) τ = 15.0 delay_trigger_affect! = function (integrator, rng) append!(integrator.de_chan[1], τ) - return append!(integrator.de_chan[2], τ) + append!(integrator.de_chan[2], τ) end delay_trigger = Dict(3 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => -1], 2 => [3 => -1]) diff --git a/docs/src/tutorials/stochastic_delay.md b/docs/src/tutorials/stochastic_delay.md index 684efec..ec04f8f 100644 --- a/docs/src/tutorials/stochastic_delay.md +++ b/docs/src/tutorials/stochastic_delay.md @@ -43,7 +43,7 @@ Unlike other examples, the elongation time $\tau$ is a random variable sampled f ```julia delay_trigger_affect! = function (integrator, rng) τ = rand(LogNormal(1, sqrt(2))) + 120 - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(3 => delay_trigger_affect!) delay_complete = Dict(1 => [3 => -1]) diff --git a/examples/bursty.jl b/examples/bursty.jl index e106832..e71e088 100644 --- a/examples/bursty.jl +++ b/examples/bursty.jl @@ -1,6 +1,6 @@ ## This example shows an application of `DelaySSA.jl` for a bursty model with delay -## A Bursty model with delay is described as +## A Bursty model with delay is described as # ab^n/(1+b)^(n+1): 0 -> n P, which triggers n P to degrade after delay time τ using DelaySSAToolkit @@ -30,7 +30,7 @@ dprob = DiscreteProblem(jumpsys, u0, tspan, ps) delay_trigger_affect! = [] for i in 1:burst_sup push!(delay_trigger_affect!, function (integrator, rng) - return append!(integrator.de_chan[1], fill(τ, i)) + append!(integrator.de_chan[1], fill(τ, i)) end) end delay_trigger_affect! diff --git a/examples/delay_degradation.jl b/examples/delay_degradation.jl index ae3d1b2..4e1397d 100644 --- a/examples/delay_degradation.jl +++ b/examples/delay_degradation.jl @@ -37,7 +37,7 @@ dprob = DiscreteProblem(u0, tspan, p) τ = 15.0 delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(3 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => -1]) diff --git a/examples/delay_oscillator.jl b/examples/delay_oscillator.jl index 868d11d..c837076 100644 --- a/examples/delay_oscillator.jl +++ b/examples/delay_oscillator.jl @@ -3,7 +3,7 @@ using Catalyst # using Plots ################################################################################ # the following example illustrates how to deal with a oscillatory system -# d: X-> 0; k1/(1+Y^2): 0-> X; [trigger X-> Y after τ time;] k2*Y/(1+Y): Y-> 0; +# d: X-> 0; k1/(1+Y^2): 0-> X; [trigger X-> Y after τ time;] k2*Y/(1+Y): Y-> 0; rn = @reaction_network begin 1 / (1 + Y^2), 0 --> X @@ -21,7 +21,7 @@ dprob = DiscreteProblem(jumpsys, u0, tspan) # jumpsys.dep_graph delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(1 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => 1, 1 => -1]) diff --git a/examples/seir.jl b/examples/seir.jl index 17df225..2d3d003 100644 --- a/examples/seir.jl +++ b/examples/seir.jl @@ -17,7 +17,7 @@ ps = [1e-4, 1e-2] τ = 20.0 dprob = DiscreteProblem(jumpsys, u0, tspan, ps) delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(1 => delay_trigger_affect!) # delay_trigger = Dict(1=>[1=>τ]) diff --git a/examples/stochastic_delay.jl b/examples/stochastic_delay.jl index cd8dcaf..d63070e 100644 --- a/examples/stochastic_delay.jl +++ b/examples/stochastic_delay.jl @@ -17,7 +17,7 @@ dprob = DiscreteProblem(u0, tspan, p) delay_trigger_affect! = function (integrator, rng) τ = rand(LogNormal(1, sqrt(2))) + 120 - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(3 => delay_trigger_affect!) delay_complete = Dict(1 => [3 => -1]) @@ -49,7 +49,7 @@ histogram( delay_trigger_affect2! = function (integrator, rng) τ = rand(LogNormal(0, 2)) + 120 - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger2 = Dict(3 => delay_trigger_affect2!) delayjumpset2 = DelayJumpSet(delay_trigger2, delay_complete, delay_interrupt) diff --git a/test/cascade_of_delay_reaction.jl b/test/cascade_of_delay_reaction.jl index bc39d55..bbbdf5e 100644 --- a/test/cascade_of_delay_reaction.jl +++ b/test/cascade_of_delay_reaction.jl @@ -8,7 +8,7 @@ end delay_trigger_affect! = [] chain_len = 10 delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], 1.0) + append!(integrator.de_chan[1], 1.0) end u0 = zeros(chain_len) @@ -22,7 +22,7 @@ for i in 1:(chain_len - 1) push!(delay_complete_affect!, function (integrator, rng) integrator.u[i] -= 1 # A_prev minus 1 integrator.u[i + 1] += 1 # A plus 1 - return append!(integrator.de_chan[i + 1], 1.0) # add to the delay channel + append!(integrator.de_chan[i + 1], 1.0) # add to the delay channel end) end push!(delay_complete_affect!, function (integrator, rng) diff --git a/test/delay_problem_test.jl b/test/delay_problem_test.jl index ec7a207..aae74d7 100644 --- a/test/delay_problem_test.jl +++ b/test/delay_problem_test.jl @@ -15,7 +15,7 @@ ps = [1e-4, 1e-2] # parameters for ρ, r dprob = DiscreteProblem(u0, tspan, ps) delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(1 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => 1, 3 => -1]) diff --git a/test/dep_gr_delay.jl b/test/dep_gr_delay.jl index d7818bc..afc5aad 100644 --- a/test/dep_gr_delay.jl +++ b/test/dep_gr_delay.jl @@ -15,7 +15,7 @@ tspan = (0, tf) dprob = DiscreteProblem(jumpsys, u0, tspan) delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(1 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => 1], 2 => [1 => -1]) diff --git a/test/remake_test.jl b/test/remake_test.jl index 1f63f1a..3522d92 100644 --- a/test/remake_test.jl +++ b/test/remake_test.jl @@ -14,7 +14,7 @@ ps = [1e-4, 1e-2] # parameters for ρ, r dprob = DiscreteProblem(u0, tspan, ps) delay_trigger_affect! = function (integrator, rng) - return append!(integrator.de_chan[1], τ) + append!(integrator.de_chan[1], τ) end delay_trigger = Dict(1 => delay_trigger_affect!) delay_complete = Dict(1 => [2 => 1, 3 => -1])