diff --git a/README.md b/README.md index 7d2abae..951a64d 100644 --- a/README.md +++ b/README.md @@ -54,11 +54,11 @@ You should now be ready to reproduce the analysis. - `basic_omnivory_module.jl`: includes all basic building blocs including the basic set of ODEs (`model!()`) and the functions to compute the different metrics (e.g. `overshoot()`); - `pulse.jl`: functions to run pulse analysis; - `press.jl`: functions to run press analysis; -- `fig_press.jl`: script to create pulse figures (Figs. 3 (a-c), 4 (a-c), S3 (a-c), S4 (a-c)); -- `fig_pulse.jl`: script to create press figures (Figs. 3 (d-f), 4 (d-f), S3 (d-f), S4 (d-f)); +- `fig_press.jl`: script to create pulse figure panels (Figs. 3 (a-c), 4 (a-c), S3 (a-c), S4 (a-c)); +- `fig_pulse.jl`: script to create press figure panels (Figs. 3 (d-f), 4 (d-f), S3 (d-f), S4 (d-f)); - `fig_S1.jl`: script to create figure S1; -- `fig_S2.jl`: script to create figure S2. -- `pipeline.jl`: orchestrate the different scripts to reproduce the analysis. +- `fig_S2.jl`: script to create figure S2; +- `pipeline.jl`: orchestrates the different scripts to reproduce the analysis. ## How to reproduce the analysis locally @@ -71,7 +71,7 @@ julia src/pipeline.jl -## Questions +## Questions? -Script have been commented for ease of comprehension but if you still have some questions regarding the numerical implementation, do not hesitate to open an issue. +Scripts have been commented for ease of comprehension but if you still have some questions regarding the numerical implementation, do not hesitate to create an issue. diff --git a/src/fig_S1.jl b/src/fig_S1.jl index cfa71cd..3924296 100644 --- a/src/fig_S1.jl +++ b/src/fig_S1.jl @@ -3,6 +3,7 @@ include("pulse.jl") using PyPlot pygui(true) +# PRESS SIMULATIONS for ranges of K, aCP, eCP and mP. # range of K println("Simulations for a range of K values") diff --git a/src/fig_S2.jl b/src/fig_S2.jl index ccea22f..a576c73 100644 --- a/src/fig_S2.jl +++ b/src/fig_S2.jl @@ -3,7 +3,7 @@ include("press.jl") using PyPlot pygui(true) - +# PULSE SIMULATIONS for ranges of K, aCP, eCP and mP. # range of K println("Simulations for a range of K values") diff --git a/src/pipeline.jl b/src/pipeline.jl index 916b263..e9eeed7 100644 --- a/src/pipeline.jl +++ b/src/pipeline.jl @@ -1,4 +1,6 @@ -# Install packagess +# Orchestrates scripts + +# Install packages printstyled("1. Installing packages\n", color = :blue) include("install_packages.jl") diff --git a/src/press.jl b/src/press.jl index c05d844..4b376b5 100644 --- a/src/press.jl +++ b/src/press.jl @@ -1,6 +1,6 @@ using DifferentialEquations, NLsolve -# analysis for one press simulation (1 system) +# Full analysis for one press simulation (1 system) function press_unit(par, p_strength) # Parameters u0 = [1.0, 1.5, 1.5] diff --git a/src/pulse.jl b/src/pulse.jl index f88b6e8..0f067ad 100644 --- a/src/pulse.jl +++ b/src/pulse.jl @@ -1,7 +1,6 @@ -# Simulation for pulse experiment using DifferentialEquations, NLsolve -# analysis for one pulse simulation (1 system) +# Entire analysis for one pulse simulation (1 system) function pulse_unit(par, p_length, p_strength) # Parameters u0 = [1.0, 1.5, 1.5]