🎨 reproduce SI figures too

Author: Kevin Cazelles

.gitignore

@@ -1,5 +1,5 @@
-#
-figs*/*.svg
+# project specific files
+fig/*.svg
 src/figs/*.svg
 src/res
 *.zip

src/basic_omnivory_module.jl

@@ -181,7 +181,7 @@ function plot_sa_unit_rev(rg, res, id, leg = false, xlb = "", ylb = "")
 end 
 
 
-# helper function to check out degree of omnivory
+# Helper function to check out degree of omnivory
 function check_doo(res, rgs)
     type = ["Fixed" "Responsive"]
     phase = ["Equilibrium", "Pulse", "Transient", "New Equilibrium"]

src/fig_press.jl

@@ -2,18 +2,33 @@ include("basic_omnivory_module.jl")
 include("press.jl")
 using PyPlot
 
-# PRESS SIMULATION
-par = ModelPar()
-# NB: for FigS4, use
-# par = ModelPar(e_CP = 0.5, e_RC = 0.5, e_RP = 0.5)
+# PRESS SIMULATIONS
+# returns dynamics and metrics in different panels, we actually dispatch the 
+# different pannels between figure 3 and 4 with Inkscape (we did the same
+# for figures S3 and S4).
+
+# we pass "true" to this ARGS for supplementary figures
+if isempty(ARGS) || ARGS[1] != "true"
+    # default for main figures 3 and 4
+    par = ModelPar()
+    fl_fig = "fig/fig_press.svg"
+else 
+    # parameters for SI figures S3 and S4
+    par = ModelPar(e_CP = 0.5, e_RC = 0.5, e_RP = 0.5)
+    fl_fig = "fig/fig_press_si.svg"
+end 
+
+# run the simulation
 res = press(par, 0.1, 1.2)
-# check equilibria 
+
+# temporal ranges of the different phases
 rgs = [
     280:0.01:299,
     300:0.01:320,
     320:0.01:550,
     880:0.01:900
     ]
+# check degree of omnivory for the different phases
 check_doo(res, rgs)
 
 # plot helper
@@ -108,5 +123,4 @@ ylabel("Max - Min")
 plt.legend()
 
 tight_layout()
-savefig("fig/fig_3.svg")
-# savefig("fig/fig_S3.svg")
+savefig(fl_fig)

src/fig_pulse.jl

@@ -3,21 +3,35 @@ include("pulse.jl")
 using PyPlot
 pygui(true)
 
+# PULSE SIMULATIONS
+# returns dynamics and metrics in different panels, we actually dispatch the 
+# different pannels between figure 3 and 4 with Inkscape (we did the same
+# for figures S3 and S4).
 
-# PULSE SIMULATION
-par = ModelPar()
-# NB: for FigS3, use
-# par = ModelPar(e_CP = 0.5, e_RC = 0.5, e_RP = 0.5)
-# this returns all the results required for figure 3
+# we pass "true" to this ARGS for supplementary figures
+if isempty(ARGS) || ARGS[1] != "true"
+    # default for main figures 3 and 4
+    par = ModelPar()
+    fl_fig = "fig/fig_pulse.svg"
+else 
+    # parameters for SI figures S3 and S4
+    par = ModelPar(e_CP = 0.5, e_RC = 0.5, e_RP = 0.5)
+    fl_fig = "fig/fig_pulse_si.svg"
+end
+
+# run pulse simulation
 res = pulse(par, 0.1, 2.0, 2.0)
-# check equilibria (NB the par should affetc the 2 last ranges if going back to equilibrium takes more time)
+
+# temporal ranges of the different phases
 rgs = [
     180:0.01:199,
     200:0.01:205,
     205:0.01:325,
     325:0.01:350
     ]
+# check degree of omnivory for the different phases
 check_doo(res, rgs)
+
 # plot helper
 function plot_illustration(sol, eq, ttl_id, leg = true, y_max = 5)
     RCP_cols = ["#1f77b4", "#ff7f0e", "#2ca02c"]
@@ -107,6 +121,5 @@ ylabel("Max - Min")
 plt.legend()
 
 tight_layout()
-savefig("fig/fig_4.svg")
-# savefig("fig/fig_S3.svg")
+savefig(fl_fig)
 

src/pipeline.jl

@@ -2,29 +2,42 @@
 printstyled("1. Installing packages\n", color = :blue)
 include("install_packages.jl")
 
-## Pulse main 
+
+# Main 
+## Pulse 
 printstyled("2. Runing pulse analysis\n", color = :blue)
 include("fig_pulse.jl")
 printstyled("Done! fig_pulse.jl created\n\n", color = :green)
-
-## Press main 
+## Press 
 printstyled("3. Runing press analysis\n", color = :blue)
 include("fig_press.jl")
 printstyled("Done! fig_pulse.jl created\n", color = :green)
 
-## Pulse main 
+
+# Supplementary Information 
+
+# The line below is used to run the SI version of the figure: when the 1st
+# argument of 'ARGS' is true, then the parameters used are the one for the SI
+# figure. Note that we actually use `ARGS` because this is specifically
+# the vector that captures external arguments. Thus using it allows us to use 
+# arguments in the command line. So here, to run the SI version of fig_pulse, 
+# I'd use `julia fig_pulse.jl true`. To mimic this we simply add "true" to 
+# ARGS here rather than via an external argument
+push!(ARGS, "true")
+
+## Pulse
 printstyled("4. Runing pulse analysis for SI\n", color = :blue)
-include("fig_pulse.jl", ARGS = ["true"])
+include("fig_pulse.jl")
 printstyled("Done! fig_pulse_si.jl created\n\n", color = :green)
 
-## Press main 
+## Press 
 printstyled("5. Runing press analysis for SI\n", color = :blue)
-include("fig_press.jl", ARGS = ["true"])
+include("fig_press.jl")
 printstyled("Done! fig_press_si.jl created\n\n", color = :green)
 
 # Figures S2 and S3 takes ~2hours each and basically call the same functions 
 # as previous analyses so we skipped them on GitHub Actions
-printstyled("Fig S1 and S2 are skipped\n\n", color = :red)
+printstyled("NB: Fig. S1 and S2 are skipped because they are time/energy-consuming\n\n", color = :red)
 
 # Figure S2 takes ~2hours
 # printstyled("Runing simulations for FigS1\n", color = :blue)

src/press.jl

@@ -1,5 +1,6 @@
 using DifferentialEquations, NLsolve
 
+# analysis for one press simulation (1 system)
 function press_unit(par, p_strength) 
     # Parameters
     u0 = [1.0, 1.5, 1.5]

src/pulse.jl

@@ -1,12 +1,7 @@
 # Simulation for pulse experiment
 using DifferentialEquations, NLsolve
 
-function find_time_hit_res_max(res)
-    max_res = findmax(res[1,:])
-    return res.t[max_res[2]]
-end
-
-
+# analysis for one pulse simulation (1 system)
 function pulse_unit(par, p_length, p_strength) 
     # Parameters   
     u0 = [1.0, 1.5, 1.5]