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Fix: Clearer example more similar to R/Pythons
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@ludmillafigueiredo
ludmillafigueiredo committed Jan 31, 2022
1 parent b9e4afc commit e20174b
Showing 1 changed file with 32 additions and 43 deletions.
75 changes: 32 additions & 43 deletions examples/modelstudy_jl/modelstudy_jl.jl
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@@ -1,5 +1,5 @@
### A Pluto.jl notebook ###
# v0.16.1
# v0.17.7

using Markdown
using InteractiveUtils
Expand All @@ -9,12 +9,11 @@ begin
using Distributions, Random, DifferentialEquations, Plots, Test, Debugger, ComponentArrays,PlutoUI

## Paths to relevant folders
data_dir = joinpath("results", "clean_data");
data_dir = joinpath("results", "data", "process");
scripts_dir = joinpath("results", "scripts");
suppl_dir = joinpath("results", "supplementary");
semiprods_dir = joinpath("results", "semi_products");
figures_dir = joinpath("text", "figures");
tables_dir = joinpath("text", "tables");
figs_dir = joinpath("text", "figures");
tabs_dir = joinpath("text", "tables");
end

# ╔═╡ 307335ba-cf46-11eb-28b0-f199cf048ae6
Expand All @@ -37,18 +36,18 @@ $\frac{dP_i}{dt}(mutualistic) = r_{Pi}P_i - D_{Pi}P_{i}² +\sum_{j=1}^{N_a}\frac
where
_P_ is the plant species density (1 \times 2 matrix)
_P_ is the plant species density (1 x 2 matrix)
_A_ is the animal species density (2 \times 1 matrix)
_A_ is the animal species density (2 x 1 matrix)
_r_ is the intrisic growth rate of A or P (2 \times 1 matrix for each),
_r_ is the intrisic growth rate of A or P (2 x 1 matrix for each),
_D_ is the density-dependent self-limitation of A or P (2 \times 1 matrix for each),
_D_ is the density-dependent self-limitation of A or P (2 x 1 matrix for each),
_c_ is the maximal rate of trophic/mutualistic interaction (2 \times 2 matrix),
_c_ is the maximal rate of trophic/mutualistic interaction (2 x 2 matrix),
\alpha is the half saturation constants of the functional response
_alpha_ is the half saturation constants of the functional response
"""

# ╔═╡ c44e930c-3969-4db6-bab8-4f91ba640f7f
Expand Down Expand Up @@ -126,9 +125,8 @@ end
# ╔═╡ 511a8b7b-31f4-4397-9d63-4d30d67df46c
md"""
## Results
### Main text material
In this example, let's assume we use the plot of the 1x1x1 system above in the main text. The code to generate such figure can be included, even if the figure is not, to avoid unnecessary repetition and confusion. In that case, simply saving the final product with a clear name should be enough for the reader to understand and reproduce the results.
The same could be done for tables.
### Figure 1
Implementation of a system with two herbivores, two plants, and two pollinator species.
"""

# ╔═╡ f0f30840-5c78-41c3-99ec-f6f62587b557
Expand All @@ -138,14 +136,13 @@ begin
xaxis = "Time", yaxis = "Density",
##label = ["Herb. 1" "Herb. 2" "Poll. 1" "Poll. 2" "Plant 1" "Plant 2"],
lw = 2, legend = :bottomright)
savefig(joinpath(figures_dir, "fig1_maintext.png"))
savefig(joinpath(figs_dir, "fig1_main.png"))
end

# ╔═╡ 5c87b202-98d3-4922-a643-d5640bdd5979
md"""
### Suplementary material
Suplementary material can be processed and displayed directly in the file.
Say you want to create the plots of the dynamics of each single species.
### Figure S1
Implementation of a system of one herbivore, one pollinator, and one plant species, whose abundance is iniated as 0.
"""

# ╔═╡ a101389e-adb1-42ef-80ad-d360a17a96a9
Expand All @@ -157,13 +154,7 @@ begin

prob_interact_Pl0 = ODEProblem(interact!, N0_Pl0, tspan, par);
sol_interact_Pl0 = solve(prob_interact_Pl0);
end

# ╔═╡ b6730158-da2e-4dfe-9f7b-435c895cd748


# ╔═╡ 993d4cf4-0a32-4088-b94d-b1c4c8a5b0c5
begin
plot(sol_interact_Pl0,
xaxis = "Time", yaxis = "Density",
abel = ["Herbivore" "Pollinator" "Plant"],
Expand Down Expand Up @@ -281,9 +272,9 @@ version = "3.2.4"
[[Cairo_jll]]
deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99"
git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2"
uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
version = "1.16.1+0"
version = "1.16.1+1"
[[ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
Expand Down Expand Up @@ -632,9 +623,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
[[GLFW_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"]
git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157"
git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8"
uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
version = "3.3.5+0"
version = "3.3.5+1"
[[GR]]
deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
Expand Down Expand Up @@ -662,9 +653,9 @@ version = "0.21.0+0"
[[Glib_jll]]
deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"]
git-tree-sha1 = "7bf67e9a481712b3dbe9cb3dac852dc4b1162e02"
git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06"
uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
version = "2.68.3+0"
version = "2.68.3+2"
[[Graphite2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand All @@ -685,9 +676,9 @@ version = "0.9.16"
[[HarfBuzz_jll]]
deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
git-tree-sha1 = "8a954fed8ac097d5be04921d595f741115c1b2ad"
git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3"
uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
version = "2.8.1+0"
version = "2.8.1+1"
[[Highlights]]
deps = ["DocStringExtensions", "InteractiveUtils", "REPL"]
Expand Down Expand Up @@ -863,9 +854,9 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
[[Libffi_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "761a393aeccd6aa92ec3515e428c26bf99575b3b"
git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290"
uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
version = "3.2.2+0"
version = "3.2.2+1"
[[Libgcrypt_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"]
Expand Down Expand Up @@ -1045,9 +1036,9 @@ version = "1.10.7"
[[Ogg_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f"
git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f"
uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051"
version = "1.3.5+0"
version = "1.3.5+1"
[[OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
Expand Down Expand Up @@ -1742,9 +1733,9 @@ version = "1.6.38+0"
[[libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb"
git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.7+0"
version = "1.3.7+1"
[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
Expand Down Expand Up @@ -1774,17 +1765,15 @@ version = "0.9.1+5"
"""

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