From 5d88e5d9173192c8f5458743154b73fc262450ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:27:41 -0500
Subject: [PATCH 01/13] =?UTF-8?q?=F0=9F=8E=89=20initial=20layouts=20are=20?=
 =?UTF-8?q?scaled=20by=20the=20square=20root=20of=20richness?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/initial_layouts.jl | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/initial_layouts.jl b/src/initial_layouts.jl
index b74ef73..ce6cb57 100644
--- a/src/initial_layouts.jl
+++ b/src/initial_layouts.jl
@@ -1,11 +1,18 @@
 """
     initial(::Type{RandomInitialLayout}, N::T) where {T <: EcologicalNetworks.AbstractEcologicalNetwork}
 
-Random disposition of nodes in the unit square. This is a good starting
-point for any force-directed layout.
+Random disposition of nodes in a circle. This is a good starting point for any
+force-directed layout. The circle is scaled so that its radius is twice the
+square root of the network richness, which helps most layouts converge faster.
 """
 function initial(::Type{RandomInitialLayout}, N::T) where {T <: EcologicalNetworks.AbstractEcologicalNetwork}
-  return Dict([s => NodePosition() for s in species(N)])
+  L = Dict([s => NodePosition() for s in species(N)])
+  _adj = 2sqrt(richness(N))
+  for s in species(N)
+    L[s].x *= _adj
+    L[s].y *= _adj
+  end
+  return L
 end
 
 """

From 8c9d7f591b0984da21a27c7f428bbb010929126b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:30:03 -0500
Subject: [PATCH 02/13] =?UTF-8?q?=F0=9F=8E=89=20food=20web=20layout=20also?=
 =?UTF-8?q?=20scaled?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/initial_layouts.jl | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/initial_layouts.jl b/src/initial_layouts.jl
index ce6cb57..c2e822f 100644
--- a/src/initial_layouts.jl
+++ b/src/initial_layouts.jl
@@ -33,16 +33,16 @@ end
     initial(::Type{FoodwebInitialLayout}, N::T) where {T <: EcologicalNetworks.AbstractUnipartiteNetwork}
 
 Random disposition of nodes on trophic levels for food webs. Note that the
-*fractional* trophic level is used, but the layout can be modified afterwards
-to use the continuous levels.
+continuous trophic level is used, but the layout can be modified afterwards to
+use another measure of trophic rank.
 """
 function initial(::Type{FoodwebInitialLayout}, N::T) where {T <: EcologicalNetworks.AbstractUnipartiteNetwork}
-  level = NodePosition[]
-  tl = fractional_trophic_level(N)
-  for (i, s) in enumerate(species(N))
-    push!(level, NodePosition(rand(), float(tl[s]), 0.0, 0.0))
+  L = initial(RandomInitialLayout, N)
+  tl = trophic_level(N)
+  for s in species(N)
+    L[s].y = tl[s]
   end
-  return Dict(zip(species(N), level))
+  return L
 end
 
 """

From a441cfdd266e01669bc86618f5c20fa39f9e84bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:35:04 -0500
Subject: [PATCH 03/13] =?UTF-8?q?=F0=9F=94=A7=20simplify=20the=20update!?=
 =?UTF-8?q?=20code?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/forcedirected.jl | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/forcedirected.jl b/src/forcedirected.jl
index 85b0372..3109e85 100644
--- a/src/forcedirected.jl
+++ b/src/forcedirected.jl
@@ -125,9 +125,10 @@ Update the position of a node
 """
 function update!(n::NodePosition)
     Δ = sqrt(n.vx^2.0+n.vy^2.0)
-    Δ = Δ == 0.0 ? 0.0001 : Δ
-    n.x += n.vx/Δ*min(Δ, 0.01)
-    n.y += n.vy/Δ*min(Δ, 0.01)
+    if !iszero(Δ)
+        n.x += n.vx/Δ*min(Δ, 0.01)
+        n.y += n.vy/Δ*min(Δ, 0.01)
+    end
     stop!(n)
 end
 

From 1eb1fb1966976635370c239dd961422603213c7b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:35:19 -0500
Subject: [PATCH 04/13] =?UTF-8?q?=F0=9F=93=96=20more=20infos=20on=20how=20?=
 =?UTF-8?q?long=20the=20FD=20layouts=20should=20run?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/forcedirected.jl | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/forcedirected.jl b/src/forcedirected.jl
index 3109e85..c3ca591 100644
--- a/src/forcedirected.jl
+++ b/src/forcedirected.jl
@@ -139,6 +139,13 @@ One iteration of the force-directed layout routine. Because these algorithms can
 take some time to converge, it may be useful to stop every 500 iterations to
 have a look at the results. Note that to avoid oscillations, the maximum
 displacement at any given time is set to 0.01 units.
+
+These layouts tend to have O(N³) complexity, where N is the number of nodes in
+the network. This is because repulsion required to do (N×(N-1))/2 visits on
+pairs of nodes, and an optimal layout usually requires s×N steps to converge.
+With the maximal displacement set to 0.01, we have found that k ≈ 100 gives
+acceptable results. This will depend on the complexity of the network, and its
+connectance, as well as the degree and edge strengths distributions.
 """
 function position!(LA::ForceDirectedLayout, L::Dict{K,NodePosition}, N::T) where {T <: EcologicalNetworks.AbstractEcologicalNetwork} where {K}
     

From 6ab516e7964ad5d23ed45773b5b54c51547b9d23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:35:41 -0500
Subject: [PATCH 05/13] =?UTF-8?q?=F0=9F=93=A6=20version=20bump?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index f1e6601..3e610c9 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "EcologicalNetworksPlots"
 uuid = "9f7a259d-73a7-556d-a7a2-3eb122d3865b"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>"]
-version = "0.0.8"
+version = "0.0.9"
 
 [deps]
 EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"

From 104bb5358399518752a9884700c84f274bb84f11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:49:04 -0500
Subject: [PATCH 06/13] update example

---
 docs/src/layouts/forcedirected.md | 44 +++++++++++++------------------
 1 file changed, 18 insertions(+), 26 deletions(-)

diff --git a/docs/src/layouts/forcedirected.md b/docs/src/layouts/forcedirected.md
index 8cbc152..7ffe9ef 100644
--- a/docs/src/layouts/forcedirected.md
+++ b/docs/src/layouts/forcedirected.md
@@ -31,7 +31,7 @@ this network has disconnected components, and we have no gravity, we expect that
 they will be quite far from one another:
 
 ```@example default
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(ForceDirectedLayout(0.3, 0.3; gravity=0.0), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -42,7 +42,7 @@ We can turn gravity on just a little bit:
 
 ```@example default
 I = initial(RandomInitialLayout, N)
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(ForceDirectedLayout(0.3, 0.3; gravity=0.2), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -54,7 +54,7 @@ on some more):
 
 ```@example default
 I = initial(RandomInitialLayout, N)
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(ForceDirectedLayout(0.3, 0.75; gravity=0.4), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -76,7 +76,7 @@ The Fruchterman-Rheingold method is the default:
 
 ```@example default
 I = initial(RandomInitialLayout, N)
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(FruchtermanRheingold(0.3; gravity=0.2), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -88,7 +88,7 @@ at showing the modules and long paths in a network.
 
 ```@example default
 I = initial(RandomInitialLayout, N)
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(ForceAtlas2(0.8; gravity=0.2), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -101,7 +101,7 @@ visualisation:
 
 ```@example default
 I = initial(RandomInitialLayout, N)
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(SpringElectric(1.2; gravity=0.2), I, N)
 end
 plot(I, N, aspectratio=1)
@@ -120,7 +120,7 @@ All nodes repel at the same force, no impact of edge weight:
 I = initial(RandomInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.2)
 L.degree = false
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(L, I, N)
 end
 plot(I, N, aspectratio=1)
@@ -134,7 +134,7 @@ I = initial(RandomInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.2)
 L.degree = false
 L.δ = 0.1
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(L, I, N)
 end
 plot(I, N, aspectratio=1)
@@ -148,7 +148,7 @@ I = initial(RandomInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.2)
 L.degree = false
 L.δ = 2.0
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(L, I, N)
 end
 plot(I, N, aspectratio=1)
@@ -162,7 +162,7 @@ I = initial(RandomInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.2)
 L.degree = true
 L.δ = 2.0
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(L, I, N)
 end
 plot(I, N, aspectratio=1)
@@ -176,7 +176,7 @@ I = initial(RandomInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.2)
 L.degree = true
 L.δ = 0.2
-for step in 1:5000
+for step in 1:(100richness(N))
   position!(L, I, N)
 end
 plot(I, N, aspectratio=1)
@@ -187,24 +187,16 @@ scatter!(I, N, bipartite=true)
 
 One convenient way to plot food webs is to prevent them from moving on the *y*
 axis, so that every species remains at its trophic level. This can be done by
-changing the `move` field (as `ForceDirectedLayout` is a mutable type). Note
-that in this example, we *update* the layout after plotting, by replacing the
-fractional trophic level by the actual trophic level (and we color the nodes by
-their degree, which is covered more in-depth in the next section of this
-documentation).
+changing the `move` field (as `ForceDirectedLayout` is a mutable type).
 
 ```@example default
-Fweb = simplify(nz_stream_foodweb()[1])
-I = initial(FoodwebInitialLayout, Fweb)
+N = simplify(nz_stream_foodweb()[1])
+I = initial(FoodwebInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.05)
 L.move = (true, false)
-for step in 1:5000
-  position!(L, I, Fweb)
-end
-tl = trophic_level(Fweb)
-for s in species(Fweb)
-  I[s].y = tl[s]
+for step in 1:(100richness(N))
+  position!(L, I, N)
 end
-plot(I, Fweb)
-scatter!(I, Fweb, nodefill=degree(Fweb), c=:YlGn)
+plot(I, N)
+scatter!(I, N, nodefill=omnivory(N), nodesize=degree(N), c=:YlGn)
 ```
\ No newline at end of file

From 95d65f48ff63950d521de6fec17773c80998634f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 09:53:55 -0500
Subject: [PATCH 07/13] =?UTF-8?q?=E2=9A=A1=20skip=20one=20step=20if=20dist?=
 =?UTF-8?q?ance=20is=20zero?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/forcedirected.jl | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/forcedirected.jl b/src/forcedirected.jl
index c3ca591..15b5c51 100644
--- a/src/forcedirected.jl
+++ b/src/forcedirected.jl
@@ -109,14 +109,15 @@ function attract!(LA::T, n1::NodePosition, n2::NodePosition, fa) where {T <: For
     δx = n1.x - n2.x
     δy = n1.y - n2.y
     Δ = sqrt(δx^2.0+δy^2.0)
-    Δ = Δ == 0.0 ? 0.0001 : Δ
-    if LA.move[1]
-        n1.vx -= δx/Δ*fa(Δ)
-        n2.vx += δx/Δ*fa(Δ)
-    end
-    if LA.move[2]
-        n1.vy -= δy/Δ*fa(Δ)
-        n2.vy += δy/Δ*fa(Δ)
+    if !iszero(Δ)
+        if LA.move[1]
+            n1.vx -= δx/Δ*fa(Δ)
+            n2.vx += δx/Δ*fa(Δ)
+        end
+        if LA.move[2]
+            n1.vy -= δy/Δ*fa(Δ)
+            n2.vy += δy/Δ*fa(Δ)
+        end
     end
 end
 

From bebd39c68ec451e6748e188c38e983913ec375d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:07:21 -0500
Subject: [PATCH 08/13] =?UTF-8?q?=F0=9F=93=96=20use=20a=20tall=20network?=
 =?UTF-8?q?=20for=20the=20doc?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 docs/src/layouts/forcedirected.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/src/layouts/forcedirected.md b/docs/src/layouts/forcedirected.md
index 7ffe9ef..7b60231 100644
--- a/docs/src/layouts/forcedirected.md
+++ b/docs/src/layouts/forcedirected.md
@@ -190,7 +190,7 @@ axis, so that every species remains at its trophic level. This can be done by
 changing the `move` field (as `ForceDirectedLayout` is a mutable type).
 
 ```@example default
-N = simplify(nz_stream_foodweb()[1])
+N = simplify(nz_stream_foodweb()[5])
 I = initial(FoodwebInitialLayout, N)
 L = SpringElectric(1.2; gravity=0.05)
 L.move = (true, false)

From cd6c66a621e5ea1236bb282ac8bdb1d8eb108a32 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:16:09 -0500
Subject: [PATCH 09/13] =?UTF-8?q?=F0=9F=94=A7=20build=20docs=20with=20diff?=
 =?UTF-8?q?erent=20token?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/TagBot.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
index d77d3a0..a335de6 100644
--- a/.github/workflows/TagBot.yml
+++ b/.github/workflows/TagBot.yml
@@ -8,4 +8,4 @@ jobs:
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.TOKEN }}

From 3cd28dd2ef817c7c630d27ad8f44d794e3fe9d9b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:21:42 -0500
Subject: [PATCH 10/13] =?UTF-8?q?=F0=9F=93=96=20new=20modular=20example=20?=
 =?UTF-8?q?network?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 docs/src/advanced/subsets.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/src/advanced/subsets.md b/docs/src/advanced/subsets.md
index c2aa186..0456ebd 100644
--- a/docs/src/advanced/subsets.md
+++ b/docs/src/advanced/subsets.md
@@ -29,14 +29,14 @@ scatter!(I, N[core3], mc=:red)
 We can also use this ability to show the modular structure of a network:
 
 ```@example default
-N = convert(BinaryNetwork, Umod)
+N = web_of_life("A_HP_029")
 I = initial(RandomInitialLayout, N)
 for step in 1:2000
   position!(SpringElectric(1.2; gravity=0.75), I, N)
 end
 
 # Modularity
-_, P = brim(lp(N)...)
+B, P = brim(lp(convert(BinaryNetwork, N))...)
 plot(I, N, aspectratio=1)
 scatter!(I, N, msw=0.0, nodefill=P, c=:Set2)
 ```
\ No newline at end of file

From e5814ad7e5e4b7ad8c3d66eaa38a514c10bdaaa3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:36:11 -0500
Subject: [PATCH 11/13] =?UTF-8?q?=F0=9F=93=96=20update?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 docs/src/advanced/subsets.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/src/advanced/subsets.md b/docs/src/advanced/subsets.md
index 0456ebd..bbbca71 100644
--- a/docs/src/advanced/subsets.md
+++ b/docs/src/advanced/subsets.md
@@ -29,7 +29,7 @@ scatter!(I, N[core3], mc=:red)
 We can also use this ability to show the modular structure of a network:
 
 ```@example default
-N = web_of_life("A_HP_029")
+N = web_of_life("M_PA_003")
 I = initial(RandomInitialLayout, N)
 for step in 1:2000
   position!(SpringElectric(1.2; gravity=0.75), I, N)

From 88e2290e8c6100bfa2a1ee8493ac93fea42aec9a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:37:53 -0500
Subject: [PATCH 12/13] :red_circle: fix branch building

---
 .github/workflows/Documentation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
index b60c221..2eebaf2 100644
--- a/.github/workflows/Documentation.yml
+++ b/.github/workflows/Documentation.yml
@@ -4,7 +4,7 @@ on:
   release:
   push:
     branches:
-      - main
+      - master
     tags:
       - '*'
   pull_request:

From b12869dd81e7685ab882d7f90999b13fb1772bd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Thu, 26 Nov 2020 10:43:17 -0500
Subject: [PATCH 13/13] Update README.md

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 110cfe7..8a8417c 100644
--- a/README.md
+++ b/README.md
@@ -6,8 +6,8 @@ generates force-directed layouts, circular layouts, bipartite layouts,
 heatmaps, as well as layouts based on node properties. Note that `Plots.jl`
 *must* be installed in the project, and loaded, for this package to work.
 
-**Documentation:** [Stable](https://ecojulia.github.io/EcologicalNetworksPlots.jl/stable/) `//` [Latest](https://ecojulia.github.io/EcologicalNetworksPlots.jl/latest/)
+[![latest doc](https://img.shields.io/badge/documentation-stable-brightgreen)](https://ecojulia.github.io/EcologicalNetworksPlots.jl/stable/) [![latest doc](https://img.shields.io/badge/documentation-latest-green)](https://ecojulia.github.io/EcologicalNetworksPlots.jl/latest/)
 
-![CI](https://github.com/EcoJulia/EcologicalNetworksPlots.jl/workflows/CI/badge.svg?branch=master)
+![CI](https://github.com/EcoJulia/EcologicalNetworksPlots.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/EcoJulia/EcologicalNetworksPlots.jl/branch/master/graph/badge.svg?token=HKaubLliPG)](https://codecov.io/gh/EcoJulia/EcologicalNetworksPlots.jl)
 
-[![DOI](https://zenodo.org/badge/143920106.svg)](https://zenodo.org/badge/latestdoi/143920106)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![DOI](https://zenodo.org/badge/143920106.svg)](https://zenodo.org/badge/latestdoi/143920106)