Merge pull request #5 from econetoolbox/fix-figures-not-found

Fix figures not found
econetoolbox · Apr 23, 2024 · ba72eb7 · ba72eb7
2 parents 38d0063 + 9dac3d9
commit ba72eb7
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diff --git a/.github/workflows/render-website.yaml b/.github/workflows/render-website.yaml
@@ -28,6 +28,22 @@ jobs:
           packages:
             any::knitr
             any::rmarkdown
+            any::igraph
+            any::igraphdata
+            any::bipartite
+            # any::FWebs
+            any::vegan
+            any::cheddar
+            any::matlib
+            any::sbm
+            any::alluvial
+            any::econetwork
+            any::poweRlaw
+            # any::rmangal
+            # any::colSBM
+            any::network
+            any::GGally
+            any::RColorBrewe
 
       - name: Render and Publish
         uses: quarto-dev/quarto-actions/publish@v2

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,36 @@
+Package: econetoolbox.github.io
+Type: Package
+Title: Analyzing Ecological Networks
+Version: 0.1
+Authors@R: c(
+    person(given   = "Nicolas",
+           family  = "Casajus",
+           role    = c("aut", "cre", "cph"),
+           email   = "nicolas.casajus@fondationbiodiversite.fr",
+           comment = c(ORCID = "0000-0002-5537-5294")))
+Description: This files is used to list dependencies required for the course.
+URL: https://github.com/econetoolbox/econetoolbox.github.io
+BugReports: https://github.com/econetoolbox/econetoolbox.github.io/issues
+License: CC-BY 4.0
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Imports:
+    igraph,
+    igraphdata,
+    bipartite,
+    FWebs,
+    vegan,
+    cheddar,
+    matlib,
+    sbm,
+    alluvial,
+    econetwork,
+    poweRlaw,
+    rmangal,
+    colSBM,
+    network,
+    GGally,
+    RColorBrewer,
+    knitr,
+    rmarkdown
diff --git a/_quarto.yml b/_quarto.yml
@@ -68,10 +68,10 @@ book:
         - text: (day 2) network structure
           href: chapters/day2.html
         - text: (day 3) SBM
-          href: chapters/day3_files/TutorialBM.html
+          href: chapters/TutorialBM.qmd
 #        - chapters/TutorialBM.qmd
         - text: (day 4) multilevel
-          href: chapters/day4_files/TutorialDattilo.html
+          href: chapters/TutorialDattilo.qmd
 #        - chapters/TutorialDattilo.qmd
 
 

diff --git a/chapters/day3_files/ICL_fungi_tree.png → chapters/ICL_fungi_tree.png b/chapters/day3_files/ICL_fungi_tree.png → chapters/ICL_fungi_tree.png
diff --git a/chapters/day3_files/ICL_tree_bin.png → chapters/ICL_tree_bin.png b/chapters/day3_files/ICL_tree_bin.png → chapters/ICL_tree_bin.png
diff --git a/chapters/day3_files/ICL_tree_cov.png → chapters/ICL_tree_cov.png b/chapters/day3_files/ICL_tree_cov.png → chapters/ICL_tree_cov.png
diff --git a/chapters/day3_files/ICL_tree_poisson.png → chapters/ICL_tree_poisson.png b/chapters/day3_files/ICL_tree_poisson.png → chapters/ICL_tree_poisson.png
diff --git a/chapters/day3_files/Tree-Fungus.jpg → chapters/Tree-Fungus.jpg b/chapters/day3_files/Tree-Fungus.jpg → chapters/Tree-Fungus.jpg
diff --git a/chapters/TutorialBM.html b/chapters/TutorialBM.html
diff --git a/chapters/TutorialBM.qmd b/chapters/TutorialBM.qmd
@@ -1,5 +1,5 @@
 ---
-title: "Day 3 Stochastic Block Models"
+title: "Tutorial on Stochastic Block Models"
 subtitle: "April 2024"
 author: "Econet group"
 date: "04/24/2024"

diff --git a/chapters/TutorialBM_files/figure-html/alluvial cov-1.png b/chapters/TutorialBM_files/figure-html/alluvial cov-1.png
diff --git a/chapters/TutorialBM_files/figure-html/alluvial-1.png b/chapters/TutorialBM_files/figure-html/alluvial-1.png
diff --git a/chapters/TutorialBM_files/figure-html/communities plot-1.png b/chapters/TutorialBM_files/figure-html/communities plot-1.png
diff --git a/chapters/TutorialBM_files/figure-html/communities plot-2.png b/chapters/TutorialBM_files/figure-html/communities plot-2.png
diff --git a/chapters/TutorialBM_files/figure-html/plot BM network tree bin-1.png b/chapters/TutorialBM_files/figure-html/plot BM network tree bin-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot BM network tree fungi-1.png b/chapters/TutorialBM_files/figure-html/plot BM network tree fungi-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot BM network tree poisson-1.png b/chapters/TutorialBM_files/figure-html/plot BM network tree poisson-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot bipartite estim-1.png b/chapters/TutorialBM_files/figure-html/plot bipartite estim-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot bipartite expect-1.png b/chapters/TutorialBM_files/figure-html/plot bipartite expect-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot commu with colors-1.png b/chapters/TutorialBM_files/figure-html/plot commu with colors-1.png
diff --git a/chapters/TutorialBM_files/figure-html/plot commu with colors-2.png b/chapters/TutorialBM_files/figure-html/plot commu with colors-2.png
diff --git a/chapters/TutorialBM_files/figure-html/plot incidence-1.png b/chapters/TutorialBM_files/figure-html/plot incidence-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM ICL-1.png b/chapters/TutorialBM_files/figure-html/simpleSBM ICL-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-1.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-10.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-10.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-11.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-11.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-12.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-12.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-13.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-13.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-14.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-14.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-15.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-15.png
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diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-17.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-17.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-2.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-2.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-3.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-3.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-4.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-4.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-5.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-5.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-6.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-6.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-7.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-7.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-8.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-8.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBM print-9.png b/chapters/TutorialBM_files/figure-html/simpleSBM print-9.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBMfit changeModel-1.png b/chapters/TutorialBM_files/figure-html/simpleSBMfit changeModel-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBMfit plot1-1.png b/chapters/TutorialBM_files/figure-html/simpleSBMfit plot1-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBMfit plot2-1.png b/chapters/TutorialBM_files/figure-html/simpleSBMfit plot2-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBMfitPoisson plot1-1.png b/chapters/TutorialBM_files/figure-html/simpleSBMfitPoisson plot1-1.png
diff --git a/chapters/TutorialBM_files/figure-html/simpleSBMfitPoisson plot2-1.png b/chapters/TutorialBM_files/figure-html/simpleSBMfitPoisson plot2-1.png
diff --git a/chapters/TutorialBM_files/figure-html/tree_fungi_bipartite network-1.png b/chapters/TutorialBM_files/figure-html/tree_fungi_bipartite network-1.png
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