Merge branch 'master' into devel

DESCRIPTION

@@ -67,7 +67,6 @@ Suggests:
     kableExtra, 
     knitr, 
     Maaslin2,
-    miaTime, 
     miaViz, 
     microbiome, 
     microbiomeDataSets,
@@ -77,7 +76,6 @@ Suggests:
     MMUPHin,
     multiview,
     NbClust,
-    NetCoMi,
     patchwork,
     pheatmap, 
     phyloseq, 
@@ -94,18 +92,19 @@ Suggests:
     scater, 
     sechm, 
     sessioninfo,
-    SpiecEasi,
-    SPRING,
     stats,
     stringr, 
     tidyverse,
     topGO,
     vegan
 Remotes:
     github::microbiome/miaTime,
-    github::microbiome/mia
+    github::microbiome/mia,
+    github::zdk123/SpiecEasi,
+    github::stefpeschel/NetCoMi,
+    github::GraceYoon/SPRING
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 BiocType: Book
 BiocBookTemplate: 1.0.5
 SystemRequirements: quarto

inst/assets/_book.yml

@@ -6,7 +6,7 @@ book:
     - part: "OMA ecosystem"
       chapters:
         - pages/06_packages.qmd
-        - pages/04_containers.qmd
+        # - pages/04_containers.qmd
     - part: "Focus topics"
       chapters:
         - pages/10_manipulation.qmd
@@ -17,10 +17,15 @@ book:
         - pages/21_microbiome_community.qmd
         - pages/24_clustering.qmd
         - pages/30_differential_abundance.qmd
-        - pages/60_network_learning.qmd
-        - pages/61_network_comparison.qmd
         - pages/40_machine_learning.qmd
         - pages/23_multi-assay_analyses.qmd
+    - part: "Advanced topics"
+      chapters:
+        - pages/60_network_learning.qmd
+        - pages/60_network_learning.qmd
+        - pages/IntegratedLearner.qmd
+        - pages/MMUPHin_meta_analysis.qmd
+        - pages/MSEA.qmd
         - pages/19_visualization_techniques.qmd
     - part: "Training"
       chapters: