Merge branch 'devel' into permanova

.gitignore

@@ -31,3 +31,6 @@ renv.lock
 cachix/.envrc
 cachix/.devenv
 cachix/.direnv
+
+# Nix stuff
+*.nix

DESCRIPTION

@@ -1,19 +1,14 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 0.98.29
+Version: 0.98.30
 Date: 2024-10-04
 Authors@R:
-    c(person("Leo", "Lahti", role = c("aut"),
-             comment = c(ORCID = "0000-0001-5537-637X")),
-      person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
-             email = "tuomas.v.borman@utu.fi",
-             comment = c(ORCID = "0000-0002-8563-8884")),
-      person("Felix GM", "Ernst", email = "felix.gm.ernst@outlook.com",
-             role = c("aut"),
-             comment = c(ORCID = "0000-0001-5064-0928")),
-      person("and others", "(see the full list of contributors)",
-             role = c("ctb"))
-         )
+    c(
+  person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", comment = c(ORCID = "0000-0002-8563-8884")),
+  person("Leo", "Lahti", role = c("aut"), comment = c(ORCID = "0000-0001-5537-637X")),
+  person("Felix GM", "Ernst", email = "felix.gm.ernst@outlook.com", role = c("aut"), comment = c(ORCID = "0000-0001-5064-0928")),
+  person("and others", "(see the full list of contributors)", role = c("ctb"))
+  )
 Description:
     This is a reference cookbook for **Microbiome Data Science** with
     R and Bioconductor.
@@ -43,6 +38,7 @@ Suggests:
     cobiclust,
     ComplexHeatmap,
     corpcor,
+    cowplot,
     curatedMetagenomicData,
     dada2,
     dendextend,
@@ -51,16 +47,16 @@ Suggests:
     dplyr,
     DT,
     factoextra,
-    forcats,
     fido,
+    forcats,
     ggplot2,
     ggpubr,
     ggtree,
     glmnet,
     glue,
     grid,
-    gtools,
     gsEasy,
+    gtools,
     igraph,
     IntegratedLearner,
     knitr,
@@ -75,29 +71,31 @@ Suggests:
     MMUPHin,
     MOFA2,
     multiview,
-    NetCoMi,
     NbClust,
+    NetCoMi,
     NMF,
     patchwork,
     phyloseq,
     plotly,
+    plotROC,
     purrr,
     qgraph,
     RColorBrewer,
     rebook,
     reshape2,
     reticulate,
     rgl,
-    ROCR,
     scales,
     scater,
+    scuttle,
     sechm,
     sessioninfo,
     shadowtext,
     SpiecEasi,
     SPRING,
     stats,
     stringr,
+    SuperLearner,
     tidyverse,
     topGO,
     vegan,
@@ -112,7 +110,7 @@ Remotes:
     github::GraceYoon/SPRING,
     github::himelmallick/IntegratedLearner
 VignetteBuilder: knitr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 BiocType: Book
 BiocBookTemplate: 1.0.5
 SystemRequirements: quarto

PackageInstallations_Troubleshoots.qmd

@@ -16,7 +16,7 @@ First of all, please ensure that you have an up-to-date version of R
 ## Mac M1 user
 
 When attempting to install miaverse packages, you may encounter
-installation failures related to the 'scuttle' and 'scatter'
+installation failures related to the 'scuttle' and 'scater'
 dependencies, which require a gcc compiler for installation. The error
 message might resemble the following: