document: improve documentation

adrientaudiere · Dec 12, 2023 · 7f783a5 · 7f783a5
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Showing 7 changed files with 16 additions and 16 deletions.
diff --git a/MiscMetabar.Rproj b/MiscMetabar.Rproj
@@ -18,8 +18,7 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageBuildArgs: --resave-data
-PackageCheckArgs: --as-cran
+PackageCheckArgs: --as-cran 
 PackageRoxygenize: rd,collate,namespace
 
 SpellingDictionary: en_US
diff --git a/R/data.R b/R/data.R
@@ -31,20 +31,20 @@
 "data_fungi_sp_known"
 
 #' This tutorial explore the dataset from Tengeler et al. (2020) available in the `mia` package.
-#' obtain using `mia::makePhyloseqFromTreeSE(Tengeler2020)` 
-#' 
+#' obtain using `mia::makePhyloseqFromTreeSE(Tengeler2020)`
+#'
 #' This is a phyloseq version of the Tengeler2020 dataset.
-#' 
+#'
 #' Tengeler2020 includes gut microbiota profiles of 27 persons with ADHD.
-#' A standard bioinformatic and statistical analysis done to demonstrate that altered microbial 
-#' composition could be a driver of altered brain structure and function and concomitant changes 
-#' in the animals behavior. This was investigated by colonizing young, male, 
+#' A standard bioinformatic and statistical analysis done to demonstrate that altered microbial
+#' composition could be a driver of altered brain structure and function and concomitant changes
+#' in the animals behavior. This was investigated by colonizing young, male,
 #' germ-free C57BL/6JOlaHsd mice with microbiota from individuals with and without ADHD.
 #'
-#' Tengeler, A.C., Dam, S.A., Wiesmann, M. et al. Gut microbiota from persons with 
+#' Tengeler, A.C., Dam, S.A., Wiesmann, M. et al. Gut microbiota from persons with
 #' attention-deficit/hyperactivity disorder affects the brain in mice. Microbiome 8, 44 (2020).
 #' https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00816-x
-#' @format 
+#' @format
 #' A phyloseq object
-#' 
-"Tengeler2020_pq"
+#'
+"Tengeler2020_pq"
diff --git a/man/blast_to_phyloseq.Rd b/man/blast_to_phyloseq.Rd
diff --git a/man/count_seq.Rd b/man/count_seq.Rd
diff --git a/man/subsample_fastq.Rd b/man/subsample_fastq.Rd
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
diff --git a/vignettes/MiscMetabar.Rmd b/vignettes/MiscMetabar.Rmd
@@ -12,7 +12,7 @@ vignette: >
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  message=FALSE
+  message = FALSE
 )
 ```