Merge pull request #99 from adrientaudiere/dev

test: Change value in test for different version of vsearch

R/Deseq2_edgeR.R

@@ -40,7 +40,7 @@
 #' }
 #' @author Adrien Taudière
 #'
-#' @return A \code{\link{ggplot}}2 plot representing edgeR results
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot representing edgeR results
 #'
 #' @seealso \code{\link[edgeR]{exactTest}}
 #' @seealso \code{\link{plot_deseq2_pq}}
@@ -133,12 +133,12 @@ plot_edgeR_pq <-
 #'
 #' Graphical representation of DESeq2 analysis.
 #'
-#' @param data (required) a \code{\link{phyloseq-class}} or a
+#' @param data (required) a \code{\link[phyloseq]{phyloseq-class}} or a
 #' \code{\link[DESeq2]{DESeqDataSet-class}} object.
 #' @param tax_table Required if data is a
 #' \code{\link[DESeq2]{DESeqDataSet-class}} object.
 #' The taxonomic table used to find the \code{taxa} and \code{color_taxa}
-#' arguments. If data is a \code{\link{phyloseq-class}} object, data@tax_table
+#' arguments. If data is a \code{\link[phyloseq]{phyloseq-class}} object, data@tax_table
 #' is used.
 #' @param contrast (required) contrast specifies what comparison to extract
 #'   from the object to build a results table. See \code{\link[DESeq2]{results}}
@@ -155,7 +155,7 @@ plot_edgeR_pq <-
 #' @param tax_depth Taxonomic depth to test for differential
 #'   distribution among contrast. If Null the analysis is done at the OTU
 #'   (i.e. Species) level. If not Null, data need to be a column name in
-#'   the `tax_table` slot of the \code{\link{phyloseq-class}} object.
+#'   the `tax_table` slot of the \code{\link[phyloseq]{phyloseq-class}} object.
 #' @param verbose whether the function print some information during
 #'   the computation
 #' @param jitter_width width for the jitter positioning
@@ -190,7 +190,7 @@ plot_edgeR_pq <-
 #' }
 #' @author Adrien Taudière
 #'
-#' @return A \code{\link{ggplot}}2 plot representing DESeq2 results
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot representing DESeq2 results
 #'
 #' @seealso \code{\link[DESeq2]{DESeq}}
 #' @seealso \code{\link[DESeq2]{results}}

R/beta_div_test.R

@@ -34,7 +34,7 @@
 #' }
 #' @author Adrien Taudière
 #'
-#' @return A \code{\link{ggplot}}2 plot with a subtitle indicating the pvalue
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot with a subtitle indicating the pvalue
 #' and the number of permutations
 #' @details
 #' This function is mainly a wrapper of the work of others.

R/blast.R

@@ -1,5 +1,5 @@
 ################################################################################
-#' Blast some sequence against `refseq` slot of a \code{\link{phyloseq-class}}
+#' Blast some sequence against `refseq` slot of a \code{\link[phyloseq]{phyloseq-class}}
 #'   object.
 #'
 #' @description
@@ -9,7 +9,7 @@
 #'
 #' Use the blast software.
 #'
-#' @param physeq (required): a \code{\link{phyloseq-class}} object obtained
+#' @param physeq (required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 #'   using the `phyloseq` package.
 #' @param seq2search (required) path to a fasta file defining the sequences
 #'   you want to blast against the taxa (ASV, OTU) sequences from the physeq object.
@@ -181,7 +181,7 @@ blast_to_phyloseq <- function(physeq,
 
 
 ################################################################################
-#' Blast all sequence of `refseq` slot of a \code{\link{phyloseq-class}}
+#' Blast all sequence of `refseq` slot of a \code{\link[phyloseq]{phyloseq-class}}
 #'   object against a custom database.
 #'
 #' @description
@@ -371,7 +371,7 @@ blast_pq <- function(physeq,
 #'   Note that params `unique_per_seq` must be lft to TRUE and `score_filter`
 #'   must be left to FALSE.
 #' @export
-#' @return A new \code{\link{phyloseq-class}} object.
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object.
 
 
 filter_asv_blast <- function(physeq,
@@ -631,7 +631,7 @@ blast_to_derep <- function(derep,
 #' @param fasta_for_db path to a fasta file to make the blast database
 #' @param silent (logical) If true, no message are printing.
 #' @param ... Other arguments passed on to [blast_pq()] function.
-#' @return A new \code{\link{phyloseq-class}} object with more information in tax_table based on a
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with more information in tax_table based on a
 #'   blast on a given database
 #'
 #' @export

R/controls.R

@@ -154,7 +154,7 @@ dist_pos_control <- function(physeq, samples_names, method = "bray") {
 #'   6. `mean`: the mean of the three firsts methods
 #' @param min_diff_for_cutoff (int) argument for method `cutoff_diff`.
 #'   Required if method is `cutoff_diff`, `min`, `max` or `mean`
-#' @return A new \code{\link{phyloseq-class}} object.
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object.
 #' @export
 #'
 #' @examples

R/dada_phyloseq.R

@@ -16,7 +16,7 @@ if (getRversion() >= "2.15.1") {
 #' @inheritParams clean_pq
 #' @param prefix_taxa_names (default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")
 #'
-#' @return A new \code{\link{phyloseq-class}} object with `refseq` slot and new
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with `refseq` slot and new
 #'   taxa names
 #' @export
 
@@ -45,7 +45,7 @@ add_dna_to_phyloseq <- function(physeq, prefix_taxa_names = "Taxa_") {
 #' (i) taxa names in refseq, taxonomy table and otu_table and between
 #' (ii) sample names in sam_data and otu_table.
 #'
-#' @param physeq (required): a \code{\link{phyloseq-class}} object obtained
+#' @param physeq (required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 #'   using the `phyloseq` package.
 #' @param remove_empty_samples (logical) Do you want to remove samples
 #'   without sequences (this is done after removing empty taxa)
@@ -68,7 +68,7 @@ add_dna_to_phyloseq <- function(physeq, prefix_taxa_names = "Taxa_") {
 #' @param simplify_taxo (logical) if TRUE, correct the taxonomy_table using the
 #'   `MiscMetabar::simplify_taxo()` function
 #' @param prefix_taxa_names (default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")
-#' @return A new \code{\link{phyloseq-class}} object
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object
 #' @export
 clean_pq <- function(physeq,
                      remove_empty_samples = TRUE,
@@ -1605,7 +1605,7 @@ subset_taxa_pq <- function(physeq,
 #' @inheritParams clean_pq
 #' @param sam_name (required) The sample name to select
 #' @param silent (logical) If true, no message are printing.
-#' @return A new \code{\link{phyloseq-class}} object with one sample
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with one sample
 #'
 #' @export
 #'
@@ -1674,7 +1674,7 @@ select_one_sample <- function(physeq, sam_name, silent = FALSE) {
 #'   If set to NULL (the default), the basename of the file reFasta
 #'   is used.
 #' @param ... Other arguments pass on to `dada2::assignTaxonomy`.
-#' @return A new \code{\link{phyloseq-class}} object with a larger slot tax_table"
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with a larger slot tax_table"
 #'
 #' @export
 #'
@@ -1712,7 +1712,7 @@ add_new_taxonomy_pq <- function(physeq, ref_fasta, suffix = NULL, ...) {
 #'  informative columns (categorical column with one value per samples),
 #'   e.g. samples names ?
 #' @param ... Other arguments pass on to [gtsummary::tbl_summary()].
-#' @return A new \code{\link{phyloseq-class}} object with a larger slot tax_table
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with a larger slot tax_table
 #'
 #' @export
 #' @author Adrien Taudière
@@ -2615,7 +2615,7 @@ taxa_only_in_one_level <- function(physeq,
 #' @param digits (default = 2) integer indicating the number of decimal places
 #'   to be used (see `?round` for more information)
 #'
-#' @return A new \code{\link{phyloseq-class}} object with otu_table count
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object with otu_table count
 #'   normalize and log transformed (if base_log is an integer)
 #' @export
 #' @author Adrien Taudière
@@ -2795,7 +2795,7 @@ psmelt_samples_pq <-
 #' @inheritParams clean_pq
 #' @author Adrien Taudière
 #' @export
-#' @return A new \code{\link{phyloseq-class}} object
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object
 taxa_as_columns <- function(physeq) {
   physeq <- clean_pq(
     physeq,
@@ -2822,7 +2822,7 @@ taxa_as_columns <- function(physeq) {
 #' @inheritParams clean_pq
 #' @author Adrien Taudière
 #' @export
-#' @return A new \code{\link{phyloseq-class}} object
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object
 taxa_as_rows <- function(physeq) {
   physeq <- clean_pq(
     physeq,
@@ -2858,7 +2858,7 @@ taxa_as_rows <- function(physeq) {
 #' @param verbose (logical). If TRUE, print additional informations.
 #' @export
 #' @author Adrien Taudière
-#' @return A new \code{\link{phyloseq-class}} object.
+#' @return A new \code{\link[phyloseq]{phyloseq-class}} object.
 #' @seealso [accu_plot_balanced_modality()]
 #' @examples
 #' table(data_fungi_mini@sam_data$Height)

R/miscellanous.R

@@ -1,6 +1,6 @@
 ################################################################################
-#' Transform the otu_table of a \code{\link{phyloseq-class}} object into a
-#'   \code{\link{phyloseq-class}} object with a binary otu_table.
+#' Transform the otu_table of a \code{\link[phyloseq]{phyloseq-class}} object into a
+#'   \code{\link[phyloseq]{phyloseq-class}} object with a binary otu_table.
 #'
 #' @description
 #'
@@ -131,7 +131,7 @@ all_object_size <- function() {
 #' @param remove_space (logical; default TRUE): do we remove space?
 #' @author Adrien Taudière
 #'
-#' @return A  \code{\link{phyloseq-class}} object with simplified taxonomy
+#' @return A  \code{\link[phyloseq]{phyloseq-class}} object with simplified taxonomy
 #' @export
 simplify_taxo <- function(physeq, remove_space = TRUE) {
   taxo <- physeq@tax_table

R/plot_functions.R

@@ -21,7 +21,7 @@
 #' plot_mt(res)
 #' plot_mt(res, taxa = "Genus", color_tax = "Order")
 #' }
-#' @return a \code{\link{ggplot}}2 plot of result of a mt test
+#' @return a \code{\link[ggplot2]{ggplot}}2 plot of result of a mt test
 #' @export
 #' @seealso [phyloseq::mt()]
 
@@ -56,7 +56,7 @@ plot_mt <-
 
 
 ################################################################################
-#' Plot accumulation curves for \code{\link{phyloseq-class}} object
+#' Plot accumulation curves for \code{\link[phyloseq]{phyloseq-class}} object
 #'
 #' @description
 #'
@@ -87,7 +87,7 @@ plot_mt <-
 #'    Only use if `add_nb_seq` = TRUE.
 #' @param ci (default: 2, integer) Confidence interval value used to multiply the
 #'   standard error to plot confidence interval
-#' @param ... Additional arguments passed on to \code{\link{ggplot}}
+#' @param ... Additional arguments passed on to \code{\link[ggplot2]{ggplot}}
 #' if `add_nb_seq` = TRUE or to \code{\link{plot}} if `add_nb_seq` = FALSE
 #'
 #' @examples
@@ -102,7 +102,7 @@ plot_mt <-
 #'
 #' p + xlim(c(0, 400))
 #' }
-#' @return A \code{\link{ggplot}}2 plot representing the richness
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot representing the richness
 #' accumulation plot if add_nb_seq = TRUE, else, if add_nb_seq = FALSE
 #' return a base plot.
 #'
@@ -512,7 +512,7 @@ accu_samp_threshold <- function(res_accuplot, threshold = 0.95) {
 
 
 ################################################################################
-#' Plot OTU circle for \code{\link{phyloseq-class}} object
+#' Plot OTU circle for \code{\link[phyloseq]{phyloseq-class}} object
 #' @description
 #'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
@@ -733,7 +733,7 @@ circle_pq <-
 ################################################################################
 
 ################################################################################
-#' Sankey plot of \code{\link{phyloseq-class}} object
+#' Sankey plot of \code{\link[phyloseq]{phyloseq-class}} object
 #' @description
 #'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
@@ -956,7 +956,7 @@ sankey_pq <-
 ################################################################################
 
 ################################################################################
-#' Venn diagram of \code{\link{phyloseq-class}} object
+#' Venn diagram of \code{\link[phyloseq]{phyloseq-class}} object
 #' @description
 #'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
@@ -992,7 +992,7 @@ sankey_pq <-
 #'     scale_fill_hue()
 #' }
 #' }
-#' @return A \code{\link{ggplot}}2 plot representing Venn diagram of
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot representing Venn diagram of
 #' modalities of the argument \code{factor}
 #'
 #' @export
@@ -1163,7 +1163,7 @@ venn_pq <-
 
 
 ################################################################################
-#' Venn diagram of \code{\link{phyloseq-class}} object using
+#' Venn diagram of \code{\link[phyloseq]{phyloseq-class}} object using
 #' `ggVennDiagram::ggVennDiagram` function
 #' @description
 #'
@@ -1197,7 +1197,7 @@ venn_pq <-
 #'   modalities of args `fact`.
 #' @param ... Other arguments for the `ggVennDiagram::ggVennDiagram` function
 #'   for ex. `category.names`.
-#' @return A \code{\link{ggplot}}2 plot representing Venn diagram of
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot representing Venn diagram of
 #'   modalities of the argument \code{factor} or if split_by is set a list
 #'   of plots.
 #' @seealso [upset_pq()]
@@ -1787,7 +1787,7 @@ ggbetween_pq <-
 
 
 ################################################################################
-#' Summarize a \code{\link{phyloseq-class}} object using a plot.
+#' Summarize a \code{\link[phyloseq]{phyloseq-class}} object using a plot.
 #' @description
 #'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
@@ -3106,7 +3106,7 @@ iNEXT_pq <- function(physeq,
 #'   modalities of `fact` parameter
 #' @param ... Other arguments passed on to the [ComplexUpset::upset()]
 #'
-#' @return A \code{\link{ggplot}}2 plot
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot
 #' @export
 #' @author Adrien Taudière
 #'
@@ -3303,7 +3303,7 @@ upset_pq <- function(physeq,
 #'   the tax_table slot from the physeq object
 #' @param ... Other arguments passed on to the [ComplexUpset::upset_test()]
 #'
-#' @return A \code{\link{ggplot}}2 plot
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot
 #' @export
 #' @author Adrien Taudière
 #'
@@ -3516,7 +3516,7 @@ diff_fct_diff_class <-
 #' @param nb_seq (logical; default TRUE) If set to FALSE, only the number of ASV
 #'   is count. Concretely, physeq otu_table is transformed in a binary
 #'   otu_table (each value different from zero is set to one)
-#' @return A \code{\link{ggplot}}2 plot  with bar representing the number of sequence en each
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot  with bar representing the number of sequence en each
 #'   taxonomic groups
 #' @export
 #'
@@ -3579,7 +3579,7 @@ tax_bar_pq <-
 #' @param tax_level The taxonomic level to fill ridges
 #' @param ... Other params passed on to [ggridges::geom_density_ridges()]
 #'
-#' @return A \code{\link{ggplot}}2 plot  with bar representing the number of sequence en each
+#' @return A \code{\link[ggplot2]{ggplot}}2 plot  with bar representing the number of sequence en each
 #'   taxonomic groups
 #' @export
 #' @author Adrien Taudière

R/table_functions.R

@@ -1,5 +1,5 @@
 ################################################################################
-#' Make a datatable with the taxonomy of a \code{\link{phyloseq-class}} object
+#' Make a datatable with the taxonomy of a \code{\link[phyloseq]{phyloseq-class}} object
 #'
 #' @description
 #'

cran-comments.md

@@ -1,6 +1,20 @@
-Problem raised by CRAN Team the 22/08/2024 :
+Resolved 2 Notes from CRAN submission
 
-'Packages which use Internet resources should fail gracefully with an informative message
-if the resource is not available or has changed (and not give a check warning nor error).'
 
-Problem resolved in issue https://github.com/adrientaudiere/MiscMetabar/issues/97
+# Invalid URLs
+
+Found the following (possibly) invalid URLs:
+  URL: https://www.sciencedirect.com/science/article/abs/pii/S1754504815000847
+    From: man/add_funguild_info.Rd
+          man/get_funguild_db.Rd
+    Status: 403
+    Message: Forbidden
+
+> I don't understand why the URL is invalid. It works for me.
+
+
+# Bad \link{} for external packages
+
+Found the following Rd file(s) with Rd \link{} targets missing package
+
+> Solved in v. 0.9.3