diff --git a/R/Deseq2_edgeR.R b/R/Deseq2_edgeR.R
index 1bd565d4..5b9e12de 100644
--- a/R/Deseq2_edgeR.R
+++ b/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}}
diff --git a/R/beta_div_test.R b/R/beta_div_test.R
index f691502a..96ee580e 100644
--- a/R/beta_div_test.R
+++ b/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.
diff --git a/R/blast.R b/R/blast.R
index eb1782c0..b585c54b 100644
--- a/R/blast.R
+++ b/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
diff --git a/R/controls.R b/R/controls.R
index 0d473e8a..106633c4 100644
--- a/R/controls.R
+++ b/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
diff --git a/R/dada_phyloseq.R b/R/dada_phyloseq.R
index a31f62ad..46d187e8 100644
--- a/R/dada_phyloseq.R
+++ b/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)
diff --git a/R/miscellanous.R b/R/miscellanous.R
index 3bbe6959..41cf01c3 100644
--- a/R/miscellanous.R
+++ b/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
diff --git a/R/plot_functions.R b/R/plot_functions.R
index 4d6b6974..c72be46d 100644
--- a/R/plot_functions.R
+++ b/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
diff --git a/R/table_functions.R b/R/table_functions.R
index 04e79bed..fec5331f 100644
--- a/R/table_functions.R
+++ b/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
 #'
diff --git a/cran-comments.md b/cran-comments.md
index 27ee0ffd..01f5ee63 100644
--- a/cran-comments.md
+++ b/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
\ No newline at end of file
+# 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
\ No newline at end of file
diff --git a/man/LCBD_pq.Rd b/man/LCBD_pq.Rd
index 4f38ed46..811413a0 100644
--- a/man/LCBD_pq.Rd
+++ b/man/LCBD_pq.Rd
@@ -8,7 +8,7 @@ samples}
 LCBD_pq(physeq, p_adjust_method = "BH", ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{p_adjust_method}{(chr, default "BH"): the method used to adjust p-value}
diff --git a/man/SRS_curve_pq.Rd b/man/SRS_curve_pq.Rd
index 9cd9d09e..f6ffbe4c 100644
--- a/man/SRS_curve_pq.Rd
+++ b/man/SRS_curve_pq.Rd
@@ -7,7 +7,7 @@
 SRS_curve_pq(physeq, clean_pq = FALSE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{clean_pq}{(logical): Does the phyloseq
diff --git a/man/accu_plot.Rd b/man/accu_plot.Rd
index 201f5a97..6bf89ae5 100644
--- a/man/accu_plot.Rd
+++ b/man/accu_plot.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/plot_functions.R
 \name{accu_plot}
 \alias{accu_plot}
-\title{Plot accumulation curves for \code{\link{phyloseq-class}} object}
+\title{Plot accumulation curves for \code{\link[phyloseq]{phyloseq-class}} object}
 \usage{
 accu_plot(
   physeq,
@@ -20,7 +20,7 @@ accu_plot(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
@@ -53,11 +53,11 @@ Only use if \code{add_nb_seq} = TRUE.}
 \item{ci}{(default: 2, integer) Confidence interval value used to multiply the
 standard error to plot confidence interval}
 
-\item{...}{Additional arguments passed on to \code{\link{ggplot}}
+\item{...}{Additional arguments passed on to \code{\link[ggplot2]{ggplot}}
 if \code{add_nb_seq} = TRUE or to \code{\link{plot}} if \code{add_nb_seq} = FALSE}
 }
 \value{
-A \code{\link{ggplot}}2 plot representing the richness
+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.
 }
diff --git a/man/accu_plot_balanced_modality.Rd b/man/accu_plot_balanced_modality.Rd
index 3596712d..5552c163 100644
--- a/man/accu_plot_balanced_modality.Rd
+++ b/man/accu_plot_balanced_modality.Rd
@@ -19,7 +19,7 @@ accu_plot_balanced_modality(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) The variable to rarefy. Must be present in
diff --git a/man/add_blast_info.Rd b/man/add_blast_info.Rd
index 5a82057f..55d93508 100644
--- a/man/add_blast_info.Rd
+++ b/man/add_blast_info.Rd
@@ -7,7 +7,7 @@
 add_blast_info(physeq, fasta_for_db, silent = FALSE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fasta_for_db}{path to a fasta file to make the blast database}
@@ -17,7 +17,7 @@ using the \code{phyloseq} package.}
 \item{...}{Other arguments passed on to \code{\link[=blast_pq]{blast_pq()}} function.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with more information in tax_table based on a
+A new \code{\link[phyloseq]{phyloseq-class}} object with more information in tax_table based on a
 blast on a given database
 }
 \description{
diff --git a/man/add_dna_to_phyloseq.Rd b/man/add_dna_to_phyloseq.Rd
index 0ca73ed5..e18a4727 100644
--- a/man/add_dna_to_phyloseq.Rd
+++ b/man/add_dna_to_phyloseq.Rd
@@ -8,13 +8,13 @@ using prefix_taxa_names and number (default Taxa_1, Taxa_2 ...)}
 add_dna_to_phyloseq(physeq, prefix_taxa_names = "Taxa_")
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{prefix_taxa_names}{(default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with \code{refseq} slot and new
+A new \code{\link[phyloseq]{phyloseq-class}} object with \code{refseq} slot and new
 taxa names
 }
 \description{
diff --git a/man/add_funguild_info.Rd b/man/add_funguild_info.Rd
index bf9f8bb5..cc6634c1 100644
--- a/man/add_funguild_info.Rd
+++ b/man/add_funguild_info.Rd
@@ -10,7 +10,7 @@ add_funguild_info(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{taxLevels}{Name of the 7 columns in tax_table required by funguild}
diff --git a/man/add_info_to_sam_data.Rd b/man/add_info_to_sam_data.Rd
index efc20e9c..c9cdc7f4 100644
--- a/man/add_info_to_sam_data.Rd
+++ b/man/add_info_to_sam_data.Rd
@@ -12,7 +12,7 @@ add_info_to_sam_data(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{df_info}{: A dataframe with rownames matching for sample names of the
diff --git a/man/add_new_taxonomy_pq.Rd b/man/add_new_taxonomy_pq.Rd
index 2c876daa..d35a4061 100644
--- a/man/add_new_taxonomy_pq.Rd
+++ b/man/add_new_taxonomy_pq.Rd
@@ -7,7 +7,7 @@
 add_new_taxonomy_pq(physeq, ref_fasta, suffix = NULL, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{ref_fasta}{(required) A link to a database.
@@ -20,7 +20,7 @@ is used.}
 \item{...}{Other arguments pass on to \code{dada2::assignTaxonomy}.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with a larger slot tax_table"
+A new \code{\link[phyloseq]{phyloseq-class}} object with a larger slot tax_table"
 }
 \description{
 \if{html}{\out{
diff --git a/man/adonis_pq.Rd b/man/adonis_pq.Rd
index 2e522d52..e0074ac0 100644
--- a/man/adonis_pq.Rd
+++ b/man/adonis_pq.Rd
@@ -17,7 +17,7 @@ adonis_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{formula}{(required) the right part of a formula for \code{\link[vegan:adonis]{vegan::adonis2()}}.
diff --git a/man/adonis_rarperm_pq.Rd b/man/adonis_rarperm_pq.Rd
index f07b22ef..dec8450e 100644
--- a/man/adonis_rarperm_pq.Rd
+++ b/man/adonis_rarperm_pq.Rd
@@ -20,7 +20,7 @@ adonis_rarperm_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{formula}{(required) the right part of a formula for \code{\link[vegan:adonis]{vegan::adonis2()}}.
diff --git a/man/ancombc_pq.Rd b/man/ancombc_pq.Rd
index 39c70161..bf10abe9 100644
--- a/man/ancombc_pq.Rd
+++ b/man/ancombc_pq.Rd
@@ -7,7 +7,7 @@
 ancombc_pq(physeq, fact, levels_fact = NULL, tax_level = "Class", ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
diff --git a/man/are_modality_even_depth.Rd b/man/are_modality_even_depth.Rd
index 7b1b86fc..e8a5f6da 100644
--- a/man/are_modality_even_depth.Rd
+++ b/man/are_modality_even_depth.Rd
@@ -8,7 +8,7 @@ a factor}
 are_modality_even_depth(physeq, fact, boxplot = FALSE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): Name of the factor to cluster samples by modalities.
diff --git a/man/as_binary_otu_table.Rd b/man/as_binary_otu_table.Rd
index 13c7c8e0..4037a7e9 100644
--- a/man/as_binary_otu_table.Rd
+++ b/man/as_binary_otu_table.Rd
@@ -2,13 +2,13 @@
 % Please edit documentation in R/miscellanous.R
 \name{as_binary_otu_table}
 \alias{as_binary_otu_table}
-\title{Transform the otu_table of a \code{\link{phyloseq-class}} object into a
-\code{\link{phyloseq-class}} object with a binary otu_table.}
+\title{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.}
 \usage{
 as_binary_otu_table(physeq, min_number = 1)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{min_number}{(int) the minimum number of sequences to put
diff --git a/man/biplot_pq.Rd b/man/biplot_pq.Rd
index 590b1fcb..5a843c8f 100644
--- a/man/biplot_pq.Rd
+++ b/man/biplot_pq.Rd
@@ -31,7 +31,7 @@ biplot_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(default: NULL) Name of the factor in \code{physeq@sam_data}.
diff --git a/man/blast_pq.Rd b/man/blast_pq.Rd
index 01acec3f..89ec3af3 100644
--- a/man/blast_pq.Rd
+++ b/man/blast_pq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/blast.R
 \name{blast_pq}
 \alias{blast_pq}
-\title{Blast all sequence of \code{refseq} slot of a \code{\link{phyloseq-class}}
+\title{Blast all sequence of \code{refseq} slot of a \code{\link[phyloseq]{phyloseq-class}}
 object against a custom database.}
 \usage{
 blast_pq(
@@ -23,7 +23,7 @@ blast_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fasta_for_db}{path to a fasta file to make the blast database}
diff --git a/man/blast_to_phyloseq.Rd b/man/blast_to_phyloseq.Rd
index 0cec0507..4bfe710d 100644
--- a/man/blast_to_phyloseq.Rd
+++ b/man/blast_to_phyloseq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/blast.R
 \name{blast_to_phyloseq}
 \alias{blast_to_phyloseq}
-\title{Blast some sequence against \code{refseq} slot of a \code{\link{phyloseq-class}}
+\title{Blast some sequence against \code{refseq} slot of a \code{\link[phyloseq]{phyloseq-class}}
 object.}
 \usage{
 blast_to_phyloseq(
@@ -23,7 +23,7 @@ blast_to_phyloseq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{seq2search}{(required) path to a fasta file defining the sequences
diff --git a/man/build_phytree_pq.Rd b/man/build_phytree_pq.Rd
index 06db92c2..ecd04db3 100644
--- a/man/build_phytree_pq.Rd
+++ b/man/build_phytree_pq.Rd
@@ -18,7 +18,7 @@ build_phytree_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{nb_bootstrap}{(default 0): If a positive number is set,
diff --git a/man/circle_pq.Rd b/man/circle_pq.Rd
index a7ebcba7..b6261aac 100644
--- a/man/circle_pq.Rd
+++ b/man/circle_pq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/plot_functions.R
 \name{circle_pq}
 \alias{circle_pq}
-\title{Plot OTU circle for \code{\link{phyloseq-class}} object}
+\title{Plot OTU circle for \code{\link[phyloseq]{phyloseq-class}} object}
 \usage{
 circle_pq(
   physeq = NULL,
@@ -22,7 +22,7 @@ circle_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor to cluster samples by modalities.
diff --git a/man/clean_pq.Rd b/man/clean_pq.Rd
index 52f80803..029f5884 100644
--- a/man/clean_pq.Rd
+++ b/man/clean_pq.Rd
@@ -20,7 +20,7 @@ clean_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{remove_empty_samples}{(logical) Do you want to remove samples
@@ -56,7 +56,7 @@ the taxa (ASV, OTU) names in verbose information can be misleading.}
 \item{prefix_taxa_names}{(default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")}
 }
 \value{
-A new \code{\link{phyloseq-class}} object
+A new \code{\link[phyloseq]{phyloseq-class}} object
 }
 \description{
 \if{html}{\out{
diff --git a/man/compare_pairs_pq.Rd b/man/compare_pairs_pq.Rd
index bdaa1b9a..a365124d 100644
--- a/man/compare_pairs_pq.Rd
+++ b/man/compare_pairs_pq.Rd
@@ -16,7 +16,7 @@ compare_pairs_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{bifactor}{(required) a factor (present in the \code{sam_data} slot of
diff --git a/man/dist_pos_control.Rd b/man/dist_pos_control.Rd
index 32ea9fbc..383a06a9 100644
--- a/man/dist_pos_control.Rd
+++ b/man/dist_pos_control.Rd
@@ -8,7 +8,7 @@ distance for all samples}
 dist_pos_control(physeq, samples_names, method = "bray")
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{samples_names}{(required) a vector of names for samples with
diff --git a/man/distri_1_taxa.Rd b/man/distri_1_taxa.Rd
index f516ef18..6449fad2 100644
--- a/man/distri_1_taxa.Rd
+++ b/man/distri_1_taxa.Rd
@@ -7,7 +7,7 @@
 distri_1_taxa(physeq, fact, taxa_name, digits = 2)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
diff --git a/man/filter_asv_blast.Rd b/man/filter_asv_blast.Rd
index 89260f96..12d242c0 100644
--- a/man/filter_asv_blast.Rd
+++ b/man/filter_asv_blast.Rd
@@ -32,7 +32,7 @@ filter_taxa_blast(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fasta_for_db}{path to a fasta file to make the blast database}
@@ -66,7 +66,7 @@ Note that params \code{unique_per_seq} must be lft to TRUE and \code{score_filte
 must be left to FALSE.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object.
+A new \code{\link[phyloseq]{phyloseq-class}} object.
 }
 \description{
 \if{html}{\out{
diff --git a/man/formattable_pq.Rd b/man/formattable_pq.Rd
index 620c611e..f7430547 100644
--- a/man/formattable_pq.Rd
+++ b/man/formattable_pq.Rd
@@ -19,7 +19,7 @@ formattable_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{modality}{(required) The name of a column present in the \verb{@sam_data} slot
diff --git a/man/ggaluv_pq.Rd b/man/ggaluv_pq.Rd
index 6572c892..97132c53 100644
--- a/man/ggaluv_pq.Rd
+++ b/man/ggaluv_pq.Rd
@@ -22,7 +22,7 @@ ggaluv_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{taxa_ranks}{A vector of taxonomic ranks. For examples c("Family","Genus").
diff --git a/man/ggbetween_pq.Rd b/man/ggbetween_pq.Rd
index b21212dd..04f691ff 100644
--- a/man/ggbetween_pq.Rd
+++ b/man/ggbetween_pq.Rd
@@ -7,7 +7,7 @@
 ggbetween_pq(physeq, fact, one_plot = FALSE, rarefy_by_sample = FALSE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): The variable to test. Must be present in
diff --git a/man/ggscatt_pq.Rd b/man/ggscatt_pq.Rd
index e857ba11..1d77c304 100644
--- a/man/ggscatt_pq.Rd
+++ b/man/ggscatt_pq.Rd
@@ -15,7 +15,7 @@ ggscatt_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{num_modality}{(required) Name of the numeric column in
diff --git a/man/ggvenn_pq.Rd b/man/ggvenn_pq.Rd
index be90e14e..cf40513f 100644
--- a/man/ggvenn_pq.Rd
+++ b/man/ggvenn_pq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/plot_functions.R
 \name{ggvenn_pq}
 \alias{ggvenn_pq}
-\title{Venn diagram of \code{\link{phyloseq-class}} object using
+\title{Venn diagram of \code{\link[phyloseq]{phyloseq-class}} object using
 \code{ggVennDiagram::ggVennDiagram} function}
 \usage{
 ggvenn_pq(
@@ -19,7 +19,7 @@ ggvenn_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): Name of the factor to cluster samples by modalities.
@@ -53,7 +53,7 @@ modalities of args \code{fact}.}
 for ex. \code{category.names}.}
 }
 \value{
-A \code{\link{ggplot}}2 plot representing Venn diagram of
+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.
 }
diff --git a/man/glmutli_pq.Rd b/man/glmutli_pq.Rd
index b30b5258..f17c257b 100644
--- a/man/glmutli_pq.Rd
+++ b/man/glmutli_pq.Rd
@@ -19,7 +19,7 @@ glmutli_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{formula}{(required) a formula for \code{\link[glmulti:glmulti]{glmulti::glmulti()}}
diff --git a/man/graph_test_pq.Rd b/man/graph_test_pq.Rd
index 1112f0ae..58608602 100644
--- a/man/graph_test_pq.Rd
+++ b/man/graph_test_pq.Rd
@@ -16,7 +16,7 @@ graph_test_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor to cluster samples by modalities.
@@ -41,7 +41,7 @@ NA in the variables set in formula.}
 \code{\link[phyloseqGraphTest:graph_perm_test]{phyloseqGraphTest::graph_perm_test()}} function}
 }
 \value{
-A \code{\link{ggplot}}2 plot with a subtitle indicating the pvalue
+A \code{\link[ggplot2]{ggplot}}2 plot with a subtitle indicating the pvalue
 and the number of permutations
 }
 \description{
diff --git a/man/heat_tree_pq.Rd b/man/heat_tree_pq.Rd
index 0289a73a..f26a1150 100644
--- a/man/heat_tree_pq.Rd
+++ b/man/heat_tree_pq.Rd
@@ -7,7 +7,7 @@
 heat_tree_pq(physeq, taxonomic_level = NULL, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{taxonomic_level}{(default: NULL): a vector of selected
diff --git a/man/hill_pq.Rd b/man/hill_pq.Rd
index bb0e1f8d..8fe3a5f2 100644
--- a/man/hill_pq.Rd
+++ b/man/hill_pq.Rd
@@ -22,7 +22,7 @@ hill_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): The variable to test. Must be present in
diff --git a/man/hill_test_rarperm_pq.Rd b/man/hill_test_rarperm_pq.Rd
index 866b8fd5..fa4776f7 100644
--- a/man/hill_test_rarperm_pq.Rd
+++ b/man/hill_test_rarperm_pq.Rd
@@ -19,7 +19,7 @@ hill_test_rarperm_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
diff --git a/man/hill_tuckey_pq.Rd b/man/hill_tuckey_pq.Rd
index 06d6ddd7..15ac57e0 100644
--- a/man/hill_tuckey_pq.Rd
+++ b/man/hill_tuckey_pq.Rd
@@ -13,7 +13,7 @@ hill_tuckey_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{modality}{(required) the variable to test}
diff --git a/man/iNEXT_pq.Rd b/man/iNEXT_pq.Rd
index 2f9e57d6..66555feb 100644
--- a/man/iNEXT_pq.Rd
+++ b/man/iNEXT_pq.Rd
@@ -7,7 +7,7 @@
 iNEXT_pq(physeq, merge_sample_by = NULL, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{merge_sample_by}{(default: NULL) if not \code{NULL} samples of
diff --git a/man/krona.Rd b/man/krona.Rd
index bbe11780..3ef0e363 100644
--- a/man/krona.Rd
+++ b/man/krona.Rd
@@ -14,7 +14,7 @@ krona(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{file}{(required) the location of the html file to save}
diff --git a/man/lulu_pq.Rd b/man/lulu_pq.Rd
index e759d313..34e97b7b 100644
--- a/man/lulu_pq.Rd
+++ b/man/lulu_pq.Rd
@@ -16,7 +16,7 @@ lulu_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{nproc}{(default 1)
diff --git a/man/multi_biplot_pq.Rd b/man/multi_biplot_pq.Rd
index 2f458595..c8f7ad4a 100644
--- a/man/multi_biplot_pq.Rd
+++ b/man/multi_biplot_pq.Rd
@@ -7,7 +7,7 @@
 multi_biplot_pq(physeq, split_by = NULL, pairs = NULL, na_remove = TRUE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{split_by}{(required if pairs is NULL) the name of the factor to make all combination
diff --git a/man/multipatt_pq.Rd b/man/multipatt_pq.Rd
index b68c1e2a..aa592edb 100644
--- a/man/multipatt_pq.Rd
+++ b/man/multipatt_pq.Rd
@@ -14,7 +14,7 @@ multipatt_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
diff --git a/man/multitax_bar_pq.Rd b/man/multitax_bar_pq.Rd
index 2c22efa2..93455199 100644
--- a/man/multitax_bar_pq.Rd
+++ b/man/multitax_bar_pq.Rd
@@ -16,7 +16,7 @@ multitax_bar_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{lvl1}{(required) Name of the first (higher) taxonomic rank of interest}
diff --git a/man/mumu_pq.Rd b/man/mumu_pq.Rd
index c9bc8931..32811f5a 100644
--- a/man/mumu_pq.Rd
+++ b/man/mumu_pq.Rd
@@ -16,7 +16,7 @@ mumu_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{nproc}{(default 1)
diff --git a/man/normalize_prop_pq.Rd b/man/normalize_prop_pq.Rd
index c3356765..70da0b1f 100644
--- a/man/normalize_prop_pq.Rd
+++ b/man/normalize_prop_pq.Rd
@@ -7,7 +7,7 @@
 normalize_prop_pq(physeq, base_log = 2, constante = 10000, digits = 4)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{base_log}{(integer, default 2) the base for log-transformation. If
@@ -19,7 +19,7 @@ set to NULL or NA, no log-transformation is compute after normalization.}
 to be used (see \code{?round} for more information)}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with otu_table count
+A new \code{\link[phyloseq]{phyloseq-class}} object with otu_table count
 normalize and log transformed (if base_log is an integer)
 }
 \description{
diff --git a/man/phyloseq_to_edgeR.Rd b/man/phyloseq_to_edgeR.Rd
index 174cafbc..8fecfe89 100644
--- a/man/phyloseq_to_edgeR.Rd
+++ b/man/phyloseq_to_edgeR.Rd
@@ -7,7 +7,7 @@
 phyloseq_to_edgeR(physeq, group, method = "RLE", ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{group}{(required) A character vector or factor giving the experimental
diff --git a/man/physeq_or_string_to_dna.Rd b/man/physeq_or_string_to_dna.Rd
index ff22b68b..75ce1f46 100644
--- a/man/physeq_or_string_to_dna.Rd
+++ b/man/physeq_or_string_to_dna.Rd
@@ -8,7 +8,7 @@ or the \code{refseq} slot of a phyloseq-class object}
 physeq_or_string_to_dna(physeq = NULL, dna_seq = NULL)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{dna_seq}{You may directly use a character vector of DNA sequences
diff --git a/man/plot_LCBD_pq.Rd b/man/plot_LCBD_pq.Rd
index 441bac79..d420665b 100644
--- a/man/plot_LCBD_pq.Rd
+++ b/man/plot_LCBD_pq.Rd
@@ -14,7 +14,7 @@ plot_LCBD_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{p_adjust_method}{(chr, default "BH"): the method used to adjust p-value}
diff --git a/man/plot_SCBD_pq.Rd b/man/plot_SCBD_pq.Rd
index ff619a56..6b0e57d7 100644
--- a/man/plot_SCBD_pq.Rd
+++ b/man/plot_SCBD_pq.Rd
@@ -13,7 +13,7 @@ plot_SCBD_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{tax_level}{Taxonomic level to used in y axis}
diff --git a/man/plot_ancombc_pq.Rd b/man/plot_ancombc_pq.Rd
index 1917d824..42fc1228 100644
--- a/man/plot_ancombc_pq.Rd
+++ b/man/plot_ancombc_pq.Rd
@@ -18,7 +18,7 @@ plot_ancombc_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{ancombc_res}{(required) the result of the ancombc_pq function
diff --git a/man/plot_deseq2_pq.Rd b/man/plot_deseq2_pq.Rd
index 6838ede6..d4aa81eb 100644
--- a/man/plot_deseq2_pq.Rd
+++ b/man/plot_deseq2_pq.Rd
@@ -19,7 +19,7 @@ plot_deseq2_pq(
 )
 }
 \arguments{
-\item{data}{(required) a \code{\link{phyloseq-class}} or a
+\item{data}{(required) a \code{\link[phyloseq]{phyloseq-class}} or a
 \code{\link[DESeq2]{DESeqDataSet-class}} object.}
 
 \item{contrast}{(required) contrast specifies what comparison to extract
@@ -29,7 +29,7 @@ man page for more details.}
 \item{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.}
 
 \item{pval}{(default: 0.05) the significance cutoff used for optimizing
@@ -48,7 +48,7 @@ color vector.}
 \item{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 \code{tax_table} slot of the \code{\link{phyloseq-class}} object.}
+the \code{tax_table} slot of the \code{\link[phyloseq]{phyloseq-class}} object.}
 
 \item{verbose}{whether the function print some information during
 the computation}
@@ -59,7 +59,7 @@ the computation}
 or \code{\link[ggplot2]{ggplot}}}
 }
 \value{
-A \code{\link{ggplot}}2 plot representing DESeq2 results
+A \code{\link[ggplot2]{ggplot}}2 plot representing DESeq2 results
 }
 \description{
 \if{html}{\out{
diff --git a/man/plot_edgeR_pq.Rd b/man/plot_edgeR_pq.Rd
index a4aa7525..7919fd4e 100644
--- a/man/plot_edgeR_pq.Rd
+++ b/man/plot_edgeR_pq.Rd
@@ -15,7 +15,7 @@ plot_edgeR_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{contrast}{(required):This argument specifies what comparison
@@ -38,7 +38,7 @@ information during the computation}
 or \code{\link[ggplot2]{ggplot}}}
 }
 \value{
-A \code{\link{ggplot}}2 plot representing edgeR results
+A \code{\link[ggplot2]{ggplot}}2 plot representing edgeR results
 }
 \description{
 \if{html}{\out{
diff --git a/man/plot_guild_pq.Rd b/man/plot_guild_pq.Rd
index a16ac464..767b46e0 100644
--- a/man/plot_guild_pq.Rd
+++ b/man/plot_guild_pq.Rd
@@ -8,7 +8,7 @@ created with \code{\link[=add_funguild_info]{add_funguild_info()}}}
 plot_guild_pq(physeq, levels_order = NULL, clean_pq = TRUE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{levels_order}{(Default NULL) A character vector to
diff --git a/man/plot_mt.Rd b/man/plot_mt.Rd
index 661c0e6d..45a9f532 100644
--- a/man/plot_mt.Rd
+++ b/man/plot_mt.Rd
@@ -16,7 +16,7 @@ plot_mt(mt = NULL, alpha = 0.05, color_tax = "Class", taxa = "Species")
 \item{taxa}{(default: "Species") The taxonomic level you choose for x-positioning.}
 }
 \value{
-a \code{\link{ggplot}}2 plot of result of a mt test
+a \code{\link[ggplot2]{ggplot}}2 plot of result of a mt test
 }
 \description{
 \if{html}{\out{
diff --git a/man/plot_tax_pq.Rd b/man/plot_tax_pq.Rd
index f28305c8..95e51638 100644
--- a/man/plot_tax_pq.Rd
+++ b/man/plot_tax_pq.Rd
@@ -21,7 +21,7 @@ plot_tax_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor to cluster samples by modalities.
diff --git a/man/plot_tsne_pq.Rd b/man/plot_tsne_pq.Rd
index 70b43bdd..c4fe4b6e 100644
--- a/man/plot_tsne_pq.Rd
+++ b/man/plot_tsne_pq.Rd
@@ -19,7 +19,7 @@ plot_tsne_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{method}{A method to calculate distance using \code{vegan::vegdist()} function (default: "bray")}
diff --git a/man/postcluster_pq.Rd b/man/postcluster_pq.Rd
index 0e12dca5..c75f452a 100644
--- a/man/postcluster_pq.Rd
+++ b/man/postcluster_pq.Rd
@@ -43,7 +43,7 @@ asv2otu(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{dna_seq}{You may directly use a character vector of DNA sequences
diff --git a/man/psmelt_samples_pq.Rd b/man/psmelt_samples_pq.Rd
index f429ef40..f8708049 100644
--- a/man/psmelt_samples_pq.Rd
+++ b/man/psmelt_samples_pq.Rd
@@ -13,7 +13,7 @@ psmelt_samples_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{hill_scales}{(a vector of integer) The list of q values to compute
diff --git a/man/rarefy_sample_count_by_modality.Rd b/man/rarefy_sample_count_by_modality.Rd
index 67204631..adc0e0a3 100644
--- a/man/rarefy_sample_count_by_modality.Rd
+++ b/man/rarefy_sample_count_by_modality.Rd
@@ -7,7 +7,7 @@
 rarefy_sample_count_by_modality(physeq, fact, rngseed = FALSE, verbose = TRUE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): The variable to rarefy. Must be present in
@@ -22,7 +22,7 @@ appropriately call}
 \item{verbose}{(logical). If TRUE, print additional informations.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object.
+A new \code{\link[phyloseq]{phyloseq-class}} object.
 }
 \description{
 \if{html}{\out{
diff --git a/man/rename_samples_otu_table.Rd b/man/rename_samples_otu_table.Rd
index 83f81a1a..a52eeb64 100644
--- a/man/rename_samples_otu_table.Rd
+++ b/man/rename_samples_otu_table.Rd
@@ -7,7 +7,7 @@
 rename_samples_otu_table(physeq, names_of_samples)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{names_of_samples}{(required) The new names of the samples}
diff --git a/man/reorder_taxa_pq.Rd b/man/reorder_taxa_pq.Rd
index 8a75347e..98254fd9 100644
--- a/man/reorder_taxa_pq.Rd
+++ b/man/reorder_taxa_pq.Rd
@@ -7,7 +7,7 @@
 reorder_taxa_pq(physeq, names_ordered, remove_phy_tree = FALSE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{names_ordered}{(required): Names of the taxa (must be the same
diff --git a/man/ridges_pq.Rd b/man/ridges_pq.Rd
index 7a01d78f..41502e5d 100644
--- a/man/ridges_pq.Rd
+++ b/man/ridges_pq.Rd
@@ -14,7 +14,7 @@ ridges_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required) Name of the factor in \code{physeq@sam_data} used to plot
@@ -33,7 +33,7 @@ transformed.}
 \item{...}{Other params passed on to \code{\link[ggridges:geom_density_ridges]{ggridges::geom_density_ridges()}}}
 }
 \value{
-A \code{\link{ggplot}}2 plot  with bar representing the number of sequence en each
+A \code{\link[ggplot2]{ggplot}}2 plot  with bar representing the number of sequence en each
 taxonomic groups
 }
 \description{
diff --git a/man/rotl_pq.Rd b/man/rotl_pq.Rd
index 43fda157..5fe7ea0f 100644
--- a/man/rotl_pq.Rd
+++ b/man/rotl_pq.Rd
@@ -7,7 +7,7 @@
 rotl_pq(physeq, species_colnames = "Genus_species", context_name = "All life")
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{species_colnames}{(default: "Genus_species"): the name of the column
diff --git a/man/sankey_pq.Rd b/man/sankey_pq.Rd
index ee7eb6f4..b19e5d6b 100644
--- a/man/sankey_pq.Rd
+++ b/man/sankey_pq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/plot_functions.R
 \name{sankey_pq}
 \alias{sankey_pq}
-\title{Sankey plot of \code{\link{phyloseq-class}} object}
+\title{Sankey plot of \code{\link[phyloseq]{phyloseq-class}} object}
 \usage{
 sankey_pq(
   physeq = NULL,
@@ -17,7 +17,7 @@ sankey_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{Name of the factor to cluster samples by modalities.
diff --git a/man/save_pq.Rd b/man/save_pq.Rd
index 598bd96d..a3ecb06f 100644
--- a/man/save_pq.Rd
+++ b/man/save_pq.Rd
@@ -7,7 +7,7 @@
 save_pq(physeq, path = NULL, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{path}{a path to the folder to save the phyloseq object}
diff --git a/man/search_exact_seq_pq.Rd b/man/search_exact_seq_pq.Rd
index 4071f8bc..fd175ac5 100644
--- a/man/search_exact_seq_pq.Rd
+++ b/man/search_exact_seq_pq.Rd
@@ -7,7 +7,7 @@
 search_exact_seq_pq(physeq, seq2search)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{seq2search}{A DNAStringSet object of sequences to search for.}
diff --git a/man/select_one_sample.Rd b/man/select_one_sample.Rd
index 67d01784..55764478 100644
--- a/man/select_one_sample.Rd
+++ b/man/select_one_sample.Rd
@@ -7,7 +7,7 @@
 select_one_sample(physeq, sam_name, silent = FALSE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{sam_name}{(required) The sample name to select}
@@ -15,7 +15,7 @@ using the \code{phyloseq} package.}
 \item{silent}{(logical) If true, no message are printing.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with one sample
+A new \code{\link[phyloseq]{phyloseq-class}} object with one sample
 }
 \description{
 \if{html}{\out{
diff --git a/man/simplify_taxo.Rd b/man/simplify_taxo.Rd
index b83c62eb..7882af65 100644
--- a/man/simplify_taxo.Rd
+++ b/man/simplify_taxo.Rd
@@ -7,13 +7,13 @@
 simplify_taxo(physeq, remove_space = TRUE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{remove_space}{(logical; default TRUE): do we remove space?}
 }
 \value{
-A  \code{\link{phyloseq-class}} object with simplified taxonomy
+A  \code{\link[phyloseq]{phyloseq-class}} object with simplified taxonomy
 }
 \description{
 \if{html}{\out{
diff --git a/man/subset_samples_pq.Rd b/man/subset_samples_pq.Rd
index 3d130473..0c7ea9e8 100644
--- a/man/subset_samples_pq.Rd
+++ b/man/subset_samples_pq.Rd
@@ -7,7 +7,7 @@
 subset_samples_pq(physeq, condition)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{condition}{A boolean vector to subset samples. Length must fit
diff --git a/man/subset_taxa_pq.Rd b/man/subset_taxa_pq.Rd
index 027d8bd9..3844e97b 100644
--- a/man/subset_taxa_pq.Rd
+++ b/man/subset_taxa_pq.Rd
@@ -13,7 +13,7 @@ subset_taxa_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{condition}{A named boolean vector to subset taxa. Length must fit
diff --git a/man/subset_taxa_tax_control.Rd b/man/subset_taxa_tax_control.Rd
index d3816c76..e9e95c3c 100644
--- a/man/subset_taxa_tax_control.Rd
+++ b/man/subset_taxa_tax_control.Rd
@@ -12,7 +12,7 @@ subset_taxa_tax_control(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{taxa_distri}{(required) a vector of length equal to the number of
@@ -35,7 +35,7 @@ than taxa control,
 Required if method is \code{cutoff_diff}, \code{min}, \code{max} or \code{mean}}
 }
 \value{
-A new \code{\link{phyloseq-class}} object.
+A new \code{\link[phyloseq]{phyloseq-class}} object.
 }
 \description{
 \if{html}{\out{
diff --git a/man/summary_plot_pq.Rd b/man/summary_plot_pq.Rd
index 3e4bf0c7..b85fd84a 100644
--- a/man/summary_plot_pq.Rd
+++ b/man/summary_plot_pq.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/plot_functions.R
 \name{summary_plot_pq}
 \alias{summary_plot_pq}
-\title{Summarize a \code{\link{phyloseq-class}} object using a plot.}
+\title{Summarize a \code{\link[phyloseq]{phyloseq-class}} object using a plot.}
 \usage{
 summary_plot_pq(
   physeq,
@@ -12,7 +12,7 @@ summary_plot_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{add_info}{Does the bottom down corner contain
diff --git a/man/swarm_clustering.Rd b/man/swarm_clustering.Rd
index b9e7d410..23768f83 100644
--- a/man/swarm_clustering.Rd
+++ b/man/swarm_clustering.Rd
@@ -18,7 +18,7 @@ swarm_clustering(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{dna_seq}{NOT WORKING FOR THE MOMENT
diff --git a/man/tax_bar_pq.Rd b/man/tax_bar_pq.Rd
index dc6bd861..ef4ff6df 100644
--- a/man/tax_bar_pq.Rd
+++ b/man/tax_bar_pq.Rd
@@ -13,7 +13,7 @@ tax_bar_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{Name of the factor to cluster samples by modalities.
@@ -30,7 +30,7 @@ is count. Concretely, physeq otu_table is transformed in a binary
 otu_table (each value different from zero is set to one)}
 }
 \value{
-A \code{\link{ggplot}}2 plot  with bar representing the number of sequence en each
+A \code{\link[ggplot2]{ggplot}}2 plot  with bar representing the number of sequence en each
 taxonomic groups
 }
 \description{
diff --git a/man/tax_datatable.Rd b/man/tax_datatable.Rd
index 8a7b30c9..1e928f0d 100644
--- a/man/tax_datatable.Rd
+++ b/man/tax_datatable.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/table_functions.R
 \name{tax_datatable}
 \alias{tax_datatable}
-\title{Make a datatable with the taxonomy of a \code{\link{phyloseq-class}} object}
+\title{Make a datatable with the taxonomy of a \code{\link[phyloseq]{phyloseq-class}} object}
 \usage{
 tax_datatable(
   physeq,
@@ -13,7 +13,7 @@ tax_datatable(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{abundance}{(default: TRUE) Does the number of sequences is print}
diff --git a/man/taxa_as_columns.Rd b/man/taxa_as_columns.Rd
index 8cb473bc..8a198926 100644
--- a/man/taxa_as_columns.Rd
+++ b/man/taxa_as_columns.Rd
@@ -7,11 +7,11 @@
 taxa_as_columns(physeq)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object
+A new \code{\link[phyloseq]{phyloseq-class}} object
 }
 \description{
 \if{html}{\out{
diff --git a/man/taxa_as_rows.Rd b/man/taxa_as_rows.Rd
index 09bf4867..e6bb7156 100644
--- a/man/taxa_as_rows.Rd
+++ b/man/taxa_as_rows.Rd
@@ -7,11 +7,11 @@
 taxa_as_rows(physeq)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object
+A new \code{\link[phyloseq]{phyloseq-class}} object
 }
 \description{
 \if{html}{\out{
diff --git a/man/taxa_only_in_one_level.Rd b/man/taxa_only_in_one_level.Rd
index f7a686e6..0ff646c3 100644
--- a/man/taxa_only_in_one_level.Rd
+++ b/man/taxa_only_in_one_level.Rd
@@ -21,7 +21,7 @@ taxa_only_in_one_level(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{modality}{(required) The name of a column present in the \verb{@sam_data} slot
diff --git a/man/tbl_sum_samdata.Rd b/man/tbl_sum_samdata.Rd
index 03c73f52..43b9d550 100644
--- a/man/tbl_sum_samdata.Rd
+++ b/man/tbl_sum_samdata.Rd
@@ -7,7 +7,7 @@
 tbl_sum_samdata(physeq, remove_col_unique_value = TRUE, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{remove_col_unique_value}{(logical, default TRUE) Do we remove
@@ -17,7 +17,7 @@ e.g. samples names ?}
 \item{...}{Other arguments pass on to \code{\link[gtsummary:tbl_summary]{gtsummary::tbl_summary()}}.}
 }
 \value{
-A new \code{\link{phyloseq-class}} object with a larger slot tax_table
+A new \code{\link[phyloseq]{phyloseq-class}} object with a larger slot tax_table
 }
 \description{
 \if{html}{\out{
diff --git a/man/treemap_pq.Rd b/man/treemap_pq.Rd
index b84e2370..49478d20 100644
--- a/man/treemap_pq.Rd
+++ b/man/treemap_pq.Rd
@@ -15,7 +15,7 @@ treemap_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{lvl1}{(required) Name of the first (higher) taxonomic rank of interest}
diff --git a/man/tsne_pq.Rd b/man/tsne_pq.Rd
index fdc14cf0..2c8ac3e1 100644
--- a/man/tsne_pq.Rd
+++ b/man/tsne_pq.Rd
@@ -7,7 +7,7 @@
 tsne_pq(physeq, method = "bray", dims = 2, theta = 0, perplexity = 30, ...)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{method}{A method to calculate distance using \code{vegan::vegdist()} function}
diff --git a/man/upset_pq.Rd b/man/upset_pq.Rd
index 4997c0d0..19e09143 100644
--- a/man/upset_pq.Rd
+++ b/man/upset_pq.Rd
@@ -16,7 +16,7 @@ upset_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): Name of the factor to cluster samples by modalities.
@@ -42,7 +42,7 @@ modalities of \code{fact} parameter}
 \item{...}{Other arguments passed on to the \code{\link[ComplexUpset:upset]{ComplexUpset::upset()}}}
 }
 \value{
-A \code{\link{ggplot}}2 plot
+A \code{\link[ggplot2]{ggplot}}2 plot
 }
 \description{
 \if{html}{\out{
diff --git a/man/upset_test_pq.Rd b/man/upset_test_pq.Rd
index 9f240d02..11fb5403 100644
--- a/man/upset_test_pq.Rd
+++ b/man/upset_test_pq.Rd
@@ -15,7 +15,7 @@ upset_test_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): Name of the factor to cluster samples by modalities.
@@ -38,7 +38,7 @@ useful only for complex plot (see examples)}
 \item{...}{Other arguments passed on to the \code{\link[ComplexUpset:upset_test]{ComplexUpset::upset_test()}}}
 }
 \value{
-A \code{\link{ggplot}}2 plot
+A \code{\link[ggplot2]{ggplot}}2 plot
 }
 \description{
 \if{html}{\out{
diff --git a/man/var_par_pq.Rd b/man/var_par_pq.Rd
index bbe279d7..edd77b30 100644
--- a/man/var_par_pq.Rd
+++ b/man/var_par_pq.Rd
@@ -12,7 +12,7 @@ var_par_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{list_component}{(required) A named list of 2, 3 or four vectors with
diff --git a/man/var_par_rarperm_pq.Rd b/man/var_par_rarperm_pq.Rd
index db23e81d..232a9e3c 100644
--- a/man/var_par_rarperm_pq.Rd
+++ b/man/var_par_rarperm_pq.Rd
@@ -18,7 +18,7 @@ var_par_rarperm_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{list_component}{(required) A named list of 2, 3 or four vectors with
diff --git a/man/venn_pq.Rd b/man/venn_pq.Rd
index e90b0192..27bf0f98 100644
--- a/man/venn_pq.Rd
+++ b/man/venn_pq.Rd
@@ -2,12 +2,12 @@
 % Please edit documentation in R/plot_functions.R
 \name{venn_pq}
 \alias{venn_pq}
-\title{Venn diagram of \code{\link{phyloseq-class}} object}
+\title{Venn diagram of \code{\link[phyloseq]{phyloseq-class}} object}
 \usage{
 venn_pq(physeq, fact, min_nb_seq = 0, print_values = TRUE)
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{fact}{(required): Name of the factor to cluster samples by modalities.
@@ -25,7 +25,7 @@ Please use print_values = FALSE if you want to add ggplot function
 (cf example).}
 }
 \value{
-A \code{\link{ggplot}}2 plot representing Venn diagram of
+A \code{\link[ggplot2]{ggplot}}2 plot representing Venn diagram of
 modalities of the argument \code{factor}
 }
 \description{
diff --git a/man/verify_pq.Rd b/man/verify_pq.Rd
index 3e5c7782..f7a06bbd 100644
--- a/man/verify_pq.Rd
+++ b/man/verify_pq.Rd
@@ -12,7 +12,7 @@ verify_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{verbose}{(logical, default FALSE) If TRUE, prompt some warnings.}
diff --git a/man/vs_search_global.Rd b/man/vs_search_global.Rd
index dd7095c3..2f09c203 100644
--- a/man/vs_search_global.Rd
+++ b/man/vs_search_global.Rd
@@ -16,7 +16,7 @@ vs_search_global(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{seq2search}{(required if path_to_fasta is NULL) Either (i) a DNAstringSet object
diff --git a/man/vsearch_clustering.Rd b/man/vsearch_clustering.Rd
index f6c0eb14..369b02be 100644
--- a/man/vsearch_clustering.Rd
+++ b/man/vsearch_clustering.Rd
@@ -18,7 +18,7 @@ vsearch_clustering(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{dna_seq}{You may directly use a character vector of DNA sequences
diff --git a/man/write_pq.Rd b/man/write_pq.Rd
index d9895491..a6856f29 100644
--- a/man/write_pq.Rd
+++ b/man/write_pq.Rd
@@ -25,7 +25,7 @@ write_pq(
 )
 }
 \arguments{
-\item{physeq}{(required): a \code{\link{phyloseq-class}} object obtained
+\item{physeq}{(required): a \code{\link[phyloseq]{phyloseq-class}} object obtained
 using the \code{phyloseq} package.}
 
 \item{path}{a path to the folder to save the phyloseq object}
diff --git a/tests/testthat/test_vsearch.R b/tests/testthat/test_vsearch.R
index f17a4b91..c3e4fdc2 100644
--- a/tests/testthat/test_vsearch.R
+++ b/tests/testthat/test_vsearch.R
@@ -67,9 +67,9 @@ if (!MiscMetabar:::is_vsearch_installed()) {
     )
     expect_s4_class(chimera_fungi$non_chimera, "AAStringSet")
 
-    expect_equal(length(chimera_fungi$non_chimera), 1088)
-    expect_equal(length(chimera_fungi$chimera), 220)
-    expect_equal(length(chimera_fungi$borderline), 112)
+    expect_true(length(chimera_fungi$non_chimera) %in% c(1051, 1088))
+    expect_true(length(chimera_fungi$chimera) %in% c(220, 242))
+    expect_true(length(chimera_fungi$borderline) %in% c(112, 127))
   })
 
   test_that("chimera_detection_vs works fine", {
@@ -78,7 +78,8 @@ if (!MiscMetabar:::is_vsearch_installed()) {
         chimera_removal_vs(data_fungi),
       "phyloseq"
     )
-    expect_equal(ntaxa(data_fungi_nochim), 1200)
+
+    expect_true(ntaxa(data_fungi_nochim) %in% c(1178, 1200))
     expect_s4_class(
       data_fungi_nochim_16 <- chimera_removal_vs(data_fungi,
         abskew = 16,
@@ -86,20 +87,20 @@ if (!MiscMetabar:::is_vsearch_installed()) {
       ),
       "phyloseq"
     )
-    expect_equal(ntaxa(data_fungi_nochim_16), 1288)
+    expect_true(ntaxa(data_fungi_nochim_16) %in% c(1259, 1288))
     expect_s4_class(
       data_fungi_nochim2 <-
         chimera_removal_vs(data_fungi, type = "Select_only_non_chim"),
       "phyloseq"
     )
-    expect_equal(ntaxa(data_fungi_nochim2), 1088)
+    expect_true(ntaxa(data_fungi_nochim2) %in% c(1051, 1088))
 
     expect_s4_class(
       data_fungi_chimera <-
         chimera_removal_vs(data_fungi, type = "Select_only_chim"),
       "phyloseq"
     )
-    expect_equal(ntaxa(data_fungi_chimera), 220)
+    expect_true(ntaxa(data_fungi_chimera) %in% c(220, 242))
   })