remove links to make CRAN happy

Author: zachary-foster

R/as_phyloseq.R

@@ -10,7 +10,7 @@
 #'   \item{\code{data.frame}}{A table with taxon IDs, OTU IDs, and OTU counts}
 #'   \item{\code{FALSE}}{Do not include an OTU table, even if "otu_table" exists in `obj$data`}
 #' }
-#' @param otu_id_col The name of the column storing OTU IDs in the otu table.
+#' @param otu_id_col The name of the column storing OTU IDs in the OTU table.
 #' @param sample_data A table containing sample data with sample IDs matching
 #'   column names in the OTU table. Must be one of the following:
 #' \describe{
@@ -20,12 +20,12 @@
 #'   \item{\code{FALSE}}{Do not include a sample data table, even if "sample_data" exists in `obj$data`}
 #' }
 #' @param sample_id_col The name of the column storing sample IDs in the sample data table.
-#' @param phy_tree A phylogenetic tree of class \code{\link[ape:phylo]{ape::phylo}} from
-#'   the \code{\link{ape}} package with tip labels matching OTU ids. Must be one of the following:
+#' @param phy_tree A phylogenetic tree of class \code{ape:phylo} from
+#'   the \code{ape} package with tip labels matching OTU ids. Must be one of the following:
 #' \describe{
 #'   \item{\code{NULL}}{Look for a tree named "phy_tree" in `obj$data` with tip labels matching OTU ids. If it exists, use it.}
 #'   \item{\code{character}}{The name of the tree stored in `obj$data` with tip labels matching OTU ids.}
-#'   \item{\code{\link[ape:phylo]{ape::phylo}}}{A tree with tip labels matching OTU ids.}
+#'   \item{\code{ape::phylo}}{A tree with tip labels matching OTU ids.}
 #'   \item{\code{FALSE}}{Do not include a tree, even if "phy_tree" exists in `obj$data`}
 #' }
 #' 

R/heat_tree.R

@@ -229,7 +229,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 
 #' @param background_color The background color of the plot.
 #' Default: Transparent
-#' @param output_file The path to one or more files to save the plot in using \code{\link[ggplot2:ggsave]{ggplot2::ggsave}}. 
+#' @param output_file The path to one or more files to save the plot in using \code{ggplot2::ggsave}. 
 #' The type of the file will be determined by the extension given.
 #' Default: Do not save plot.
 #' 
@@ -240,7 +240,7 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' @param verbose If \code{TRUE} print progress reports as the function runs.
 #' 
 #' @param ... (other named arguments)
-#' Passed to the \code{\link{igraph}} layout function used.
+#' Passed to the \code{igraph} layout function used.
 #' 
 #' 
 #' @section labels:
@@ -316,22 +316,22 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' @section layout:
 #' 
 #' Layouts determine the position of node elements on the graph.
-#' They are implemented using the \code{\link{igraph}} package.
-#' Any additional arguments passed to \code{heat_tree} are passed to the  \code{\link{igraph}}
+#' They are implemented using the \code{igraph} package.
+#' Any additional arguments passed to \code{heat_tree} are passed to the  \code{igraph}
 #' function used.
 #' The following \code{character} values are understood:
 #' 
 #' \describe{
-#'   \item{"automatic"}{Use \code{\link[igraph:nicely]{igraph::nicely}}. Let \code{\link{igraph}} choose the layout.}
-#'   \item{"reingold-tilford"}{Use \code{\link[igraph:as_tree]{igraph::as_tree}}. A circular tree-like layout.}
-#'   \item{"davidson-harel"}{Use \code{\link[igraph:with_dh]{igraph::with_dh}}. A type of simulated annealing.}
-#'   \item{"gem"}{Use \code{\link[igraph:with_gem]{igraph::with_gem}}. A force-directed layout.}
-#'   \item{"graphopt"}{Use \code{\link[igraph:with_graphopt]{igraph::with_graphopt}}. A force-directed layout.}
-#'   \item{"mds"}{Use \code{\link[igraph:with_mds]{igraph::with_mds}}. Multidimensional scaling.}
-#'   \item{"fruchterman-reingold"}{Use \code{\link[igraph:with_fr]{igraph::with_fr}}. A force-directed layout.}
-#'   \item{"kamada-kawai"}{Use \code{\link[igraph:with_kk]{igraph::with_kk}}. A layout based on a physical model of springs.}
-#'   \item{"large-graph"}{Use \code{\link[igraph:with_lgl]{igraph::with_lgl}}. Meant for larger graphs.}
-#'   \item{"drl"}{Use \code{\link[igraph:with_drl]{igraph::with_drl}}. A force-directed layout.}
+#'   \item{"automatic"}{Use \code{igraph::nicely}. Let \code{igraph} choose the layout.}
+#'   \item{"reingold-tilford"}{Use \code{igraph::as_tree}. A circular tree-like layout.}
+#'   \item{"davidson-harel"}{Use \code{igraph::with_dh}. A type of simulated annealing.}
+#'   \item{"gem"}{Use \code{igraph::with_gem}. A force-directed layout.}
+#'   \item{"graphopt"}{Use \code{igraph::with_graphopt}. A force-directed layout.}
+#'   \item{"mds"}{Use \code{igraph::with_mds}. Multidimensional scaling.}
+#'   \item{"fruchterman-reingold"}{Use \code{igraph::with_fr}. A force-directed layout.}
+#'   \item{"kamada-kawai"}{Use \code{igraph::with_kk}. A layout based on a physical model of springs.}
+#'   \item{"large-graph"}{Use \code{igraph::with_lgl}. Meant for larger graphs.}
+#'   \item{"drl"}{Use \code{igraph::with_drl}. A force-directed layout.}
 #' }
 #' 
 #'