resolve link issues with CRAN check

Author: zachary-foster

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metacoder
 Title: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
-Version: 0.3.7
+Version: 0.3.8
 Authors@R: c(person("Zachary", "Foster", email =
         "zacharyfoster1989@gmail.com", role = c("aut", "cre")),
         person("Niklaus", "Grunwald", email =
@@ -53,8 +53,7 @@ Suggests:
     biomformat,
     DESeq2
 VignetteBuilder: knitr
-RoxygenNote: 7.3.1
-Date: 2024-02-19
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 biocViews: 
 LinkingTo: Rcpp

R/as_phyloseq.R

@@ -20,12 +20,12 @@
 #'   \item{\code{FALSE}}{Do not include a sample data table, even if "sample_data" exists in `obj$data`}
 #' }
 #' @param sample_id_col The name of the column storing sample IDs in the sample data table.
-#' @param phy_tree A phylogenetic tree of class \code{\link[ape]{phylo}} from
+#' @param phy_tree A phylogenetic tree of class \code{\link[ape:phylo]{ape::phylo}} from
 #'   the \code{\link{ape}} package with tip labels matching OTU ids. Must be one of the following:
 #' \describe{
 #'   \item{\code{NULL}}{Look for a tree named "phy_tree" in `obj$data` with tip labels matching OTU ids. If it exists, use it.}
 #'   \item{\code{character}}{The name of the tree stored in `obj$data` with tip labels matching OTU ids.}
-#'   \item{\code{\link[ape]{phylo}}}{A tree with tip labels matching OTU ids.}
+#'   \item{\code{\link[ape:phylo]{ape::phylo}}}{A tree with tip labels matching OTU ids.}
 #'   \item{\code{FALSE}}{Do not include a tree, even if "phy_tree" exists in `obj$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}}. 
+#' @param output_file The path to one or more files to save the plot in using \code{\link[ggplot2:ggsave]{ggplot2::ggsave}}. 
 #' The type of the file will be determined by the extension given.
 #' Default: Do not save plot.
 #' 
@@ -322,16 +322,16 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' The following \code{character} values are understood:
 #' 
 #' \describe{
-#'   \item{"automatic"}{Use \code{\link[igraph]{nicely}}. Let \code{\link{igraph}} choose the layout.}
-#'   \item{"reingold-tilford"}{Use \code{\link[igraph]{as_tree}}. A circular tree-like layout.}
-#'   \item{"davidson-harel"}{Use \code{\link[igraph]{with_dh}}. A type of simulated annealing.}
-#'   \item{"gem"}{Use \code{\link[igraph]{with_gem}}. A force-directed layout.}
-#'   \item{"graphopt"}{Use \code{\link[igraph]{with_graphopt}}. A force-directed layout.}
-#'   \item{"mds"}{Use \code{\link[igraph]{with_mds}}. Multidimensional scaling.}
-#'   \item{"fruchterman-reingold"}{Use \code{\link[igraph]{with_fr}}. A force-directed layout.}
-#'   \item{"kamada-kawai"}{Use \code{\link[igraph]{with_kk}}. A layout based on a physical model of springs.}
-#'   \item{"large-graph"}{Use \code{\link[igraph]{with_lgl}}. Meant for larger graphs.}
-#'   \item{"drl"}{Use \code{\link[igraph]{with_drl}}. A force-directed layout.}
+#'   \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.}
 #' }
 #' 
 #'