preparing for CRAN release

NEWS.md

@@ -1,6 +1,6 @@
 # News 
 
-## Current
+##  metacoder 0.2.1
 
 ### Bug fixes
 

R/heat_tree.R

@@ -221,8 +221,6 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' Passed to the \code{\link{igraph}} layout function used.
 #' 
 #' 
-#' @section Elements
-#'
 #' @section labels:
 #' 
 #' The labels of nodes, edges, and trees can be added.
@@ -232,8 +230,6 @@ heat_tree.Taxmap <- function(.input, ...) {
 #' 
 #' Accepts a vector, the same length \code{taxon_id} or a factor of its length.
 #'
-#' @section Element Properties
-#'
 #' @section sizes:
 #' 
 #' The size of nodes, edges, labels, and trees can be mapped to various conditions.
@@ -422,7 +418,6 @@ heat_tree.Taxmap <- function(.input, ...) {
 #'           node_size_interval = c(10, 100))
 #' 
 #' }
-#' @keywords internal
 #' @method heat_tree default
 #' @rdname heat_tree
 heat_tree.default <- function(taxon_id, supertaxon_id, 

R/remove_ambiguous.R

@@ -73,6 +73,9 @@ ambiguous_patterns <- function(unknown = TRUE, uncultured = TRUE,
 #'   determining a match.
 #'
 #' @return TRUE/FALSE vector corresponding to \code{taxon_names}
+#' 
+#' @examples 
+#' is_ambiguous(c("unknown", "uncultured", "homo sapiens", "kfdsjfdljsdf"))
 #'
 #' @export
 is_ambiguous <- function(taxon_names, unknown = TRUE, uncultured = TRUE,
@@ -104,6 +107,14 @@ is_ambiguous <- function(taxon_names, unknown = TRUE, uncultured = TRUE,
 #'
 #' @return A \code{\link[taxa]{taxmap}} object
 #'
+#' @examples 
+#' obj <- parse_tax_data(c("Plantae;Solanaceae;Solanum;lycopersicum",
+#'                         "Plantae;Solanaceae;Solanum;tuberosum",
+#'                         "Plantae;Solanaceae;Solanum;unknown",
+#'                         "Plantae;Solanaceae;Solanum;uncultured",
+#'                         "Plantae;UNIDENTIFIED"))
+#' filter_ambiguous_taxa(obj)
+#'
 #' @export
 filter_ambiguous_taxa <- function(obj, unknown = TRUE, uncultured = TRUE,
                                   name_regex = ".", ignore_case = TRUE,