Went through docs, resolves #109, added classification to get_data …

…for taxonomy and taxmap

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Provides taxonomic classes for
     with data. Methods provided are "taxonomically aware", in
     that they know about ordering of ranks, and methods that
     filter based on taxonomy also filter associated data.
-Version: 0.1.0.9115
+Version: 0.1.0.9116
 Authors@R: c(
     person("Scott", "Chamberlain", role = c("aut", "cre"), email = "[email protected]"),
     person("Zachary", "Foster", role = "aut", email = "[email protected]")

R/taxmap--class.R

@@ -3,8 +3,8 @@
 #' A class designed to store a taxonomy and associated information. This class
 #' builds on the [taxonomy()] class. User defined data can be stored in the list
 #' `obj$data`, where `obj` is a taxmap object. Data that is associated with taxa
-#' can be manipulated in a variety of ways using functions like `filter_taxa`
-#' and `filter_obs`. To associate the items of lists/vectors with taxa, name
+#' can be manipulated in a variety of ways using functions like [filter_taxa()]
+#' and [filter_obs()]. To associate the items of lists/vectors with taxa, name
 #' them by [taxon_ids()]. For tables, add a column named `taxon_id` that stores
 #' [taxon_ids()].
 #'
@@ -18,7 +18,7 @@
 #'   [hierarchy()] or character vectors in a list. Cannot be used with `...`.
 #' @param data A list of tables with data associated with the taxa.
 #' @param funcs A named list of functions to include in the class. Referring to
-#'   the names of these in functions like `filter_taxa` will execute the
+#'   the names of these in functions like [filter_taxa()] will execute the
 #'   function and return the results. If the function has at least one argument,
 #'   the taxmap object is passed to it.
 #' @family classes
@@ -467,6 +467,7 @@ Taxmap <- R6::R6Class(
       "taxon_names",
       "taxon_ids",
       "taxon_indexes",
+      "classifications",
       "n_supertaxa",
       "n_supertaxa_1",
       "n_subtaxa",

R/taxonomy--class.R

@@ -311,13 +311,15 @@ Taxonomy <- R6::R6Class(
       output <- unname(subset[is_root])
 
       # Look up values
-      if (!is.null(value)) {
+      if (! is.null(value)) {
         possible_values <- self$get_data(value)[[1]]
         if (is.null(names(possible_values))) {
           output <- possible_values[output]
         } else {
           output <- possible_values[self$taxon_ids()[output]]
         }
+      } else {
+        names(output) <- self$taxon_ids()[output]
       }
 
       return(output)
@@ -975,10 +977,20 @@ Taxonomy <- R6::R6Class(
   ),
 
   private = list(
-    nse_accessible_funcs = c("taxon_names", "taxon_ids", "taxon_indexes",
-                             "n_supertaxa", "n_supertaxa_1", "n_subtaxa",
-                             "n_subtaxa_1", "taxon_ranks", "is_root", "is_stem",
-                             "is_branch", "is_leaf", "is_internode"),
+    nse_accessible_funcs = c("taxon_names",
+                             "taxon_ids",
+                             "taxon_indexes",
+                             "classifications",
+                             "n_supertaxa",
+                             "n_supertaxa_1",
+                             "n_subtaxa",
+                             "n_subtaxa_1",
+                             "taxon_ranks",
+                             "is_root",
+                             "is_stem",
+                             "is_branch",
+                             "is_leaf",
+                             "is_internode"),
 
     make_graph = function() {
       apply(self$edge_list, 1, paste0, collapse = "->")

R/taxonomy--docs.R

@@ -222,7 +222,7 @@ NULL
 #' Get "branch" taxa
 #'
 #' Return the "branch" taxa for a [taxonomy()] or [taxmap()] object. A branch is
-#' anything that is not a root, stem, or, leaf. Its the interior of the tree
+#' anything that is not a root, stem, or leaf. Its the interior of the tree
 #' after the first split starting from the roots. Can also be used to get the
 #' branches of a subset of taxa.
 #' \preformatted{
@@ -302,10 +302,6 @@ NULL
 #' # Return something besides taxon indexes
 #' internodes(ex_taxmap, value = "taxon_names")
 #'
-#' # Visualize which taxa are internodes
-#' library(metacoder)
-#' heat_tree(ex_taxmap, node_label = taxon_names,
-#'           node_color = ifelse(is_internode, "red", "grey"))
 #' }
 #' @name internodes
 NULL
@@ -736,13 +732,15 @@ NULL
 
 #' Get data in a taxonomy or taxmap object by name
 #'
-#' Given a vector of names, return a list of data (usually lists/vectors)
-#' contained in a [taxonomy()] or [taxmap()] object. Each item will be named by
-#' taxon ids when possible.
+#' Given a vector of names, return a  table of the indicated data
+#' contained in a [taxonomy()] or [taxmap()] object.
 #' \preformatted{
 #' obj$get_data_frame(name = NULL, ...)
 #' get_data_frame(obj, name = NULL, ...)}
 #'
+#' Note: This function will not work with variables in datasets in [taxmap()]
+#' objects unless their rows correspond 1:1 with all taxa.
+#'
 #' @param obj A [taxonomy()] or [taxmap()]  object
 #' @param name (`character`) Names of data to return. If not supplied, return
 #'   all data listed in [all_names()].