filter_taxa now has better error messages for invalid inputs

resolves #117

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: 0.2.0.9103
+Version: 0.2.0.9104
 Authors@R: c(
     person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus+r@gmail.com"),
     person("Zachary", "Foster", role = "aut", email = "zacharyfoster1989@gmail.com")

NEWS.md

@@ -7,6 +7,7 @@ Current
 
 ### Bug fixes
 
+* `filter_taxa` now has better error messages for invalid inputs ([issue #117](https://github.com/ropensci/taxa/issues/117)).
 * Fix a bug that caused an error in `filter_taxa` when no taxa pass filter ([issue #116](https://github.com/ropensci/taxa/issues/116)).
 
 taxa 0.2.0

R/taxonomy--class.R

@@ -687,7 +687,7 @@ Taxonomy <- R6::R6Class(
         reassign_obs <- parse_possibly_named_logical(
           reassign_obs,
           self$data,
-          default = formals(self$filter_taxa)$reassign_obs
+          default <- formals(self$filter_taxa)$reassign_obs
         )
         process_one <- function(data_index) {
 
@@ -996,7 +996,6 @@ Taxonomy <- R6::R6Class(
       apply(self$edge_list, 1, paste0, collapse = "->")
     },
 
-    # Remove taxa not in "el_indexes"
     remove_taxa = function(el_indexes) {
       # Remove taxa objects
       self$taxa <- self$taxa[self$taxon_ids()[el_indexes]]
@@ -1005,10 +1004,8 @@ Taxonomy <- R6::R6Class(
       self$edge_list <- self$edge_list[el_indexes, , drop = FALSE]
 
       # Replace and edges going to removed taxa with NA
-      to_replace <- ! self$edge_list$from %in% self$taxon_ids()
-      if (sum(to_replace) > 0) {
-        self$edge_list[to_replace, "from"] <- as.character(NA)
-      }
+      self$edge_list[! self$edge_list$from %in% self$taxon_ids(), "from"] <-
+        as.character(NA)
     },
 
     # Takes one ore more NSE expressions and resolves them to indexes of edgelist rows
@@ -1022,15 +1019,45 @@ Taxonomy <- R6::R6Class(
         return(self$taxon_indexes())
       }
 
+      # Check that index input is valid
+      is_num <- vapply(selection, is.numeric, logical(1))
+      unused <- lapply(selection[is_num],
+                       function(x) {
+                         invalid_indexes <- x[x < 1 | x > length(self$taxon_ids())]
+                         if (length(invalid_indexes) > 0) {
+                           stop(call. = FALSE,
+                                paste0("The following taxon indexes are invalid:\n",
+                                       limited_print(invalid_indexes, type = "silent")))
+                         }
+                       })
+
       # Convert taxon_ids to indexes
       is_char <- vapply(selection, is.character, logical(1))
       selection[is_char] <- lapply(selection[is_char],
-                                   function(x) match(x, self$taxon_ids()))
+                                   function(x) {
+                                     result <- match(x, self$taxon_ids())
+                                     invalid_ids <- x[is.na(result)]
+                                     if (length(invalid_ids) > 0) {
+                                       stop(call. = FALSE,
+                                            paste0("The following taxon IDs do not exist:\n",
+                                                   limited_print(invalid_ids, type = "silent")))
+                                     }
+                                     return(result)
+                                   })
 
       # Convert logical to indexes
       is_tf <- vapply(selection, is.logical, logical(1))
       selection[is_tf] <- lapply(selection[is_tf],
-                                 function(x) which(x))
+                                 function(x) {
+                                   if (length(x) != length(self$taxon_ids())) {
+                                     stop(call. = FALSE,
+                                          paste0("TRUE/FALSE vector (length = ",
+                                                 length(x),
+                                                 ") must be the same length as the number of taxa (",
+                                                 length(self$taxon_ids()), ")"))
+                                   }
+                                   which(x)
+                                 })
 
       # Combine index lists.
       intersect_with_dups <- function(a, b) {

tests/testthat/test--taxonomy.R

@@ -1,6 +1,7 @@
 ## Testing `taxonomy` class
 
 library(taxa)
+library(testthat)
 context("taxonomy")
 
 
@@ -268,6 +269,14 @@ test_that("Filtering taxa", {
   expected_names <- expected_names[! expected_names %in% c("Solanum", "lycopersicum", "tuberosum")]
   expect_true(all(expected_names == result$taxon_names()))
 
+  # Errors for invalid indexes
+  expect_error(filter_taxa(x, 100), "The following taxon indexes are invalid:")
+
+  # Errors for invalid IDs
+  expect_error(filter_taxa(x, "zzz"), "The following taxon IDs do not exist:")
+
+  # Errors for invalid logical
+  expect_error(filter_taxa(x, TRUE), "must be the same length as the number of taxa")
 })