Add "gigaclass" to rank_ref_zoo

references issue #885

Author: zachary-foster

R/downstream-utils.R

@@ -15,7 +15,15 @@ prune_too_low <- function(x, rank, ignore_no_rank = FALSE, zoo = FALSE,
   # the pruning
   rr <- if (zoo) taxize_ds$rank_ref_zoo else taxize_ds$rank_ref
   rank_target_no <- as.numeric(rr[which_rank(rank, zoo = zoo), "rankid"])
-  rank_nos <- as.numeric(rr$rankid[vapply(x$rank, function(z) which_rank(z, zoo = zoo), 1)])
+  rank_nos <- as.numeric(rr$rankid[vapply(x$rank, FUN.VALUE = numeric(1), function(z) {
+    out <- which_rank(z, zoo = zoo)
+    if (length(out) == 0) {
+      stop('The rank "', z, '" is not part of rank_ref so cannot be assigned a relative position.',
+           '\n\n  Post an issue at https://github.com/ropensci/taxize/issues/ to get the rank added.')
+    } else {
+      return(out)
+    }
+  })])
   if (ignore_no_rank) rank_nos[rank_nos %in% c(300, 400)] <- 0
   x[!rank_nos > rank_target_no, ]
 }

R/tp_accnames.R

@@ -13,7 +13,6 @@
 #' # No accepted names found
 #' tp_accnames(id = 25509881)
 #' }
-
 tp_accnames <- function(id, key = NULL, ...) {
   url = sprintf('http://services.tropicos.org/Name/%s/AcceptedNames', id)
 	key <- getkey(key, "TROPICOS_KEY")

data/rank_ref_zoo.rda

@@ -44,7 +44,7 @@ ids_zoo <- c(
   '01', # domain
   '05','10','20','25', # kingdom
   '30','40','45', # phylum/division
-  '50','60','70','80','81','82', # class
+  '47', '50','60','70','80','81','82', # class
   '83','84','85','86','87', # cohort
   '90','100','110','120','125', # order
   '126','127', # section/subsection
@@ -60,7 +60,7 @@ ranks_zoo <- c(
   'domain', # domain
   'superkingdom','kingdom','subkingdom','infrakingdom,superphylum', # kingdom
   'phylum,division','subphylum,subdivision','infraphylum,infradivision', # phylum/division
-  'superclass','class','subclass','infraclass','subterclass','parvclass', # class
+  'gigaclass', 'superclass','class','subclass','infraclass','subterclass','parvclass', # class
   'megacohort','supercohort','cohort','subcohort','infracohort', # cohort
   'superorder','order','suborder','infraorder','parvorder', # order
   'section','subsection', # section/subsection
@@ -72,12 +72,12 @@ ranks_zoo <- c(
   'biotype,isolate,pathogroup,serogroup,serotype,strain,aberration', # genetic variants
   'unspecified,no rank,unranked,clade' # unspecified
 )
-rank_ref_zoo <- data.frame(
+rank_ref_zoo <- tibble::tibble(
   rankid = ids_zoo,
   ranks = ranks_zoo
 )
 # NOTE: "version = 2" is so that we don't have to require R > 3.5
-save(rank_ref_zoo, file = "data/rank_ref_zoo.RData", version = 2)
+usethis::use_data(rank_ref_zoo, overwrite = TRUE)
 # NOTES: 
 # - genetic variants: placed slightly higher above 'unspecified' just to denote
 #   they're not no rank, but they're not really a taxonomic rank either