allow assignment with only genus or only species binomial

NEWS.md

@@ -13,6 +13,9 @@
   It also works with a locally cached database.
 * `funguild_assign()` now accepts Sintax ("`k:`", "`p:`"...) or Unite ("`k__`,
   "`p__`", ...) style taxonomy strings.
+* `funguild_assign()` now works in many cases when the *Taxonomy* column
+  contains only genus or species names. The most complete results will still be 
+  achieved when the whole taxonomy string is included.
 
 # FUNGuildR 0.2.0
 

R/funguildr.R

@@ -135,10 +135,7 @@ funguild_assign <- function(otu_table, db = get_funguild_db(),
   }
   assertthat::assert_that(is.data.frame(otu_table),
                           tax_col %in% colnames(otu_table))
-  otu_table$taxkey <-
-    stringr::str_replace_all(otu_table[[tax_col]], "\\b[kpcofgs](:|__)", "") %>%
-    stringr::str_replace_all("[_ ;,:]", "@") %>%
-    paste0("@")
+  otu_table$taxkey <- make_taxkey(otu_table[[tax_col]])
   all_taxkey <- unique(otu_table$taxkey) %>% na.omit()
   `.` <- taxon <- taxkey <- searchkey <- taxonomicLevel <- NULL # to pass R CMD check
   db <- dplyr::mutate(

R/utils.R

@@ -25,3 +25,9 @@ check_is_json <- function(response) {
   )
   response
 }
+
+make_taxkey <- function(x) {
+  out <- gsub("\\b[kpcofgs](:|__)", "", x)
+  out <- gsub("[_ ;,:]", "@", out)
+  paste0("@", out, "@")
+}