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Matching Neotoma taxa
# Coding to obtain a long list of fully resolved taxonomies for taxa in the Netoma Paleoecological Database.
# This work is to support (generally) export to other databases, allowing researchers to match at multiple
# levels, and across resources, providing a clear and unambiguous reference for taxonomies within Neotoma.
# Coded by: Simon Goring
# Neotoma Paleoecological Database: http://neotomadb.org
library(neotoma)
library(taxize)
neotoma_taxa <- neotoma::get_table("taxa")
neo_runs <- seq(1, nrow(neotoma_taxa), by = 10)
get_class <- function(x) {
# This just clears up some of the "uncertainty" fields in the taxon names.
# This doesn't catch things like "sensu stricto" and others.
taxa <- gsub("(\\?|\\-type|cf\\.\\s|aff\\.|\\sundiff\\.)", "", x, perl=TRUE)
taxize::classification(taxa, db="itis", rows = 1)
}
all_taxa_list <- list()
for (i in (i-1):nrow(neotoma_taxa)) {
cat(paste0(neotoma_taxa$TaxaGroupID[i], ": ", neotoma_taxa$TaxonName[i],
' - ', round(i/nrow(neotoma_taxa) * 100, 2), '% complete . . . '))
all_taxa_list[[i]] <- list(neotoma_taxa[i,],
suppressMessages(get_class(neotoma_taxa$TaxonName[i])))
if (!is.na(all_taxa_list[[i]][[2]])) {
cat('Success!\n')
} else {
cat('Ugh. :(\n')
}
# Output throughout the run, it's slower, but then we don't run into issues later.
saveRDS(all_taxa_list, file = "../TaxonAlignment/all_taxa.RDS")
}
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