knitr::opts_chunk$set( warning = FALSE, message = FALSE, collapse = TRUE, comment = "#>" )
splister
matches taxa against a references list
The package API:
match_exact
: Exact match of each namematch_fuzzy
: Fuzzy match of each namepull_names
: yank out names into character vectorcase_names
: change casexxx
: asdfdevtools::install_github("sckott/splister")
library('splister')
x <- read.csv(system.file("examples", "iucn_dat.csv", package = "splister"), stringsAsFactors = FALSE)[,-1] y <- system.file("examples", "worms_sample.csv", package = "splister") spp <- x$sciname[1:20000L] res <- matcher(spplist = spp, ref = y, against = "scientificName") df <- data.frame(original = spp, taxon = unlist(res), match = sapply(res, attr, "match")) df[df$match == "replace", ] #> original taxon match #> 2080 Alburnus mento Alburnus mentoides replace #> 7080 Bahaba chaptis Alburnus mentoides replace #> 12080 Caridina evae Alburnus mentoides replace #> 17080 Copadichromis inornatus Alburnus mentoides replace
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