In ropenscilabs/splister: Match Species Lists Against Reference List

splister

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 name
• match_fuzzy: Fuzzy match of each name
• pull_names: yank out names into character vector
• case_names: change case
• xxx: asdf

Installation

devtools::install_github("sckott/splister")

library('splister')

Examples

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

Meta

• Please report any issues or bugs.
• License: MIT
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

ropenscilabs/splister documentation built on Sept. 22, 2020, 4:46 p.m.