Photos from Robertson & Allen (2015) 1, Reef Life Survey, Matthieu Leray & William L Wied
In order to get taxon details from the World Register of Marine Species (WoRMS) online database (specifically the hyperlink to the taxon page), we used the worms R package. First, we created a list of taxa (genus and species) which you can download here:
Next, we interated through the list with a simple for-loop and then appended the results to a dataframe. You can download the complete results of the database scrap for each taxa here:
library("worms")
library("tidyverse")
rm(worms_results, i, taxon_names)
taxon_names <- readr::read_delim("leraywied2019_taxon_names.txt", delim = "\t")
taxon_names <- data.frame(taxon_names)
worms_results <- c()
for(i in 1:nrow(taxon_names)) {
tmp_taxa <- taxon_names[i,]
tmp_results <- data.frame(wormsbynames(tmp_taxa, ids = TRUE,
match = TRUE,
verbose = TRUE,
chunksize = 150,
like = "false",
marine_only = "true",
sleep_btw_chunks_in_sec = 0.1))
worms_results <- rbind(worms_results, tmp_results)
rm(list = ls(pattern = "tmp_"))
}
worms_results$id <- NULL
worms_results$id <- 1:nrow(worms_results)
worms_results <- worms_results %>% dplyr::relocate(id)
readr::write_csv(data.frame(worms_results), "leraywied2019_worms_results.csv")
Robertson D.R. and Allen GR 2015. Shorefishes of the Tropical Eastern Pacific: online information system. Version 2.0 Smithsonian Tropical Research Institute, Balboa, Panamá. ↩︎
