Fishes of Coiba National Park

The size of the pdf is about 46Mb.

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:

Download the Taxa table

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:

Download the WoRMS results

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")

  1. 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. ↩︎

Matthieu Leray
Matthieu Leray
Staff Scientist

Drivers, functions, and evolution of marine biodiversity.