Corals & other macro-invertebrates of the Eastern Pacific coast of Panama

This field guide that can be printed on waterproof paper to help identify corals and others macro-invertebrates that occur on the Eastern Pacific coast of Panama. The guide includes species that have been reported on coral reefs in the Coiba National Park and in the Pearl Islands.

The size of the pdf is about 54Mb.

Photos from Maté et al. (2017) 1, Veron et al. (2016) 2, Reef Life Survey, Matthieu Leray & Arthur Anker.

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("leray2020_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), "leray2020_worms_results.csv")

  1. Maté JJ, Brandt M, Grassian B & Chiriboga A (2017) Field Guide to Select Eastern Pacific Corals and Associated Coral Reef Biota, P.W. Glynn et al. (eds.), Coral Reefs of the Eastern Tropical Pacific, Coral Reefs of the World 8 ↩︎

  2. Veron JEN, Stafford-Smith MG, Turak E. & DeVantier L.M. (2016). Corals of the World. Accessed 24 Jan 2019, version 0.01. ↩︎

Matthieu Leray
Matthieu Leray
Staff Scientist

Drivers, functions, and evolution of marine biodiversity.