In xavi-rp/PreSPickR: Downloading Species Presences (Occurrences) From Public Repositories

PreSPickR: An Example

The aim of this package is to download species presences (occurrences) data from public repositories. For now it is implemented for Bioatles, which has data from the Balearic Islands (http://bioatles.caib.es), and for GBIF.

Bioatles data is projected in European Datum 1950 (31N). The function bioatles(), which downloads the occurrences, also transform the data set in Lat/Long Geographic Coordinates System WGS84. It is based on several functions included in the packages "rvest" (Wickham, 2016) and "xml2" (Wickham et al., 2017). Finally, it saves the data in a csv file.

Equally, GetBIF() is used to download species occurrences from GBIF. It is based on several functions included in the package "rgbif" (Chamberlain, 2017). It uses the so-called "/occurrence/download route" (see vignettes of the "rgbif" package) which is more appropriate for big data sets. GetBIF() retrieve your GBIF credentials (user, password and email) and automatically makes checks using a loop until the request of the data set made to GBIF is ready. In that moment it starts the download. Finally, it saves the data in a csv file. The data is in Lat/Long Geographic Coordinates System WGS84.

This vignette is just an example of how to use the package.

library("PreSPickR")

You can pass the list of species names to be downloaded in a .csv file (without header) or as a vector. Make sure that the spelling is correct!

Bioatles

bioatles(sp_list = "species_bioatles.csv")

bioatles(sp_list = c("Chamaerops humilis", "Asphodelus aestivus"))

You can also pass the arguments sp_dir to specify the directory of the file and out_name for the the output name of the downloaded file.

GBIF

GetBIF(credentials = "~/gbif_credentials.RData", sp_list = "species_gbif.csv", out_name = "sp_records_gbif")

Your GBIF credentials can be stored in a .RData or passed to the function using the arguments gbif_usr, gbif_pwrd and email.

References

• Scott Chamberlain (2017). rgbif: Interface to the Global 'Biodiversity' Information Facility 'API'. R package version 0.9.8. https://CRAN.R-project.org/package=rgbif
• Hadley Wickham (2016). rvest: Easily Harvest (Scrape) Web Pages. R package version 0.3.2. https://CRAN.R-project.org/package=rvest
• Hadley Wickham, James Hester and Jeroen Ooms (2017). xml2: Parse XML. R package version 1.1.1. https://CRAN.R-project.org/package=xml2

xavi-rp/PreSPickR documentation built on March 27, 2022, 7:30 a.m.