collect_from_WORMS: Collect species names from WoRMS
In dswdejonge/TripleD: Construct a TripleD database.

Description Usage Arguments Details Value

This wrapper function collects accepted species names from WoRMS for all reported species in the data files and the bioconversion file.

collect_from_WORMS(
  species = NULL,
  conversion_data = NULL,
  input_folder = "inputfiles",
  data_folder = "data",
  out_folder = "data",
  as_CSV = FALSE
)

`species`	The initial database for species with reported specimen names. If NULL (default) the function will automatically search the data_folder for 'species_initial.rda'.
`conversion_data`	Dataframe with bioconversion data matching the given requirements from the attributes_bioconversion file. If NULL (default) the bioconversion.csv will be searched for and loaded from the input_folder.
`input_folder`	The folder where to find the bioconversion.csv file. Default is 'inputfiles'.
`data_folder`	If the species database is not provided, the function will search for it (species_initial.rda') in this folder. Default is 'data'.
`out_folder`	The external data is stored in this folder. Default is 'data'.
`as_CSV`	If you also want to store the collected external data as CSV, set to TRUE. Default is FALSE.

Taxonomic data is collected from the WoRMS database using the worrms R-package. You need internet connection to do this. All reported taxonomic names of the specimens in the initial database and in the bioconversion file are matched against the WoRMS database (also fuzzy matches, i.e. where typos and phonetic spelling is allowed).

This function does not return an object, but stores the information in the specified out_folder under the name 'worms.rda'.

dswdejonge/TripleD documentation built on June 18, 2020, 12:24 p.m.