pdb function

Download data from the paleobiology database.

pdb(
  taxon,
  interval = "all",
  what = "occs",
  full = FALSE,
  base = "https://paleobiodb.org/data1.2/",
  file = "list.csv",
  cc = NULL,
  envtype = NULL,
  append_additional = NULL
)

Arguments

• taxon: A taxon (base_name) for which to download records.
• interval: A character string indicating over which temporal interval to download data (defaults to "all"), e.g. "Phanerozoic" or "Jurassic".
• what: The type of data to download (for details, see https://paleobiodb.org/data1.2/). Defaults to "occs", which downloads occurrence data. Setting this parameter to "colls" will instead download collection data.
• full: A logical indicating whether or not the full dataset is to be downloaded (defaults to FALSE). At the expense of larger file size, the full dataset contains a large number of additional columns containing data such as stratigraphy, phylogeny and (paleo)geography, which is useful for various purposes but not strictly necessary for graphing paleodiversity.
• base: Character string containing base url to use. Defaults to https://paleobiodb.org/data1.2/. Entering "dev" serves as a shortcut to use https://dev.paleobiodb.org/data1.2/ instead (can sometimes be helpful if one of the two is unavailable).
• file: Character string containing which file name to look for. Defaults to list.csv.
• cc: Selection for continent (e.g. EUR for Europe, see paleobiodb.org documentation)
• envtype: Selection for environment type (e.g. marine)
• append_additional: Any additional character string to append to URL for pdb dataset

Returns

A data.frame() containing the downloaded paleobioDB dataset. The column "identified_name" will be copied into the column "tna", and (if what==occs) the columns "max_ma" and "min_ma" will be copied into the columns named "eag" and "lag" respectively, maintaining compatibility with the output of the deprecated package "paleobioDB" for those variable names.

Examples

pdb("Stegosauria")->Stegosauria