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Get information about fossil occurrence records

Source: R/pbdb_queries.R
pbdb_occurrences.Rd

Returns information about fossil occurrence records stored in the Paleobiology Database.

Usage

pbdb_occurrences(...)

Arguments

...

Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/occs/list.

  • limit: Limits the number of records returned. The value may be a positive integer, zero, or "all".

  • taxon_name: Return only records associated with the specified taxonomic name(s). You may specify multiple names.

  • base_name: Return records associated with the specified taxonomic name(s) and any of their children (e.g. base_name = "Canis" will return "Canis", "Canis lupus", "Canis mosbachensis", etc.)

  • lngmin: Numeric. The longitude boundaries will be normalized to fall between -180 and 180. Note that if you specify lngmin then you must also specify lngmax. Returns only records whose geographic location falls within the given bounding box (defined by lngmin, lngmax, latmin, latmax). It generates two adjacent bounding boxes if the range crosses the antimeridian.

  • lngmax: Numeric. The longitude boundaries will be normalized to fall between -180 and 180.

  • latmin: Numeric value between -90 and 90. Note that if you specify latmin then you must also specify latmax.

  • latmax: Numeric value between -90 and 90.

  • min_ma: Return only records whose temporal locality is at least this old, specified in millions of years.

  • max_ma: Return only records whose temporal locality is at most this old, specified in millions of years.

  • interval: Return only records whose temporal locality falls within the named geologic time interval (e.g. "Miocene").

  • cc: Return only records whose location falls within the specified geographic regions. The value of this parameter should be one or more two-character country codes and/or three-character continent codes as a comma-separated list (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 and https://paleobiodb.org/data1.2/config.txt?show=continents). If the parameter value starts with !, then records falling into these regions are excluded instead of included. Any country codes starting with ^ are subtracted from the filter.

  • show: Show extra variables (e.g. "coords", "classext", "ident").

Value

A data frame with the fossil occurrences.

Details

Documentation for all the parameters is available at https://paleobiodb.org/data1.2/occs/list. We describe the most common filters that paleontologists and ecologists might use in the parameter list above.

Be aware that depending on the query, some columns may not be returned by the API if those are empty across all the rows.

Examples

if (FALSE) { # \dontrun{
  pbdb_occurrences(id = c(10, 11), show = c("coords", "classext", "ident"))
  pbdb_occurrences(
    limit = "all", vocab = "pbdb", taxon_name = "Canis",
    show = c("coords", "classext", "ident")
  )
  pbdb_occurrences(
    limit = "all", vocab = "pbdb", base_name = "Canidae",
    show = c("coords", "classext", "ident")
  )
} # }