Collections

pbdb_collection(id; kwargs...)

Get information about a single fossil collection record from the Paleobiology Database.

Arguments

• id: Identifier of the collection (required).
• kwargs...: Additional query parameters. Common options include:
  • vocab: Set to "pbdb" to use full field names instead of compact 3-letter codes.
  • show: Extra information blocks to include (e.g. "loc", "stratext", "lithext").
  • Geographic filters accepted by PBDB (e.g. lngmin, lngmax, latmin, latmax).

Returns

A DataFrame describing the specified collection.

Examples

pbdb_collection("col:1003")
pbdb_collection(1003)
pbdb_collection(
	"col:1003";
	show = ["loc", "stratext"],
	extids = true
)

pbdb_collections(; kwargs...)

Get information about multiple fossil collections.

Arguments

• kwargs...: Filtering and output parameters. Common options include:
  • base_name: Restrict to collections containing occurrences of the named taxon (including descendants).
  • interval: Geologic time interval (e.g. "Miocene").
  • min_ma, max_ma: Minimum and maximum age in millions of years.
  • lngmin, lngmax, latmin, latmax: Geographic bounding box.
  • cc: Country/continent codes (ISO-3166 two-letter; three-letter continent codes).
  • show: Extra blocks ("ref", "loc", "stratext", "lithext").
  • limit: Limit the number of records (Int or "all").
  • vocab: Vocabulary for field names ("pbdb" for full names, "com" for compact codes).

Returns

A DataFrame of collections matching the query.

Examples

pbdb_collections(base_name = "Cetacea", interval = "Miocene"; show = ["ref", "loc", "stratext"])

pbdb_collections_geo(level; kwargs...)

Geographic clusters (summary) of collections. level is required.

Use this method when you prefer a positional level per Julia convention. All other parameters are passed as keywords and accept the same filters as pbdb_collections.

Arguments

• level: Cluster level (required). See pbdb_config(show = "clusters") for available levels.
• kwargs...: Any colls/summary filters (e.g., lngmin, lngmax, latmin, latmax, base_name, interval, vocab).

Returns

A DataFrame summarizing the selected collections by geographic clusters.

Examples

pbdb_collections_geo(2; lngmin = 0.0, lngmax = 15.0, latmin = 0.0, latmax = 15.0)

pbdb_collections_geo(; level, kwargs...)

Geographic clusters (summary) of collections. level is required.

This keyword-only form is provided for compatibility with existing code that prefers level as a keyword. All other filters are identical to pbdb_collections_geo(level; ...).

Arguments

• level: Cluster level (required). See pbdb_config(show = "clusters") for available levels.
• kwargs...: Any colls/summary filters (e.g., lngmin, lngmax, latmin, latmax, base_name, interval, vocab).

Returns

A DataFrame summarizing the selected collections by geographic clusters.

Examples

pbdb_collections_geo(level = 2; lngmin = 0.0, lngmax = 15.0, latmin = 0.0, latmax = 15.0)

pbdb_ref_collections(; kwargs...)

Get bibliographic references from which collection data were entered.

Arguments

• kwargs...: Filtering options, e.g.:
  • id: One or more collection identifiers.
  • base_name: Restrict to collections associated with a given taxon (and all descendants).
  • ref_author, ref_pubyr, pub_title: Reference filters as in pbdb_references.
  • order: Sort order (see PBDB docs).
  • vocab: Field naming vocabulary.

Returns

A DataFrame listing references associated with the selected collections.

Examples

pbdb_ref_collections(base_name = "Canidae", interval = "Quaternary", cc = "ASI")

pbdb_config(; kwargs...)

Query the PBDB configuration endpoint.

The configuration endpoint provides metadata tables that describe available cluster levels, continents, vocabularies, and other reference information needed for interpreting and filtering PBDB data.

Arguments

• kwargs...: Commonly used parameters include:
  • show: Which configuration table to return. Examples:

- `"clusters"`: Available geographic cluster levels (for use with `pbdb_collections_geo`).
- `"continents"`: Continent codes recognized by PBDB.
- `"vocabularies"`: Available vocabularies for field names.
- `"ecologies"`, `"lithologies"`, etc. (see PBDB documentation for a full list).
- Full list:
	- 'clusters',
	- 'ranks',
	- 'continents',
	- 'countries',
	- 'collblock',
	- 'lithblock',
	- 'lithologies',
	- 'minorliths',
	- 'lithification',
	- 'lithadj',
	- 'envs',
	- 'envtypes',
	- 'tecs',
	- 'collmet',
	- 'datemet',
	- 'colltype',
	- 'collcov',
	- 'presmodes',
	- 'resgroups',
	- 'museums',
	- 'abundance',
	- 'plant',
	- 'pgmodels',
	- 'prefs',
	- 'all'

Returns

A DataFrame with the requested configuration information.

Examples

# List available geographic cluster levels
pbdb_config(show = "clusters")

# List continent codes
pbdb_config(show = "continents")

# List taxonomic ranks
pbdb_config(show = "ranks")