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Time intervals and scales

PaleobiologyDB.pbdb_interval — Function
pbdb_interval(; kwargs...)

Get information about a single geologic time interval, selected by name or id.

Arguments

  • kwargs...: One of the following must be provided (but not both):
    • name: Interval name (e.g. "Miocene").
    • id: PBDB interval identifier.
    Additional options:
    • vocab: Set to "pbdb" to return full field names (default for text formats).
    • order: Return the interval in a specific order (rarely used here; see PBDB docs).

Returns

A DataFrame describing the selected interval.

Examples

pbdb_interval(name = "Miocene")
pbdb_interval(id = 1)
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PaleobiologyDB.pbdb_intervals — Function
pbdb_intervals(; kwargs...)

Get information about multiple geologic time intervals.

Arguments

  • kwargs...: Filtering and output parameters. Common options include:
    • min_ma: Return only intervals at least this old (Ma).
    • max_ma: Return only intervals at most this old (Ma).
    • order: Return intervals in the requested order (e.g. "age" or "name").
    • vocab: Field naming vocabulary ("pbdb" for full names).

Returns

A DataFrame with the selected intervals.

Examples

pbdb_intervals(min_ma = 0, max_ma = 5)
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PaleobiologyDB.pbdb_scale — Function
pbdb_scale(id; kwargs...)

Get information about a single time scale, selected by identifier.

Arguments

  • id: PBDB scale identifier (required).
  • kwargs...: Additional parameters, e.g.:
    • vocab: Set to "pbdb" to return full field names.

Returns

A DataFrame with information about the requested time scale.

Examples

pbdb_scale(1)
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PaleobiologyDB.pbdb_scales — Function
pbdb_scales(; kwargs...)

Get information about multiple time scales.

Arguments

  • kwargs...: Optional parameters, e.g.:
    • vocab: Set to "pbdb" to return full field names.

Returns

A DataFrame listing the requested time scales (or all, if no filter provided).

Examples

pbdb_scales()
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Stratigraphy

PaleobiologyDB.pbdb_strata — Function
pbdb_strata(; kwargs...)

Get information about geological strata, selected by name, rank, and/or geography.

Arguments

  • kwargs...: Filtering and output parameters. Common options include:
    • name: Full or partial name (wildcards % and _ allowed).
    • rank: One of "formation", "group", or "member".
    • lngmin, lngmax, latmin, latmax: Bounding box (if you provide one of lngmin/latmin, you must provide the paired max).
    • loc: WKT geometry string to constrain by polygon/geometry.
    • vocab: Set to "pbdb" to return full field names (default for text formats).

Returns

A DataFrame with strata records matching the query.

Examples

pbdb_strata(rank = "formation", lngmin = -120, lngmax = -100, latmin = 30, latmax = 50)
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PaleobiologyDB.pbdb_strata_auto — Function
pbdb_strata_auto(; kwargs...)

Autocomplete: list of strata matching a given prefix or partial name.

Arguments

  • kwargs...: Common options include:
    • name: Prefix or partial name (≥ 3 significant characters). May end with a space + g or f to hint at group/formation.
    • rank: Optional rank filter ("formation" or "group").
    • lngmin, lngmax, latmin, latmax: Optional bounding box to constrain suggestions.
    • limit: Maximum number of matches.

Returns

A DataFrame of matching stratum names, ranks, and occurrence counts (JSON endpoint is converted to DataFrame).

Examples

pbdb_strata_auto(name = "Pin")
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References

The reference functions retrieve bibliographic data associated with taxa, occurrences, or collections, and can fetch a specific reference record directly.

# References for a taxon group
refs = pbdb_ref_taxa(name = "Canidae", show = ["both", "comments"])

# References cited in occurrence records
occ_refs = pbdb_ref_occurrences(base_name = "Canis", ref_pubyr = 2000)

# A specific reference record
ref_detail = pbdb_reference(1003, show = "both")
PaleobiologyDB.pbdb_reference — Function
pbdb_reference(id; kwargs...)

Get information about a single bibliographic reference.

Arguments

  • id: Reference identifier (required).
  • kwargs...: Additional parameters, for example:
    • vocab: Set to "pbdb" to use full field names.
    • show: Extra information blocks (e.g. "counts" to report numbers of taxa/opinions/occurrences/specimens; "both" to include both formatted reference and individual fields).

Returns

A DataFrame with information about the requested reference.

Examples

pbdb_reference(1003; show = "both")
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PaleobiologyDB.pbdb_references — Function
pbdb_references(; kwargs...)

Get information about multiple bibliographic references.

Arguments

  • kwargs...: Filtering and output parameters. Common options include:
    • ref_author: Match on author last name(s).
    • ref_pubyr: Publication year.
    • pub_title: Publication title.
    • order: Sort order; one or more of "author", "pubyr", "reftitle", "pubtitle", "pubtype", "created", "modified", "rank", with optional ".asc"/".desc" suffix.
    • vocab: Set to "pbdb" for full field names.

Returns

A DataFrame with references matching the query.

Examples

pbdb_references(ref_author = "Polly")
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Opinions

PaleobiologyDB.pbdb_opinion — Function
pbdb_opinion(id; kwargs...)

Get information about a single taxonomic opinion.

Arguments

  • id: Identifier of the opinion (required).
  • kwargs...: Additional parameters, for example:
    • vocab: Set to "pbdb" to return full field names.
    • show: Extra information blocks (e.g. "basis", "entname", "refattr").

Returns

A DataFrame with the requested opinion.

Examples

pbdb_opinion(1000; show = "full")
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PaleobiologyDB.pbdb_opinions — Function
pbdb_opinions(; kwargs...)

Get information about multiple taxonomic opinions.

Arguments

  • kwargs...: Filtering options. Common parameters include:
    • id: One or more opinion identifiers.
    • op_author: Filter by opinion author name(s).
    • ops_created_before, ops_created_after: Date/time filters.
    • op_type: Opinion type filter ("all", "class", "valid", "accepted", "junior", "invalid").
    • vocab: Vocabulary for field names.

Returns

A DataFrame with opinions matching the query.

Examples

pbdb_opinions(op_pubyr = 1818)
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Counting

PaleobiologyDB.pbdb_count — Function
pbdb_count(endpoint; kwargs...) -> Union{Int, Missing}

Return the total number of records matching a query without downloading the records themselves.

Internally issues the query with limit=0 and format=json, then reads the records_found field from the PBDB JSON response envelope. This is fast because no record data is transferred.

Arguments

  • endpoint: PBDB path such as "occs/list", "colls/list", etc.
  • base_url: Override the default base URL.
  • readtimeout: HTTP read timeout in seconds (default 300).
  • retries: Number of retries on failure (default 3).
  • kwargs...: Any PBDB filter parameters (same as pbdb_query).

Returns

An Int with the total number of matching records, or missing if the API does not return a records_found field for the given endpoint.

Examples

pbdb_count("occs/list"; base_name = "Canidae")
pbdb_count("colls/list"; interval = "Miocene", cc = "ASI")
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pbdb_count(resource::Symbol; kwargs...) -> Union{Int, Missing}

Return the total number of records for the given resource type without downloading the records themselves.

resource must be one of: collections, occurrences, opinions, references, specimens, taxa.

Examples

pbdb_count(:occurrences; base_name = "Canidae")
pbdb_count(:collections; interval = "Miocene", cc = "ASI")

# Dynamic dispatch and splatting work:
params = Dict(:base_name => "Canidae")
pbdb_count(:occurrences; params...)
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