Retrieve collections from the Paleobiology Database

A function to retrieve collections from the Paleobiology Database (PBDB), matched to Macrostrat units.

Usage

get_fossils(
  unit_id = NULL,
  column_id = NULL,
  interval_name = NULL,
  age = NULL,
  age_top = NULL,
  age_bottom = NULL,
  lithology = NULL,
  lithology_id = NULL,
  lithology_type = NULL,
  lithology_class = NULL,
  environ = NULL,
  environ_id = NULL,
  environ_type = NULL,
  environ_class = NULL,
  econ = NULL,
  econ_id = NULL,
  econ_type = NULL,
  econ_class = NULL,
  project_id = NULL,
  strat_name_id = NULL,
  sf = FALSE
)

Arguments

unit_id: integer. Filter PBDB collections to those within one or more unit(s) as specified by their unique identification number(s).
column_id: integer. Filter PBDB collections to those within one or more column(s) as specified by their unique identification number(s).
interval_name: character. Filter PBDB collections to those that overlap with a named chronostratigraphic time interval (e.g., "Permian").
age: numeric. Filter PBDB collections to those that overlap with the specified numerical age, in millions of years before present.
age_top: numeric. Filter PBDB collections to those that overlap with the age range between the specified numerical age and age_bottom. Should be in millions of years before present. age_bottom must also be specified, and this must be older than age_top.
age_bottom: numeric. Filter PBDB collections to those that overlap with the age range between the specified numerical age and age_top. Should be in millions of years before present. age_top must also be specified, and this must be younger than age_bottom.
lithology: character. Filter PBDB collections to those containing a named lithology (e.g., "shale", "sandstone").
lithology_id: integer. Filter PBDB collections to those containing one or more lithology(ies) identified by their unique identification number(s).
lithology_type: character. Filter PBDB collections to those containing a named lithology type (e.g., "carbonate", "siliciclastic").
lithology_class: character. Filter PBDB collections to those containing a named lithology class (e.g., "sedimentary", "igneous", "metamorphic").
environ: character. Filter PBDB collections to those containing a named environment (e.g., "delta plain", "pond").
environ_id: integer. Filter PBDB collections to those containing one or more environment(s) as specified by their unique identification number(s).
environ_type: character. Filter PBDB collections to those containing a named environment type (e.g., "fluvial", "eolian", "glacial").
environ_class: character. Filter PBDB collections to those containing a named environment class (e.g., "marine", "non-marine").
econ: character. Filter PBDB collections to those containing a named economic attribute (e.g., "brick", "ground water", "gold").
econ_id: integer. Filter PBDB collections to those containing one or more economic attribute(s) as specified by their unique identification number(s).
econ_type: character. Filter PBDB collections to those containing a named economic attribute type (e.g., "construction", "aquifer", "mineral").
econ_class: character. Filter PBDB collections to those containing a named economic attribute class (e.g., "material", "water", "precious commodity").
project_id: integer. Filter sections to those contained within a Macrostrat project as specified by its unique identification number.
strat_name_id: integer. Filter PBDB collections to those containing a unit that matches one or more stratigraphic name(s) as specified by their unique identification number(s).
sf: logical. Should the results be returned as an sf object? Defaults to FALSE.

Value

A dataframe containing the following columns:

collection_no: The unique identification number of the collection, as assigned in the PBDB.
collection_name: The unique name of the collection, as assigned in the PBDB.
t_age: The top age of the unit containing the collection, estimated using the continuous time age model, in millions of years before present.
b_age: The bottom age of the unit containing the collection, estimated using the continuous time age model, in millions of years before present.
pbdb_occs: The count of PBDB occurrences in the specified PBDB collection.
genus_no: A vector containing the unique identification number for each genus that appears in the collection, corresponding to the genus_no column in the Paleobiology Database.
taxon_no: The count of unique taxa in the specified PBDB collection.
unit_id: The unique identification number of the Macrostrat unit containing the specified PBDB collection.
col_id: The unique identification number of the Macrostrat column containing the specified PBDB collection.
refs: Reference for the source of the data.
strat_name_concept_id: The unique identification number of the stratigraphic name concept containing the specified PBDB collection.

If sf = TRUE, an sf object is returned instead.

Details

More information can be found for the inputs for this function using the definition functions (beginning with def_). Terminology related to the PBDB can be found at https://paleobiodb.org/#/ or in the suggested references below.

Developer(s)

Christopher D. Dean

Reviewer(s)

Lewis A. Jones

References

Peters, S.E. and McClennen, M. (2016). The Paleobiology Database application programming interface. Paleobiology, 42(1), pp. 1–7. doi:10.1017/pab.2015.39 .

Uhen, M.D., Allen, B., Behboudi, N., Clapham, M.E., Dunne, E., Hendy, A., Holroyd, P.A., Hopkins, M., Mannion, P., Novack-Gottshall, P. and Pimiento, C. (2023). Paleobiology Database User Guide Version 1.0. PaleoBios, 40(11), pp. 1–56. doi:10.5070/P9401160531 .

Examples

# \donttest{
 # Get fossils by Macrostrat column ID
 ex1 <- get_fossils(column_id = 10)
 # Get fossils by Macrostrat unit ID
 ex2 <- get_fossils(unit_id = 6279)
 # Get fossils by lithology and age
 ex3 <- get_fossils(lithology = "sandstone", age_top = 66, age_bottom = 73)
 # Get fossils by environment type and age
 ex4 <- get_fossils(environ_type = "fluvial", age =  253)
# }