get_fossils {rmacrostrat} | R Documentation |
Retrieve collections from the Paleobiology Database
Description
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 |
|
column_id |
|
interval_name |
|
age |
|
age_top |
|
age_bottom |
|
lithology |
|
lithology_id |
|
lithology_type |
|
lithology_class |
|
environ |
|
environ_id |
|
environ_type |
|
environ_class |
|
econ |
|
econ_id |
|
econ_type |
|
econ_class |
|
project_id |
|
strat_name_id |
|
sf |
|
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.
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.
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.
See Also
External data:
def_drilling_sites()
,
def_measurements()
,
get_eodp()
,
get_measurements()
Examples
# 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)