paleobioDB: paleobioDB: An R-package for downloading, visualizing and...

In ropensci/paleobioDB: Download and Process Data from the Paleobiology Database

paleobioDB: An R-package for downloading, visualizing and processing data from the Paleobiology Database

Description

We have developed paleobioDB, an R-package designed to make easy and flexible queries of the Paleobiology Database, as well as to visualize and download selected data. This package will make it easy to access paleontological data in a way that should allow those data to be further analyzed, including via packages and libraries available in R.

Details

We programmed two different groups of functions. First, we developed a set of general and flexible functions to wrap the PaleobioDB API. These functions connect R with each of the endpoints of the PaleobioDB API. Second, based on these base functions, we programmed a second set of functions intended to explore and visualize the fossil occurrences in their geographic, temporal and taxonomic dimensions.

Author(s)

Sara Varela [e-mail]

Javier Gonzalez [e-mail]

Luciano Fabris Sgarbi [e-mail]

References

Sara Varela, Javier González-Hernández, Luciano Fabris Sgarbi, Charles Marshall, Mark D. Uhen, Shanan Peters, Michael McClennen, 2015. paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. Ecography, 38: 419-425. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/ecog.01154")}

See Also

https://paleobiodb.org

Examples

## Not run: 
canidae <- pbdb_occurrences(
  vocab = "pbdb",
  limit = "all",
  base_name = "canidae",
  interval = "Quaternary",
  show = c("coords", "classext", "ident")
)

## to explore the number of subtaxa
pbdb_subtaxa(canidae)

## to explore the temporal resolution of the fossil records
pbdb_temporal_resolution(canidae)

## returns a data frame and a plot with the temporal span
## of the species, genera, etc.
pbdb_temp_range(canidae, rank = "genus", names = FALSE)

## returns a data frame and a plot showing the species, genera, etc.
## richness across time
pbdb_richness(canidae, rank = "species", temporal_extent = c(0, 10), res = 1)

## returns a data frame and a plot showing the evolutionary
## and extinction rates across time

## evolutionary rates: orig_ext = 1
pbdb_orig_ext(
  canidae,
  rank = "species", temporal_extent = c(0, 10), res = 1,
  orig_ext = 1
)

## extinction rates: orig_ext = 2
pbdb_orig_ext(
  canidae,
  rank = "species", temporal_extent = c(0, 10), res = 1,
  orig_ext = 2
)

## maps the fossil occurrences
pbdb_map(canidae, main = "Canidae", pch = 19, cex = 0.7)

## maps the sampling effort
pbdb_map_occur(canidae, res = 5)

## maps the species, genera, etc. richness
pbdb_map_richness(canidae, rank = "species", res = 5)


## End(Not run)

ropensci/paleobioDB documentation built on March 5, 2024, 3:08 a.m.