Function reference • palaeoverse

Data cleaning and preparing

Functions for cleaning and preparing occurrence or taxonomic data for downstream analyses.

tax_check(): Taxonomic spell check

phylo_check(): Check phylogeny tip names

tax_unique(): Filter occurrences to unique taxa

palaeorotate(): Palaeorotate fossil occurrences

look_up(): Look up geological intervals and assign geological stages

tax_expand_lat(): Generate pseudo-occurrences from latitudinal range data

tax_expand_time(): Generate pseudo-occurrences from temporal range data

Data binning

Functions for binning occurrence data.

bin_lat(): Assign fossil occurrences to latitudinal bins

bin_space(): Assign fossil occurrences to spatial bins

bin_time(): Assign fossil occurrences to time bins

Data summarisation

Functions to summarise occurrence-level data.

tax_range_space(): Calculate the geographic range of fossil taxa

tax_range_time(): Calculate the temporal range of fossil taxa

Data visualization

Functions to aid in the visualisation of data and analysis results.

axis_geo() axis_geo_phylo(): Add an axis with a geological timescale

tax_range_strat(): Generate a stratigraphic section plot

Auxiliary functions

Functions to support further functionality.

lat_bins(): Generate latitudinal bins

time_bins(): Generate time bins

group_apply(): Apply a function over grouping(s) of data

Built-in data

palaeoverse comes with a selection of built-in datasets that are used in examples to illustrate various use cases.

GTS2012: Geological Timescale 2012

GTS2020: Geological Timescale 2020

interval_key: Example dataset: Interval key for the look_up function

reefs: Example dataset: Phanerozoic reefs from the PaleoReefs Database

tetrapods: Example dataset: Early tetrapod data from the Paleobiology Database