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paleoDiv (version 0.4.0)

Extracting and Visualizing Paleobiodiversity

Description

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database , extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

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Install

install.packages('paleoDiv')

Monthly Downloads

234

Version

0.4.0

License

GPL (>= 3)

Maintainer

Darius Nau

Last Published

October 17th, 2024

Functions in paleoDiv (0.4.0)

diversity_table

diversity_table
ggcol

Replicate the standard color scheme from ggplot2
abdistr_

Count number of entries in occurrence or collection data.frame for specific points in geological time
mk.sptab

Generate a taxon-range table based on an occurrence dataset.
pdb.diff

Subtract one occurrence data.frame from another, for disentangling overlapping taxonomies or quantifying stem-lineage diversity.
jitterp

plot data as a jitter-plot
phylo.spindles

Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.
pdb.union

Form the union of two occurrence data.frames or remove duplicates from occurrence data.frame. Useful if parts of a clade are not included in the downloaded dataset and need to be added separately.
ts.periods

Add a horizontal, period-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.
rmean

Calculate a rolling mean for a vector x.
pdb.autodiv

A wrapper around pdb(), occ.cleanup() and mk.sptab() to automatically download and clean occurrence data from the paleobiology database and build species-level taxon-range tables for multiple taxa in one step.
rmeana

Calculate a rolling mean based on distance within a second variable.
ts.stages

Add a horizontal, stage-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.
tree_archosauria

tree_archosauria
tree.ages.spp

Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.
tree.age.combine

Combine two calibration matrixes and fill in NA values in one with values from another
tree.ages

Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.
violins

Wrapper around viol() to conveniently plot multiple violins on a single plot, analogous to the behavior of boxplot()
tsconv

Convert geological ages for accurate plotting alongside a calibrated phylogeny
viol

Generate a violin plot
add.alpha

Add transparency to any color
redraw.phylo

Redraw the lines of a phylogenetic tree.
ages_archosauria

ages_archosauria
multijitter

Wrapper around jitterp that plots multiple jitter plots on the same plotting device (analogous to violins())
stax.sel

Extract subsets of an occurrence data.frame.
occ.cleanup

Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.
synonymize

Combine selected entries in a taxon-range table to remove duplicates
archosauria

archosauria
divdistr_

Calculate total species diversity for any point in time based on a taxon-range table
div.gg

Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2
ab.gg

Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2
divdistr_int

Count number of taxon records overlapping a specific time interval.
darken

Darken or lighten colors by adding/subtracting to or hsv channel values
convert.sptab

Convert geological ages in taxon-range tables as constructed by mk.sptab() for plotting alongside a time-calibrated phylogeny.
pdb

Download data from the paleobiology database.