Extracting and Visualizing Paleobiodiversity

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Documentation for package ‘paleoDiv’ version 0.4.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ab.gg	Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2
abdistr_	Count number of entries in occurrence or collection data.frame for specific points in geological time
add.alpha	Add transparency to any color
ages_archosauria	ages_archosauria
archosauria	archosauria
convert.sptab	Convert geological ages in taxon-range tables as constructed by mk.sptab() for plotting alongside a time-calibrated phylogeny.
darken	Darken or lighten colors by adding/subtracting to or hsv channel values
div.gg	Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2
divdistr_	Calculate total species diversity for any point in time based on a taxon-range table
divdistr_int	Count number of taxon records overlapping a specific time interval.
diversity_table	diversity_table
ggcol	Replicate the standard color scheme from ggplot2
jitterp	plot data as a jitter-plot
mk.sptab	Generate a taxon-range table based on an occurrence dataset.
multijitter	Wrapper around jitterp that plots multiple jitter plots on the same plotting device (analogous to violins())
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.
pdb	Download data from the paleobiology database.
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.
pdb.diff	Subtract one occurrence data.frame from another, for disentangling overlapping taxonomies or quantifying stem-lineage 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.
phylo.spindles	Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.
redraw.phylo	Redraw the lines of a phylogenetic tree.
rmean	Calculate a rolling mean for a vector x.
rmeana	Calculate a rolling mean based on distance within a second variable.
stax.sel	Extract subsets of an occurrence data.frame.
synonymize	Combine selected entries in a taxon-range table to remove duplicates
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.
tree.ages.spp	Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.
tree_archosauria	tree_archosauria
ts.periods	Add a horizontal, period-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.
ts.stages	Add a horizontal, stage-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.
tsconv	Convert geological ages for accurate plotting alongside a calibrated phylogeny
viol	Generate a violin plot
violins	Wrapper around viol() to conveniently plot multiple violins on a single plot, analogous to the behavior of boxplot()