Extracting and Visualizing Paleobiodiversity
Make a data.frame() that can be used to plot diversity data with densi...
Count number of entries in occurrence or collection data.frame for spe...
Add transparency to any color
Convert geological ages in taxon-range tables as constructed by mk.spt...
Darken or lighten colors by adding/subtracting to or hsv channel value...
Make a data.frame() that can be used to plot diversity data with densi...
Calculate total species diversity for any point in time based on a tax...
Count number of taxon records overlapping a specific time interval.
Replicate the standard color scheme from ggplot2
plot data as a jitter-plot
Generate a taxon-range table based on an occurrence dataset.
Wrapper around jitterp that plots multiple jitter plots on the same pl...
Clean up occurrence dataset by removing commonly used character combin...
A wrapper around pdb(), occ.cleanup() and mk.sptab() to automatically ...
Subtract one occurrence data.frame from another, for disentangling ove...
Download data from the paleobiology database.
Form the union of two occurrence data.frames or remove duplicates from...
Plots a phylogenetic tree with spindle-diagrams, optimized for showing...
Redraw the lines of a phylogenetic tree.
Calculate a rolling mean for a vector x.
Calculate a rolling mean based on distance within a second variable.
Extract subsets of an occurrence data.frame.
Combine selected entries in a taxon-range table to remove duplicates
Combine two calibration matrixes and fill in NA values in one with val...
Automatically build matrix for time-calibration of phylogenetic trees ...
Automatically build matrix for time-calibration of phylogenetic trees ...
Add a horizontal, period-level phanerozoic timescale to any plot, espe...
Add a horizontal, stage-level phanerozoic timescale to any plot, espec...
Convert geological ages for accurate plotting alongside a calibrated p...
Generate a violin plot
Wrapper around viol() to conveniently plot multiple violins on a singl...
Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.