R: Extracting and Visualizing Paleobiodiversity

# Extracting and Visualizing Paleobiodiversity

## 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()