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()
