div.gg {paleoDiv}

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

Description

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

Usage

div.gg(data, taxa, agerange = c(252, 66), precision_ma = 1, prefix = "sptab_")

Arguments

data

list()-object containing taxon-range tables

taxa

Selection of taxa to include

agerange

Range of geological ages to include in data.frame()

precision_ma

Size of intervals (in ma) at which to calculate diversity within the age range.

prefix

Prefix under which to find taxon-range tables in data

Details

Each taxon receives one entry per subtaxon (e.g. species) occurring for each time interval at which it occurs. The number of entries per taxon at any given point is thus proportional to the diversity of the taxon, and can be used to trick density functions (e.g. hist(), density()) into plotting diversity diagrams of various types. This is most useful when using ggplot2::geom_violin(), geom_histogram() or geom_density() functions. A simpler alternative to achieve a similar result would be to use the taxon-range-tables directly with these functions. However, this will lead to a relative underestimate of diversity for taxa with long-lived subtaxa, since each subtaxon will only be counted once. The div.gg()-function circumvents this problem by representing each taxon for each time interval in which it occurs, i.e. the relative number of entries in the returned data.frame will be proportional to the relative number of taxa with ranges overlapping each point in time.

Value

A data.frame() with two columns: ma, for the numerical age, and tax, for the taxon.

Examples

data(archosauria)
div.gg(archosauria, taxa=c("Pterosauria","Aves"), agerange=c(252,0),precision_ma=1)->flyers
library(ggplot2)
ggplot(data=flyers, aes(x=tax, y=ma))+ylim(252,0)+geom_violin(scale="count")
ggplot(data=flyers, aes(col=tax, x=ma))+xlim(252,0)+geom_density(adjust=0.5)