paleoDiv (version 0.4.6)

ab.gg: 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

ab.gg(data, taxa = NULL, agerange = c(252, 66), precision_ma = 1)

Value

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

Arguments

data

list()-object containing occurrence data.frames or single occurrence data.frame()

taxa

Selection of taxa to include. If NULL, then abundance is tabulated for each unique factor level of data$tna

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.

Details

Each taxon receives one entry per occurrence per time interval. The number of entries per taxon at any given point is thus proportional to the abundance of the taxon in the fossil record, and can be used for plotting with frequency- or density-based functions (e.g. hist(), ggplot2::geom_violin(), etc.). Note that using age values in the original occurrence table instead of this function will often be fully sufficient if the number of occurrences is considered an adequate proxy for abundance. However, instead using the ab.gg() and thus visualizing the results of the abdistr_() function has the benefit of the ability to account for a column of abundance values within the occurrence dataset, if available.

Examples

data(archosauria)
ab.gg(data=archosauria, taxa=c("Ankylosauria","Stegosauria"))->thyreophora
library(ggplot2)
ggplot(data=thyreophora, aes(x=tax, y=ma, col=tax))+ylim(252,0)+geom_violin(scale="count")