plotOccData: Plotting Occurrence Data Across Taxa

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Plotting Occurrence Data Across Taxa

Description

plotOccData takes occurrence data which has been sorted into a by-taxon list, such as that output by taxonSortPBDBocc or may be output by simulations using sampleRanges and produces a plot showing the age uncertainty associated with individual occurrences, with occurrences of the same taxon grouped by color.

Usage

plotOccData(
  occList,
  groupLabel = NULL,
  occColors = NULL,
  lineWidth = NULL,
  xlims = NULL
)

Arguments

occList	A list where every element is a table of occurrence data for a different taxon, such as that returned by taxonSortPBDBocc. The occurrence data can be either a two-column matrix composed of the lower and upper age bounds on each taxon occurrence, or has two named variables which match any of the field names given by the PBDB API under either the 'pbdb' vocab or 'com' (compact) vocab for early and late age bounds.
groupLabel	A character vector with a single string giving the name for the occurrence dataset used, such as the taxonomic name of the group examined. If not given (the default) a generic plot title is appended.
occColors	A vector of numbers or characters indicating colors on a color palette for use with the basic plot function. Must be the same length as occList. If empty, as with the default, the colors used are sampled randomly from the rainbow function.
lineWidth	A numeric value giving the length to be used for the width of lines plotted in plotOccData. If not given (the default), this is calculated using an algorithm that selects an optimal line width for plotting.
xlims	A two element vector controlling the width of the horizontal time-scale the occurrence bars are plotted against. By default, this is not given and calculated internally.

Details

This function was originally conceived of in the following blog post: Link

Value

This function will invisibly return a list, with each per-taxon element containing the two-column matrix of age bounds for occurrences.

Author(s)

David W. Bapst

See Also

Occurrence data as commonly used with paleotree functions can be obtained with link{getPBDBocc}, and sorted into taxa by taxonSortPBDBocc, and further explored with this function and occData2timeList. Also, see the example graptolite dataset at graptPBDB and the example graptolite dataset at graptPBDB

Examples

#load example graptolite PBDB occ dataset
data(graptPBDB)

#get formal genera
occSpecies <- taxonSortPBDBocc(graptOccPBDB, rank = "species")

#plot it!
plotOccData(occSpecies)

#this isn't too many occurrences, because there are so few
    #formal grapt species in the PBDB

#genera is messier...

#get formal genera
occGenus <- taxonSortPBDBocc(graptOccPBDB, rank = "genus")

#plot it!
plotOccData(occGenus)

#some of those genera have occurrences with very large
   #age uncertainties on them!

dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.