Plotting Occurrence Data Across Taxa
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.
A list where every element is a table of occurrence data for a different taxon,
such as that returned by
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.
A vector of numbers or characters indicating colors on a color
palette for use with basic plot. Must be the same length as occList. If empty, the
default, the colors used are sampled randomly from the
A numeric value giving the length to be used for the width of lines
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.
This function was originally conceived of in the following blog post: Link
This function will invisibly return a list, with each per-taxon element containing the two-column matrix of age bounds for occurrences.
David W. Bapst
and the example graptolite dataset at
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#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!