paleotree (version 2.5)

graptPBDB: Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database

Description

Example datasets consisting of (a) occurrence data and (b) taxonomic data downloaded from the Paleobiology Database API for the Graptolithina.

format

The example occurrence dataset (graptOccPBDB) is a data.frame consisting of 5900 occurrences (rows) and 35 variables (columns). The example taxonomy dataset (graptTaxaPBDB) is a data.frame consisting of 364 formal taxa (rows) and 53 variables (columns). Variables are coded in the 'pbdb' vocabulary of the PBDB API v1.2.

source

See examples for the full R code used to obtain the data from the API. You can find the Paleobiology Database at http://paleobiodb.org The occurrence data was entered by (in order of relative portion) P. Novack-Gottshall, M. Krause, M. Foote, A. Hendy, T. Hanson, M. Sommers and others. This same data was authorized mainly by A. Miller, W. Kiessling, M. Foote, A. Hendy, S. Holland, J. Sepkoski and others.

Details

This example PBDB data is included here for testing functions involving occurrence data and taxonomy in paleotree.

See Also

taxonSortPBDBocc, occData2timeList, makePBDBtaxonTree, plotOccData

Examples

#original code used to obtain this dataset on March 21st, 2015
		# using version 1.2 of the Paleobiology Database API

# (sorry, URLs removed as they lead to the PBDB test server...)

save(graptOccPBDB,graptTaxaPBDB,file="graptPBDB.rdata")

# load archived example data
data(graptPBDB)

# let's visualize who entered the majority of the occurrence data
pie(sort(table(graptOccPBDB$enterer)))
# and now who authorized it
pie(sort(table(graptOccPBDB$authorizer)))
# I apologize for using pie charts.

# Let's look at age resolution of these occurrences
hist(graptOccPBDB$early_age-graptOccPBDB$late_age,
		main="Age Resolution of Occurrences", xlab="Ma")

#distribution of taxa among taxonomic ranks
table(graptTaxaPBDB$taxon_rank)
barplot(table(graptTaxaPBDB$taxon_rank))