velociraptr
R Functions for downloading, cleaning, culling, or analyzing fossil data from the Paleobiology Database. Developed and maintained by Andrew Zaffos as part of the Paleobiology Database and Macrostrat Database tech development initiatives at the University of Wisconsin - Madison.
The following is a list of functions included in the package and basic descriptions of what they do. See the internal help files for further information on usage - e.g., ?downloadPBDB.
Installation
For RStudio users, the best way to install this package directly from GitHub is by using the devtools package.
devtools::install_github("paleobiodb/paleobiodb_utilities",subdir="velociraptr")Contents
Download Functions
Cleaning and Culling Functions
Reshaping Functions
Diversity Functions
subsampleIndividuals( )subsampleEvenness( )taxonAlpha( )meanAlpha( )taxonBeta( )sampleBeta( )totalBeta( )multiplicativeBeta( )completeTurnovers( )- ````notEndemic( )`````
totalGamma( )
Confidence Interval Functions
downloadPBDB( )
Downloads a data frame of Paleobiology Database fossil occurrences.
downloadTime( )
Downloads a geologic timescale from the Macrostrat.org database.
downloadPaleogeography( )
Download a paleogeographic map for an age expressed as millions of years ago from the Macrostrat.org database.
constrainAges( )
Assign fossil occurrences to different intervals within a geologic timescale, then remove occurrences that are not temporally constrained to a single interval within that timescale.
multiplyAges( )
Create mutliple instances of a single occurrence for each geologic interval it occurs in.
ageRanges( )
Find the age range (first occurrence and last occurrence) for each taxon in a PBDB dataset. Can be run for any level of the taxonomic hierarchy (e.g., family, genus).
cleanTaxonomy( )
Removes NAs and subgenera from a taxonomic column.
cullMatrix( )
Functions for recursively culling community matrices of rare taxa and depauperate samples.
presenceMatrix( )
Creates a community matrix of taxon presences and absences from a data frame with a column of "sites" and a column of "species".
abundanceMatrix( )
Creates a community matrix of taxon abundances, with "sites" as rows and "species" as columns, from a data frame.
subsampleIndividuals( )
Calculate the richness of a sample after subsampling to a set number of individuals.
subsampleEvenness( )
Calculate the richness of a sample after subsampling based on the evenness of the abundance distribution.
taxonAlpha( )
Calculates the contribution to alpha diversity of each taxon in a communiy matrix using the additive diversity partitioning paradigm.
meanAlpha( )
Calculates the alpha diversity of a community matrix.
taxonBeta( )
Calculates the contribution to beta diversity of each taxon in a community matrix using the additive diversity partitioning paradigm.
taxonBeta( )
Calculates the contribution to beta diversity of each sample in a community matrix using the additive diversity partitioning paradigm.
totalBeta( )
Calculates the beta diversity of a community matrix using the additive diversity partitioning paradigm.
multiplicativeBeta( )
Calculates the beta diversity of a community matrix using the multiplicative paradigm.
completeTurnovers( )
Calculates Whittaker's effective species turnover, the number of complete effective species turnovers among samples in the dataset.
notEndemic( )
Proportional effective species turnover, the proportion of species in the community matrix not limited to a single sample - i.e., the proportion of "non-endemic" taxa.
totalGamma( )
Calculates the gamma diversity of a community matrix.
uniformExtinction( )
Places a confidence interval on time of extinction using the Strauss and Sadler method.
uniformOrigination( )
Places a confidence interval on time of origination using the Strauss and Sadler method.
adaptiveExtinction( )
Places a confidence interval on time of extinction using the Adaptive Beta Method.
adaptiveOrigination( )
Places a confidence interval on time of origination using the Adaptive Beta Method.