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divDyn (version 0.8.0)

Diversity Dynamics using Fossil Sampling Data

Description

Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) .

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Version

Install

install.packages('divDyn')

Monthly Downloads

399

Version

0.8.0

License

CC BY 4.0

Maintainer

Adam Kocsis

Last Published

June 12th, 2019

Functions in divDyn (0.8.0)

keys

Keys to process stratigraphic, environmental and lithological information from the Paleobiology Database
singletons

List of singleton taxa
shades

Quantile plot of time series
subsample

Subsampling wrapper function
survivors

Proportions of survivorship
subtrialCR

Subsampling trial functions
indices

Scalar indices of diversity
sumstat

Occurrence database summary
streaklog

Utility functions for slicing gappy time series
stratkeys

The FossilWorks-based lookup table for the stratigraphic assignments of collections in the Paleobiology Database
ratesplit

Test of rate split (selectivity)
repmatch

Replicate matching and merging
tabinate

Apply function to TAxon/BIN subset of occurrences and iterATE
tens

The 10 million year resolution timescale of the Paleobiology Database
tsplot

Time series plotting using a custom time scale
tsbars

Function to plot a series a values with bars that have variable widths
modeltab

Origination/extinction response table for statistical modelling.
omit

Omission of taxa that have a poor occurrence record
ranges

Plotting ranges and occurrence distributions through time
stages

95 bin Phanerozoic time scale based on the stratigraphic stages of Ogg et al. (2016).
corals

Fossil occurrences of scleractinian (stony) corals from the Paleobiology Database
slice

Discretization of continuous time dimension - slicing
parts

Plot time series counts or proportions as polygons
fill

Filling of missing values in a vector, based on the marginal values of the gaps
georange

Estimation of geographic ranges from occurrence data
categorize

Mapping multiple entries to categories
fadlad

FAD - LAD matrix from occurrence data
divDyn

Time series from metrics of diversity dynamics
cleansp

Cleanse Species Name Vector
affinity

Environmental affinities of taxa
binstat

Sampling statistics and diversity indices in every bin
seqduplicated

Determination and omission of consecutive duplicates in a vector.