Diversity Dynamics using Fossil Sampling Data

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Documentation for package ‘divDyn’ version 0.8.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

affinity	Environmental affinities of taxa
binstat	Sampling statistics and diversity indices in every bin
categorize	Mapping multiple entries to categories
cleansp	Cleanse Species Name Vector
collapse	Determination and omission of consecutive duplicates in a vector.
corals	Fossil occurrences of scleractinian (stony) corals from the Paleobiology Database
divDyn	Time series from metrics of diversity dynamics
fadlad	FAD - LAD matrix from occurrence data
fill	Filling of missing values in a vector, based on the marginal values of the gaps
georange	Estimation of geographic ranges from occurrence data
indices	Scalar indices of diversity
keys	Keys to process stratigraphic, environmental and lithological information from the Paleobiology Database
matchtime	Match the dates of a time-dependent variable with a predefined vector
matchtime-method	Match the dates of a time-dependent variable with a predefined vector
modeltab	Origination/extinction response table for statistical modelling.
omit	Omission of taxa that have a poor occurrence record
parts	Plot time series counts or proportions as polygons
ranges	Plotting ranges and occurrence distributions through time
ratesplit	Test of rate split (selectivity)
repmatch	Replicate matching and merging
seqduplicated	Determination and omission of consecutive duplicates in a vector.
shades	Quantile plot of time series
singletons	List of singleton taxa
slice	Discretization of continuous time dimension - slicing
stages	95 bin Phanerozoic time scale based on the stratigraphic stages of Gradstein et al. 2020.
stages2018	95 bin Phanerozoic time scale based on the stratigraphic stages of Ogg et al. (2016) with updated dates in some intervals (2018).
stratkeys	The FossilWorks-based lookup table for the stratigraphic assignments of collections in the Paleobiology Database
streaklog	Utility functions for slicing gappy time series
subsample	Subsampling wrapper function
subtrialCR	Subsampling trial functions
subtrialOXW	Subsampling trial functions
subtrialSQS	Subsampling trial functions
sumstat	Occurrence database summary
survivors	Proportions of survivorship
tabinate	Apply function to TAxon/BIN subset of occurrences and iterATE
tens	The 10 million year resolution timescale of the Paleobiology Database
tsbars	Function to plot a series a values with bars that have variable widths
tsplot	Time series plotting using a custom time scale
whichmaxstreak	Utility functions for slicing gappy time series