# Diversity Dynamics using Fossil Sampling Data

## 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