Function reference • divDyn

Diversity dynamics

Primary functions to calculate variables fo diversity dynamics, i.e. richness, origination and extinction rates and sampling.

divDyn(): Time series from metrics of diversity dynamics

binstat(): Sampling statistics and diversity indices in every bin

indices(): Scalar indices of diversity

ratesplit(): Test of rate split (selectivity)

sumstat(): Occurrence database summary

Sampling standardization

Wrapper function and algorithms used for sampling-standardization via subsampling.

subsample(): Subsampling wrapper function

subtrialCR() subtrialOXW() subtrialSQS(): Subsampling trial functions

Auxilliary functions

Additional functions relevant for complex analyses of diversity dynamics.

georange(): Estimation of geographic ranges from occurrence data

fadlad(): FAD - LAD matrix from occurrence data

survivors(): Proportions of survivorship

affinity(): Environmental affinities of taxa

singletons(): List of singleton taxa

modeltab(): Origination/extinction response table for statistical modelling.

matchtime(): Match the dates of a time-dependent variable with a predefined vector

cleansp(): Cleanse Species Name Vector

omit(): Omission of taxa that have a poor occurrence record

tabinate(): Apply function to TAxon/BIN subset of occurrences and iterATE

Plotting tools

Tools that help visualize paleobiological data.

tsplot(): Time series plotting using a custom time scale

tsbars(): Function to plot a series a values with bars that have variable widths

shades(): Quantile plot of time series

parts(): Plot time series counts or proportions as polygons

ranges(): Plotting ranges and occurrence distributions through time

Example data

Data examples to demonstrate the structure the package was designed to work with.

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

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

tens: The 10 million year resolution timescale of the Paleobiology Database

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

Utilities

Utilities used to manipulate base R objects.

seqduplicated() collapse(): Determination and omission of consecutive duplicates in a vector.

fill(): Filling of missing values in a vector, based on the marginal values of the gaps

categorize(): Mapping multiple entries to categories

slice(): Discretization of continuous time dimension - slicing

streaklog() whichmaxstreak(): Utility functions for slicing gappy time series

repmatch(): Replicate matching and merging