Package: divDyn 0.8.2

Adam T. Kocsis

divDyn: Diversity Dynamics using Fossil Sampling Data

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 as 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) <doi:10.1101/423780>.

Authors:Adam T. Kocsis, John Alroy, Carl J. Reddin, Wolfgang Kiessling

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NEWS

# Install 'divDyn' in R:
install.packages('divDyn', repos = c('https://divdyn.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/divdyn/divdyn/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • corals - Fossil occurrences of scleractinian (stony) corals from the Paleobiology Database
  • keys - Keys to process stratigraphic, environmental and lithological information 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

On CRAN:

diversityextinctionfossil-dataoccurrencesoriginationpaleobiology

32 exports 10 stars 1.66 score 1 dependencies 1 mentions 109 scripts 468 downloads

Last updated 2 years agofrom:0963c8ccbe. Checks:OK: 1 WARNING: 8. Indexed: yes.

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Doc / VignettesOKSep 13 2024
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Exports:affinitybinstatcategorizecleanspcollapsedivDynfadladfillgeorangeindicesmatchtimemodeltabomitpartsrangesratesplitrepmatchseqduplicatedshadessingletonsslicestreaklogsubsamplesubtrialCRsubtrialOXWsubtrialSQSsumstatsurvivorstabinatetsbarstsplotwhichmaxstreak

Dependencies:Rcpp

Handout to the R package divDyn v0.8.2 for diversity dynamics using fossil sampling data

Adam T. Kocsis, Carl J. Reddin, Wolfgang Kiessling

Rendered fromhandout.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2022-09-05
Started: 2018-07-07

Readme and manuals

Help Manual

Help pageTopics
Environmental affinities of taxaaffinity
Sampling statistics and diversity indices in every binbinstat
Mapping multiple entries to categoriescategorize
Cleanse Species Name Vectorcleansp
Fossil occurrences of scleractinian (stony) corals from the Paleobiology Databasecorals
Time series from metrics of diversity dynamicsdivDyn
FAD - LAD matrix from occurrence datafadlad
Filling of missing values in a vector, based on the marginal values of the gapsfill
Estimation of geographic ranges from occurrence datageorange
Scalar indices of diversityindices
Keys to process stratigraphic, environmental and lithological information from the Paleobiology Databasekeys
Match the dates of a time-dependent variable with a predefined vectormatchtime matchtime,character-method matchtime,list-method matchtime,numeric-method
Origination/extinction response table for statistical modelling.modeltab
Omission of taxa that have a poor occurrence recordomit
Plot time series counts or proportions as polygonsparts
Plotting ranges and occurrence distributions through timeranges
Test of rate split (selectivity)ratesplit
Replicate matching and mergingrepmatch
Determination and omission of consecutive duplicates in a vector.collapse seqduplicated
Quantile plot of time seriesshades
List of singleton taxasingletons
Discretization of continuous time dimension - slicingslice
95 bin Phanerozoic time scale based on the stratigraphic stages of Gradstein et al. 2020.stages
95 bin Phanerozoic time scale based on the stratigraphic stages of Ogg et al. (2016) with updated dates in some intervals (2018).stages2018
The FossilWorks-based lookup table for the stratigraphic assignments of collections in the Paleobiology Databasestratkeys
Utility functions for slicing gappy time seriesstreaklog whichmaxstreak
Subsampling wrapper functionsubsample
Subsampling trial functionssubtrialCR subtrialOXW subtrialSQS
Occurrence database summarysumstat
Proportions of survivorshipsurvivors
Apply function to TAxon/BIN subset of occurrences and iterATEtabinate
The 10 million year resolution timescale of the Paleobiology Databasetens
Function to plot a series a values with bars that have variable widthstsbars
Time series plotting using a custom time scaletsplot