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) .

divDyn

R package for quantifying diversity dynamics using fossil sampling data

News

• The next update of the package (V0.8.2) is now availble from the CRAN servers! As this is a major update, I suggest everyone to update their copy. See the change log below for the changes.

• The paper describing the package is available from the Wiley Online Library. You can download it from this link: https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13161 (or contact me, if you have problems). If you decide to use the methods implemented in this package, please refer to this document. The examples implemented can be reproduced with the files deposited at https://github.com/divDyn/ddPhanero using this (updated) vignette: https://github.com/divDyn/ddPhanero/blob/master/doc/dd_phanero_web.html

About the package

If you are interested in what this package does, or have questions about its use, please check out the first vignette: 'Handout to the R package 'divDyn' v0.8.2 for diversity dynamics from fossil occurrence data' here: https://github.com/divDyn/r-package/blob/master/vignettes/handout.pdf

As the package is still getting developed, please note that some interface changes might occurr based on the feedback of people and my own experience on what is easier to use. If you have any requirements or recommendations about what to add (or more importantly, if you find a mistake), do not hesitate to contact me at [email protected].

Installing

1. From CRAN (v0.8.2)

You can install the appropriate binaries normally, by running install.packages("divDyn")

2. Using the source tarball to install (v0.8.2)

This you can do with running

install.packages(
  "https://github.com/divDyn/assets/raw/master/r_archive/source/divDyn_0.8.2.tar.gz", 
  repos=NULL, type="source")

from the R console. Note that there is some code in the package that requires compilation. To do this, the most straightforward way is to install/use Rtools (https://cran.r-project.org/bin/windows/Rtools/) on Windows, and XCode https://developer.apple.com/xcode/ on Mac.

The sources of the older versions are also in the _archive/source folder. You can access earlier versions by changing the version number in the command above.

3. Using the repository files and 'devtools' to install (v0.8.2)

To do this:

• You need a compiler, as for method 2
• Make sure that the 'devtools' package is installed
• Run devtools::install_github("divDyn/r-package")

If the frist method is not working for you, and you do not want to mess around with a compiler and such, then contact me and I will find a way to compile binaries for you.

Change log

See the change log here: Change Log