sumstat

The function calculates global statistics of the entire database

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>.

Adam Kocsis

divDyn

Diversity Dynamics using Fossil Sampling Data

Adam T. Kocsis

John Alroy

Carl J. Reddin

Wolfgang Kiessling

Deutsche Forschungsgemeinschaft 

FAU GeoZentrum Nordbayern 

sumstat function

<dl><dt>x</dt>
<dd><code>(data.frame)</code>: The occurrence dataset.</dd>
<dt>tax</dt>
<dd><code>(character)</code>: The column name of taxon names.</dd>
<dt>bin</dt>
<dd><code>(character)</code>: The column name of bin names.</dd>
<dt>coll</dt>
<dd><code>(character)</code>: The column name of collection numbers. (optional)</dd>
<dt>ref</dt>
<dd><code>(character)</code>: The column name of reference numbers. (optional)</dd>
<dt>duplicates</dt>
<dd><code>(logical)</code>: The function will check whether there are duplicate occurrences (multiple species/genera). When set to <code>NULL</code>, nothing will happen, but the function will notify you if duplicates are present. If set to <code>TRUE</code>, the function will not do anything with these, if set to <code>FALSE</code>, the duplicates will be omitted.</dd></dl>

Arguments

Occurrence database summary — sumstat

<dl>

<dt>x</dt>
<dd><code>(data.frame)</code>: The occurrence dataset.</dd>


<dt>tax</dt>
<dd><code>(character)</code>: The column name of taxon names.</dd>


<dt>bin</dt>
<dd><code>(character)</code>: The column name of bin names.</dd>


<dt>coll</dt>
<dd><code>(character)</code>: The column name of collection numbers. (optional)</dd>


<dt>ref</dt>
<dd><code>(character)</code>: The column name of reference numbers. (optional)</dd>


<dt>duplicates</dt>
<dd><code>(logical)</code>: The function will check whether there are duplicate occurrences (multiple species/genera). When set to <code>NULL</code>, nothing will happen, but the function will notify you if duplicates are present. If set to <code>TRUE</code>, the function will not do anything with these, if set to <code>FALSE</code>, the duplicates will be omitted.</dd>

</dl>

sumstat: Occurrence database summary

Description

Usage

Value

Arguments

Details

Examples