occ.cleanup

Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

Darius Nau

paleoDiv

Extracting and Visualizing Paleobiodiversity

occ.cleanup function

<dl><dt>x</dt>
<dd>A occurrence data.frame or character vector containing the variable to clean up (defaults to x$tna)</dd>
<dt>remove</dt>
<dd>Which values to remove. If NULL, a default set of commonly occurring character combinations is used ("n. gen.", "n. sp.", "cf.","aff.", punctuation, as well as double, leading and ending spaces). If user-defined, remove needs to be formatted as a character vector with the values to be removed as names, i.e. in the format of c("remove_this" = "", "removethistoo"="")</dd>
<dt>return.df</dt>
<dd>A logical indicating whether to return the entire data.frame (if TRUE) or just the column of taxonomic names.</dd></dl>

Arguments

Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon. — occ.cleanup

<dl>

<dt>x</dt>
<dd>A occurrence data.frame or character vector containing the variable to clean up (defaults to x$tna)</dd>


<dt>remove</dt>
<dd>Which values to remove. If NULL, a default set of commonly occurring character combinations is used ("n. gen.", "n. sp.", "cf.","aff.", punctuation, as well as double, leading and ending spaces). If user-defined, remove needs to be formatted as a character vector with the values to be removed as names, i.e. in the format of c("remove_this" = "", "removethistoo"="")</dd>


<dt>return.df</dt>
<dd>A logical indicating whether to return the entire data.frame (if TRUE) or just the column of taxonomic names.</dd>

</dl>

Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.

occ.cleanup: Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.

Description

Usage

Value

Arguments

Examples