resampling_core

Rarefy BioTIME data Applies sample-based rarefaction to standardise the
number of samples per year within a cell-level time series.

internal

The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.

Alban Sagouis

BioTIMEr

Tools to Use and Explore the 'BioTIME' Database

Faye Moyes

Inês S. Martins

Shane A. Blowes

Viviana Brambilla

Cher F. Y. Chow

Ada Fontrodona-Eslava

Laura Antão

Jonathan M. Chase

Maria Dornelas

Anne E. Magurran

European Research Council grant AdG BioTIME 250189 

European Research Council grant PoC BioCHANGE 727440 

European Research Council grant AdG MetaCHANGE 101098020 

The Leverhulme Centre for Anthropocene Biodiversity grant RC-2018-021 

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig 

Martin Luther University Halle-Wittenberg 

University of St Andrews 

resampling_core function

<dl><dt>x</dt>
<dd>(<code>data.frame</code>) BioTIME gridded data to be resampled (in the
format of the output of the <code>gridding</code> function).</dd>
<dt>measure</dt>
<dd>(<code>character</code>) currency to be retained during the
sample-based rarefaction. Can be either defined by a single column name or a
vector of two or more column names.</dd>
<dt>summarise</dt>
<dd>(<code>logical</code>). <code>TRUE</code> by default. If <code>FALSE</code>,
the function returns abundance and/or biomass summed at the SAMPLE_DESC level
git pull(i.e., per sample), rather than per species per year.</dd></dl>

Arguments

Rarefy BioTIME data Applies sample-based rarefaction to standardise the
number of samples per year within a cell-level time series. — resampling_core

<dl>

<dt>x</dt>
<dd>(<code>data.frame</code>) BioTIME gridded data to be resampled (in the
format of the output of the <code>gridding</code> function).</dd>


<dt>measure</dt>
<dd>(<code>character</code>) currency to be retained during the
sample-based rarefaction. Can be either defined by a single column name or a
vector of two or more column names.</dd>


<dt>summarise</dt>
<dd>(<code>logical</code>). <code>TRUE</code> by default. If <code>FALSE</code>,
the function returns abundance and/or biomass summed at the SAMPLE_DESC level
git pull(i.e., per sample), rather than per species per year.</dd>

</dl>

Rarefy BioTIME data Applies sample-based rarefaction to standardise the
number of samples per year within a cell-level time series.

resampling_core: Rarefy BioTIME data Applies sample-based rarefaction to standardise the number of samples per year within a cell-level time series.

Description

Usage

Value

Arguments