obtainRichness

This function is used to obtain richness estimates for a multi-species ISDM.

Integration of disparate datasets is needed in order to make efficient use of all available data and thereby address the issues currently threatening biodiversity.
Data integration is a powerful modeling framework which allows us to combine these datasets together into a single model, yet retain the strengths of each individual dataset.
We therefore introduce the package, 'intSDM': an R package designed to help ecologists develop a reproducible workflow of integrated species distribution models, using data both provided from the user as well as data obtained freely online.
An introduction to data integration methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.

Philip Mostert

intSDM

Reproducible Integrated Species Distribution Models Across
Norway using 'INLA'

Angeline Bruls

Ragnhild {Bjørkås}

Wouter Koch

Ellen Martin

obtainRichness function

<dl><dt>modelObject</dt>
<dd>A <code>fitISDM</code> object of class <code>modSpeceis</code>.</dd>
<dt>predictionData</dt>
<dd>An <code>sf</code> data.frame object of containing the locations and covariates that are predicted on.</dd>
<dt>predictionIntercept</dt>
<dd>The name of the prediction dataset to use in the model.</dd>
<dt>sampleSize</dt>
<dd>The size of the sampling area for the prediction intercept dataset. Defaults to <code>1</code>.</dd>
<dt>inclProb</dt>
<dd>Include the individual probabilities for each species. Defaults to <code>TRUE</code></dd></dl>

Arguments

obtainRichness: Function to obtain richness estimates from a fitISDM object. — obtainRichness

<dl>

<dt>modelObject</dt>
<dd>A <code>fitISDM</code> object of class <code>modSpeceis</code>.</dd>


<dt>predictionData</dt>
<dd>An <code>sf</code> data.frame object of containing the locations and covariates that are predicted on.</dd>


<dt>predictionIntercept</dt>
<dd>The name of the prediction dataset to use in the model.</dd>


<dt>sampleSize</dt>
<dd>The size of the sampling area for the prediction intercept dataset. Defaults to <code>1</code>.</dd>


<dt>inclProb</dt>
<dd>Include the individual probabilities for each species. Defaults to <code>TRUE</code></dd>

</dl>

obtainRichness: `obtainRichness`: Function to obtain richness estimates from a `fitISDM` object.

Description

Usage

Value

Arguments