formatStructured

Function used to format structure data into a coherent framework.

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

formatStructured function

<dl><dt>dataOCC</dt>
<dd>The species occurrence data. May be either a <code>SpatialPointsDataFrame</code>, <code>sf</code> or <code>data.frame</code> object.</dd>
<dt>type</dt>
<dd>The type of observation model for the data. May be either: <code>PO</code>, <code>PA</code> or <code>Counts</code>.</dd>
<dt>varsOld</dt>
<dd>The names of the old variables in the model which need to be converted to something new.</dd>
<dt>varsNew</dt>
<dd>The name of the new variables in the model which will be used in the full model.</dd>
<dt>projection</dt>
<dd>The CRS object to add to the species occurrence data.</dd>
<dt>boundary</dt>
<dd>An sf object of the boundary of the study area, used to check if the data points are over the region.</dd></dl>

Arguments

formatStructured: Function to add structured data into the workflow. — formatStructured

<dl>

<dt>dataOCC</dt>
<dd>The species occurrence data. May be either a <code>SpatialPointsDataFrame</code>, <code>sf</code> or <code>data.frame</code> object.</dd>


<dt>type</dt>
<dd>The type of observation model for the data. May be either: <code>PO</code>, <code>PA</code> or <code>Counts</code>.</dd>


<dt>varsOld</dt>
<dd>The names of the old variables in the model which need to be converted to something new.</dd>


<dt>varsNew</dt>
<dd>The name of the new variables in the model which will be used in the full model.</dd>


<dt>projection</dt>
<dd>The CRS object to add to the species occurrence data.</dd>


<dt>boundary</dt>
<dd>An sf object of the boundary of the study area, used to check if the data points are over the region.</dd>

</dl>

formatStructured: formatStructured: Function to add structured data into the workflow.

Description

Usage

Value

Arguments