connectivity

Calculate mean, variance and difference. The result is produced in form of maps plotted with predefined settings.
Currently, the settings for plot cannot be customized.
Default value is <code>TRUE</code> for all logical arguments

The geohabnet package is designed to perform a geographically or spatially explicit risk analysis of habitat connectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067> proposed the concept of cropland connectivity as a risk factor for plant pathogen or pest invasions. As the functions in geohabnet were initially developed thinking on cropland connectivity, users are recommended to first be familiar with the concept by looking at the Xing et al paper. In a nutshell, a habitat connectivity analysis combines information from maps of host density, estimates the relative likelihood of pathogen movement between habitat locations in the area of interest, and applies network analysis to calculate the connectivity of habitat locations.
The functions of geohabnet are built to conduct a habitat connectivity analysis relying on geographic parameters (spatial resolution and spatial extent), dispersal parameters (in two commonly used dispersal kernels: inverse power law and negative exponential models), and network parameters (link weight thresholds and network metrics).
The functionality and main extensions provided by the functions in geohabnet to habitat connectivity analysis are
a) Capability to easily calculate the connectivity of locations in a landscape using a single function, such as sensitivity_analysis() or msean().
b) As backbone datasets, the geohabnet package supports the use of two publicly available global datasets to calculate cropland density. The backbone datasets in the geohabnet package include crop distribution maps from Monfreda, C., N. Ramankutty, and J. A. Foley (2008) <doi:10.1029/2007gb002947> "Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000, Global Biogeochem. Cycles, 22, GB1022" and International Food Policy Research Institute (2019) <doi:10.7910/DVN/PRFF8V> "Global Spatially-Disaggregated Crop Production Statistics Data for 2010 Version 2.0, Harvard Dataverse, V4". Users can also provide any other geographic dataset that represents host density.
c) Because the geohabnet package allows R users to provide maps of host density (as originally in Xing et al (2021)), host landscape density (representing the geographic distribution of either crops or wild species), or habitat distribution (such as host landscape density adjusted by climate suitability) as inputs, we propose the term habitat connectivity.
d) The geohabnet package allows R users to customize parameter values in the habitat connectivity analysis, facilitating context-specific (pathogen- or pest-specific) analyses.
e) The geohabnet package allows users to automatically visualize maps of the habitat connectivity of locations resulting from a sensitivity analysis across all customized parameter combinations.
The primary function is sean() and sensitivity analysis().
Most functions in geohabnet provide as three main outcomes: i) A map of mean habitat connectivity across parameters selected by the user, ii) a map of variance of habitat connectivity across the selected parameters, and iii) a map of the difference between the ranks of habitat connectivity and habitat density.
Each function can be used to generate these maps as 'final' outcomes.
Each function can also provide intermediate outcomes, such as the adjacency matrices built to perform the analysis, which can be used in other network analysis.
Refer to article at <https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html> to see examples of each function and how to access each of these outcome types.
To change parameter values, the file called parameters.yaml stores the parameters and their values, can be accessed using get_parameters() and set new parameter values with set_parameters().
Users can modify up to ten parameters.

Krishna Keshav

geohabnet

Geographical Risk Analysis Based on Habitat Connectivity

Aaron Plex

Garrett Lab

Karen Garrett

University of Florida 

connectivity function

<dl><dt>host</dt>
<dd>SpatRaster. Host density map aka <code>SpatRaster</code> object</dd>
<dt>indices</dt>
<dd>SpatRaster. Collection of risk indices.</dd>
<dt>global</dt>
<dd>Logical. <code>TRUE</code> if global analysis is desired, <code>FALSE</code> otherwise.
<code>east</code> and <code>west</code> are required when <code>TRUE</code>.</dd>
<dt>east</dt>
<dd>SpatRaster. Collection of risk indices on eastern extent.</dd>
<dt>west</dt>
<dd>SpatRaster. Collection of risk indices on western extent.
When <code>TRUE</code>, <code>geoscale</code> is ignored. Default is <code>TRUE</code>.</dd>
<dt>geoscale</dt>
<dd>Vector. geographical scale. Default is <code>NULL</code>.</dd>
<dt>res</dt>
<dd>Numeric. Map resolution. This value is used in aggregation and dis-aggregation operation.
Default is <code>reso()</code>.</dd>
<dt>pmean</dt>
<dd>Logical. <code>TRUE</code> if map of mean should be plotted, <code>FALSE</code> otherwise.</dd>
<dt>pvar</dt>
<dd>Logical. <code>TRUE</code> if variance map should be plotted, <code>FALSE</code> otherwise.</dd>
<dt>pdiff</dt>
<dd>Logical. <code>TRUE</code> if difference map should be plotted, <code>FALSE</code> otherwise.</dd>
<dt>outdir</dt>
<dd>Character. Output directory for saving raster in TIFF format.
Default is <code><a href="/link/tempdir()?package=geohabnet&version=2.1.3" data-mini-rdoc="geohabnet::tempdir()">tempdir()</a></code>.</dd></dl>

Arguments

Calculate and plot maps — connectivity

<dl>

<dt>host</dt>
<dd>SpatRaster. Host density map aka <code>SpatRaster</code> object</dd>


<dt>indices</dt>
<dd>SpatRaster. Collection of risk indices.</dd>


<dt>global</dt>
<dd>Logical. <code>TRUE</code> if global analysis is desired, <code>FALSE</code> otherwise.
<code>east</code> and <code>west</code> are required when <code>TRUE</code>.</dd>


<dt>east</dt>
<dd>SpatRaster. Collection of risk indices on eastern extent.</dd>


<dt>west</dt>
<dd>SpatRaster. Collection of risk indices on western extent.
When <code>TRUE</code>, <code>geoscale</code> is ignored. Default is <code>TRUE</code>.</dd>


<dt>geoscale</dt>
<dd>Vector. geographical scale. Default is <code>NULL</code>.</dd>


<dt>res</dt>
<dd>Numeric. Map resolution. This value is used in aggregation and dis-aggregation operation.
Default is <code>reso()</code>.</dd>


<dt>pmean</dt>
<dd>Logical. <code>TRUE</code> if map of mean should be plotted, <code>FALSE</code> otherwise.</dd>


<dt>pvar</dt>
<dd>Logical. <code>TRUE</code> if variance map should be plotted, <code>FALSE</code> otherwise.</dd>


<dt>pdiff</dt>
<dd>Logical. <code>TRUE</code> if difference map should be plotted, <code>FALSE</code> otherwise.</dd>


<dt>outdir</dt>
<dd>Character. Output directory for saving raster in TIFF format.
Default is <code><a href='https://rdrr.io/r/base/tempfile.html'>tempdir()</a></code>.</dd>

</dl>

connectivity: Calculate and plot maps

Description

Usage

Value

Arguments

Details

References

See Also