Date repository last updated: January 23, 2024
The envi
package is a suite of R
functions to estimate the ecological niche of a species and predict the spatial distribution of the ecological niche -- a version of environmental interpolation -- with spatial kernel density estimation techniques. A two-group comparison (e.g., presence and absence locations of a single species) is conducted using the spatial relative risk function that is estimated using the sparr package. Internal cross-validation and basic visualization are also supported.
To install the release version from CRAN:
install.packages("envi")
To install the development version from GitHub:
devtools::install_github("lance-waller-lab/envi")
lrren
Main function. Estimate an ecological niche using the spatial relative risk function and predict its location in geographic space.
perlrren
Sensitivity analysis for lrren
whereby observation locations are spatially perturbed ("jittered") with specified radii, iteratively.
plot_obs
Display multiple plots of the estimated ecological niche from lrren
output.
plot_predict
Display multiple plots of the predicted spatial distribution from lrren
output.
plot_cv
Display multiple plots of internal k-fold cross-validation diagnostics from lrren
output.
plot_perturb
Display multiple plots of output from perlrren
including predicted spatial distribution of the summary statistics.
div_plot
Called within plot_obs
, plot_predict
, and plot_perturb
, provides functionality for basic visualization of surfaces with diverging color palettes.
seq_plot
Called within plot_perturb
, provides functionality for basic visualization of surfaces with sequential color palettes.
pval_correct
Called within lrren
and perlrren
, calculates various multiple testing corrections for the alpha level.
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