README.md

In envi: Environmental Interpolation using Spatial Kernel Density Estimation

envi: Environmental Interpolation using Spatial Kernel Density Estimation

Date repository last updated: February 01, 2023

Overview

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.

Installation

To install the release version from CRAN:

install.packages("envi")

To install the development version from GitHub:

devtools::install_github("lance-waller-lab/envi")

Available functions

Function Description 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.

Authors

* **Ian D. Buller** - *Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland (current)* - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (former)* - *Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, Georgia. (original)* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582) See also the list of [contributors](https://github.com/lance-waller-lab/envi/graphs/contributors) who participated in this package, including: * **Lance A. Waller** - *Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia.* - [GitHub](https://github.com/lance-waller) - [ORCID](https://orcid.org/0000-0001-5002-8886) ## Usage ### For the lrren() function wzxhzdk:0       wzxhzdk:1   ### For the perlrren() function wzxhzdk:2         ### Funding This package was developed while the author was originally a doctoral student in the [Environmental Health Sciences doctoral program](https://www.sph.emory.edu/departments/eh/degree-programs/phd/index.html) at [Emory University](https://www.emory.edu/home/index.html) and later as a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). Any modifications since December 05, 2022 were made while the author was an employee of Social & Scientific Systems, Inc., a division of [DLH Corporation](https://www.dlhcorp.com). ### Acknowledgments When citing this package for publication, please follow: citation("envi") ### Questions? Feedback? For questions about the package, please contact the maintainer [Dr. Ian D. Buller](mailto:[e-mail]) or [submit a new issue](https://github.com/lance-waller-lab/envi/issues).

envi documentation built on Feb. 16, 2023, 7:38 p.m.