sdmApp

Species Distribution Models Application

sdmApp: Statistical Details

Package	Status	Usage	GitHub	Miscellaneous

sdmApp is a R package containing a Shiny application that allows non-expert R users to easily model species distribution. It offers a reproducible work flow for species distribution modeling into a single and user friendly environment. sdmApp takes Raster data (in format supported by the Raster package) and species occurrence data (several format supported) as input argument. This package provides an interactive graphical user interface (GUI). This document will give an overview of the main functionalities of the graphical user interface. The main features of the GUI is:

• Uploading data (raster and species occurrence files)

• View correlation between raster

• Use CENFA to select species predictors

• Apply a spatial blocking for cross-validation based on the blockCV package

• Apply species distribution models with or without a spatial blocking strategy

• Export results

• Keep reproduce (R code) by being able do download the underlying code from sdmApp.

The GUI is build around 5 main windows, which can be selected from the navigation bar at the top of the screen. Initially, some of these windows will be empty and their content changes once data (both raster and species occurrence files) have been uploaded.

Set working environment

sdmApp uses Maxent model which used the Java implementation. Therefore you need :

• the Java JDK software is installed;
• the package rJava is installed;
• the file maxent.jar is copied in the correct folder.

Installation

To install the package from github use:

remotes::install_github("Abson-dev/sdmApp", dependencies = TRUE)
library(sdmApp)
sdmApp()

To install the package from CRAN use:

install.package("sdmApp", dependencies = TRUE)
library(sdmApp)
sdmApp()

Citation

citation("sdmApp")

To cite package sdmApp in publications use:

HEMA A, NDAO B, LEROUX L, DIOUF A (2021). sdmApp: A User-Friendly Application for Species Distribution Modeling. R package version 0.0.2, https://CRAN.R-project.org/package=sdmApp.

A BibTeX entry for LaTeX users is

@Manual{, title = {sdmApp: A User-Friendly Application for Species Distribution Modeling}, author = {Aboubacar HEMA and Babacar NDAO and Louise LEROUX and Abdoul Aziz DIOUF}, year = {2021}, note = {R package version 0.0.2}, url = {https://CRAN.R-project.org/package=sdmApp}, }

License

The sdmApp sticker was made through R art kindly shared by this link and released under a CC-BY-SA 4.0 license.

Guidelines for contributing

I welcome contributions and suggestions for improving this package. Please do not hesitate to submit any issues you may encounter.