Package: USE 0.1.6

USE: Uniform Sampling of the Environmental Space

Provides functions for uniform sampling of the environmental space, designed to assist species distribution modellers in gathering ecologically relevant pseudo-absence data. The method ensures balanced representation of environmental conditions and helps reduce sampling bias in model calibration. Based on the framework described by Da Re et al. (2023) <doi:10.1111/2041-210X.14209>.

Authors:Daniele Da Re [aut, cre], Enrico Tordoni [aut], Manuele Bazzichetto [aut]

USE_0.1.6.tar.gz
USE_0.1.6.zip(r-4.7-any)USE_0.1.6.zip(r-4.6-any)USE_0.1.6.zip(r-4.5-any)
USE_0.1.6.tgz(r-4.6-any)USE_0.1.6.tgz(r-4.5-any)
USE_0.1.6.tar.gz(r-4.7-any)USE_0.1.6.tar.gz(r-4.6-any)
USE_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
USE/json (API)

# Install 'USE' in R:

install.packages('USE', repos = c('https://danddr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/danddr/use/issues

Pkgdown/docs site:https://danddr.github.io

Datasets:

Worldclim_tmp - A subset of WorldClim bioclimatic variables

On CRAN:

environment sampling-methods species-distribution-modelling uniform

5.04 score 7 stars 31 scripts 353 downloads 7 exports 41 dependencies

Last updated from:8732c2dd25. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	123
source / vignettes	OK	422
linux-release	OK	131
macos-release	OK	145
macos-oldrel	OK	187
windows-devel	OK	68
windows-release	OK	82
windows-oldrel	OK	66
wasm-release	OK	113

Exports:optimRes paSampling princompCustom rastPCA SpatialProba thresh.inspect uniformSampling

Dependencies:class classInt cli cowplot cpp11 DBI e1071 farver FNN ggplot2 glue gtable isoband kernlab KernSmooth ks labeling lattice lifecycle Matrix mclust mgcv multicool mvtnorm nlme pracma proxy R6 RColorBrewer Rcpp rlang s2 S7 scales sf terra units vctrs viridisLite withr wk

USE vignette

1. Create Virtual Species | 2. Generating the environmental space | 3. Uniform sampling of the environmental space | 4. Uniform sampling of the pseudo-absences within the environmental space | 5. Effect of the kernel density threshold on the environmental sub-space sampled to collect pseudo-absences

Rendered fromUSE_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-09-05
Started: 2023-01-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get optimal resolution of the sampling grid	optimRes
Sampling pseudo-absences for the training and testing datasets.	paSampling
Principal Component Analysis for Rasters	rastPCA
Virtual species probability of occurrence	SpatialProba
Inspect the effect of the kernel threshold parameter on the environmental space partitioning	thresh.inspect
Uniform sampling of the environmental space	uniformSampling
A subset of WorldClim bioclimatic variables	Worldclim_tmp