Package: eSDM 0.4.2

Sam Woodman

eSDM: Ensemble Tool for Predictions from Species Distribution Models

A tool which allows users to create and evaluate ensembles of species distribution model (SDM) predictions. Functionality is offered through R functions or a GUI (R Shiny app). This tool can assist users in identifying spatial uncertainties and making informed conservation and management decisions. The package is further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.

Authors:Sam Woodman [aut, cre]

eSDM_0.4.2.tar.gz
eSDM_0.4.2.zip(r-4.5)eSDM_0.4.2.zip(r-4.4)eSDM_0.4.2.zip(r-4.3)
eSDM_0.4.2.tgz(r-4.4-any)eSDM_0.4.2.tgz(r-4.3-any)
eSDM_0.4.2.tar.gz(r-4.5-noble)eSDM_0.4.2.tar.gz(r-4.4-noble)
eSDM_0.4.2.tgz(r-4.4-emscripten)eSDM_0.4.2.tgz(r-4.3-emscripten)
eSDM.pdf |eSDM.html✨
eSDM/json (API)
NEWS

# Install 'eSDM' in R:

install.packages('eSDM', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/swfsc/esdm/issues

Datasets:

gshhg.l.L16 - Low resolution GSHHG world map
preds.1 - Sample SDM density predictions
preds.2 - Sample SDM density predictions
preds.3 - Sample SDM density predictions
validation.data - Sample validation data

On CRAN:

3.91 score 23 scripts 376 downloads 8 exports 56 dependencies

Last updated 4 months agofrom:c2fb2cccfb. Checks:OK: 1 ERROR: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 17 2024
R-4.5-win	ERROR	Nov 17 2024
R-4.5-linux	ERROR	Nov 17 2024
R-4.4-win	ERROR	Nov 17 2024
R-4.4-mac	ERROR	Nov 17 2024
R-4.3-win	ERROR	Nov 17 2024
R-4.3-mac	ERROR	Nov 17 2024

Exports:ensemble_create ensemble_rescale eSDM_GUI evaluation_metrics model_abundance overlay_sdm pts2poly_centroids pts2poly_vertices

Dependencies:base64enc bitops bslib cachem caTools class classInt cli commonmark crayon DBI digest dplyr e1071 fansi fastmap fontawesome fs generics glue gplots gtools htmltools httpuv jquerylib jsonlite KernSmooth later lifecycle magrittr MASS memoise mime pillar pkgconfig promises proxy purrr R6 rappdirs Rcpp rlang ROCR s2 sass sf shiny sourcetools tibble tidyselect units utf8 vctrs withr wk xtable

Example analysis - Woodman et al 2019

Samuel Woodman

Rendered fromexample-analysis.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2021-05-03
Started: 2019-05-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Ensemble tool for predictions from Species Distribution Models	eSDM-package eSDM
Create ensemble of SDM predictions	ensemble_create ensemble_create.data.frame ensemble_create.sf
Rescale SDM predictions	ensemble_rescale
Open the eSDM GUI	eSDM_GUI
Calculate SDM evaluation metrics	evaluation_metrics
Low resolution GSHHG world map	gshhg.l.L16
Calculate predicted abundance	model_abundance
Overlay SDM predictions onto base geometry	overlay_sdm
Sample SDM density predictions	preds preds.1 preds.2 preds.3
Create polygons from centroid coordinates	pts2poly_centroids
Create polygons from vertex coordinates	pts2poly_vertices
Sample validation data	validation.data