SSDM: Stacked Species Distribution Modelling
Version 0.2.3

Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.

Browse man pages Browse package API and functions Browse package files

AuthorSylvain Schmitt, Robin Pouteau, Dimitri Justeau, Florian de Boissieu, Philippe Birnbaum
Date of publication2017-05-09 21:17:38 UTC
MaintainerSylvain Schmitt <sylvain.schmitt@agroparistech.fr>
LicenseGPL (>= 3) | file LICENSE
Version0.2.3
URL https://github.com/sylvainschmitt/SSDM
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SSDM")

Man pages

Algorithm.SDM-class: An S4 class to represent an SDM based on a single algorithm
ensemble: Methods to assemble multiple algorithms in an ensemble SDM
ensemble_modelling: Build an ensemble SDM that assembles multiple algorithms
Ensemble.SDM-class: An S4 class to represent an ensemble SDM
Env: A stack of three environmental variables
evaluate: Evaluate
gui: SSDM package Graphic User Interface
load.model: Load ensemble SDMs and SSDMs.
load_occ: Load occurrence data
load_var: Load environmental variables
mapDiversity: Map Diversity
modelling: Build an SDM using a single algorithm
Occurrences: Plant occurrences data frame
plot.model: Plot SDMs, ensemble SDMs, and SSDMs
save.model: Save ensemble SDMs and SSDMs
SSDM: SSDM: Stacked species distribution modelling
Stacked.SDM-class: An S4 class to represent SSDMs
stacking: Stack different ensemble SDMs in an SSDM
stack_modelling: Build an SSDM that assembles multiple algorithms and species.
update-Stacked.SDM-method: Update a previous SSDM

Functions

Algorithm.SDM Source code
Algorithm.SDM-class Man page
Ensemble.SDM Source code
Ensemble.SDM-class Man page
Env Man page
MEM Source code
Occurrences Man page
PRR Source code
SSDM Man page
SSDM-package Man page
Stacked.SDM Source code
Stacked.SDM-class Man page
checkargs Source code
ensemble Man page
ensemble,Algorithm.SDM-method Man page
ensemble_modelling Man page Source code
evaluate Man page Man page
evaluate,Algorithm.SDM-method Man page
evaluate,MAXENT.SDM-method Man page
evaluate,Stacked.SDM-method Man page
gui Man page Source code
load.model Man page
load_enm Man page Source code
load_occ Man page Source code
load_stack Man page Source code
load_var Man page Source code
mapDiversity Man page Man page
mapDiversity,Stacked.SDM-method Man page
modelling Man page Source code
onAttach Source code
onLoad Source code
onUnload Source code
plot,SDM,ANY-method Man page
plot,Stacked.SDM,ANY-method Man page
plot.model Man page
richness Source code
save.enm Man page
save.enm,Ensemble.SDM-method Man page
save.model Man page
save.stack Man page
save.stack,Stacked.SDM-method Man page
stack_modelling Man page Source code
stacking Man page
stacking,Ensemble.SDM-method Man page
sum,Algorithm.SDM-method Man page
update,Stacked.SDM-method Man page

Files

inst
inst/shiny
inst/shiny/gui
inst/shiny/gui/ui.R
inst/shiny/gui/server.R
inst/extdata
inst/extdata/RAINFALL.tif
inst/extdata/SUBSTRATE.tif
inst/extdata/Occurrences.csv
inst/extdata/TEMPERATURE.tif
inst/doc
inst/doc/GUI.html
inst/doc/SSDM.html
inst/doc/GUI.Rmd
inst/doc/SSDM.Rmd
inst/doc/SSDM.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test_load_occ.R
tests/testthat/test_load_var.R
tests/testthat/test_modelling.R
tests/testthat/test_Algorithm.SDM.R
tests/testthat/test_stacking.R
tests/testthat/test_stack_modelling.R
tests/testthat/test_ensemble_modelling.R
tests/testthat/test_checkargs.R
tests/testthat/test_ensemble.R
NAMESPACE
NEWS.md
data
data/Env.rda
data/Occurrences.rda
R
R/evaluate.axes.R
R/project.R
R/plot.model.R
R/evaluate.R
R/modelling.R
R/Env.R
R/Algorithm.SDM.R
R/checkargs.R
R/load_occ.R
R/ensemble_modelling.R
R/mapDiversity.R
R/data.values.R
R/Ensemble.SDM.R
R/update.stack.R
R/save.model.R
R/load_model.R
R/PA.select.R
R/get_PA.R
R/get_model.R
R/Occurrences.R
R/gui.R
R/stacking.R
R/ensemble.R
R/SSDM.R
R/Stacked.SDM.R
R/load_var.R
R/SDM.R
R/zzz.R
R/stack_modelling.R
vignettes
vignettes/GUI.Rmd
vignettes/SSDM.Rmd
vignettes/GUI
vignettes/GUI/stack.png
vignettes/GUI/load_occ.png
vignettes/GUI/basic.png
vignettes/GUI/Advanced.png
vignettes/GUI/species.png
vignettes/GUI/load_var.png
vignettes/GUI/Intermediate.png
vignettes/GUI/launch.png
vignettes/GUI/save.png
vignettes/SSDM
vignettes/SSDM/workflow.png
vignettes/SSDM/plot.png
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plot.model.Rd
man/save.model.Rd
man/Occurrences.Rd
man/evaluate.Rd
man/Ensemble.SDM-class.Rd
man/stack_modelling.Rd
man/Algorithm.SDM-class.Rd
man/load_occ.Rd
man/gui.Rd
man/ensemble_modelling.Rd
man/Stacked.SDM-class.Rd
man/ensemble.Rd
man/update-Stacked.SDM-method.Rd
man/stacking.Rd
man/mapDiversity.Rd
man/load_var.Rd
man/Env.Rd
man/modelling.Rd
man/SSDM.Rd
man/load.model.Rd
LICENSE
SSDM documentation built on May 19, 2017, 10:15 p.m.