SSDM: Stacked Species Distribution Modelling

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.

AuthorSylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
Date of publication2017-03-22 22:21:55 UTC
MaintainerSylvain Schmitt <sylvain.schmitt@agroparistech.fr>
LicenseGPL (>= 3) | file LICENSE
Version0.2.2
https://github.com/sylvainschmitt/SSDM

View on CRAN

Functions

Algorithm.SDM-class Man page
ensemble Man page
ensemble,Algorithm.SDM-method Man page
ensemble_modelling Man page
Ensemble.SDM-class Man page
Env Man page
evaluate Man page
evaluate Man page
evaluate,Algorithm.SDM-method Man page
evaluate,MAXENT.SDM-method Man page
evaluate,Stacked.SDM-method Man page
gui Man page
load_enm Man page
load.model Man page
load_occ Man page
load_stack Man page
load_var Man page
mapDiversity Man page
mapDiversity Man page
mapDiversity,Stacked.SDM-method Man page
modelling Man page
Occurrences Man page
plot.model Man page
plot,SDM,ANY-method Man page
plot,Stacked.SDM,ANY-method Man page
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
SSDM Man page
SSDM-package Man page
Stacked.SDM-class Man page
stacking Man page
stacking,Ensemble.SDM-method Man page
stack_modelling Man page
sum,Algorithm.SDM-method Man page
update,Stacked.SDM-method Man page

Files

SSDM
SSDM/inst
SSDM/inst/shiny
SSDM/inst/shiny/gui
SSDM/inst/shiny/gui/ui.R
SSDM/inst/shiny/gui/server.R
SSDM/inst/extdata
SSDM/inst/extdata/RAINFALL.tif
SSDM/inst/extdata/SUBSTRATE.tif
SSDM/inst/extdata/Occurences.txt
SSDM/inst/extdata/TEMPERATURE.tif
SSDM/tests
SSDM/tests/testthat.R
SSDM/tests/testthat
SSDM/tests/testthat/test_load_occ.R
SSDM/tests/testthat/test_load_var.R
SSDM/tests/testthat/test_modelling.R
SSDM/tests/testthat/test_Algorithm.SDM.R
SSDM/tests/testthat/test_stacking.R
SSDM/tests/testthat/test_stack_modelling.R
SSDM/tests/testthat/test_ensemble_modelling.R
SSDM/tests/testthat/test_checkargs.R
SSDM/tests/testthat/test_ensemble.R
SSDM/NAMESPACE
SSDM/NEWS.md
SSDM/data
SSDM/data/Env.rda
SSDM/data/Occurrences.rda
SSDM/R
SSDM/R/evaluate.axes.R SSDM/R/project.R SSDM/R/plot.model.R SSDM/R/evaluate.R SSDM/R/modelling.R SSDM/R/Env.R SSDM/R/Algorithm.SDM.R SSDM/R/checkargs.R SSDM/R/load_occ.R SSDM/R/ensemble_modelling.R SSDM/R/mapDiversity.R SSDM/R/data.values.R SSDM/R/Ensemble.SDM.R SSDM/R/update.stack.R SSDM/R/save.model.R SSDM/R/load_model.R SSDM/R/PA.select.R SSDM/R/get_PA.R SSDM/R/get_model.R SSDM/R/Occurrences.R SSDM/R/gui.R SSDM/R/stacking.R SSDM/R/ensemble.R SSDM/R/SSDM.R SSDM/R/Stacked.SDM.R SSDM/R/load_var.R SSDM/R/SDM.R SSDM/R/zzz.R SSDM/R/stack_modelling.R
SSDM/README.md
SSDM/MD5
SSDM/DESCRIPTION
SSDM/man
SSDM/man/plot.model.Rd SSDM/man/save.model.Rd SSDM/man/Occurrences.Rd SSDM/man/evaluate.Rd SSDM/man/Ensemble.SDM-class.Rd SSDM/man/stack_modelling.Rd SSDM/man/Algorithm.SDM-class.Rd SSDM/man/load_occ.Rd SSDM/man/gui.Rd SSDM/man/ensemble_modelling.Rd SSDM/man/Stacked.SDM-class.Rd SSDM/man/ensemble.Rd SSDM/man/update-Stacked.SDM-method.Rd SSDM/man/stacking.Rd SSDM/man/mapDiversity.Rd SSDM/man/load_var.Rd SSDM/man/Env.Rd SSDM/man/modelling.Rd SSDM/man/SSDM.Rd SSDM/man/load.model.Rd
SSDM/LICENSE

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