SSDM: Stacked Species Distribution Modelling

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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.

Author
Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Philippe Birnbaum
Date of publication
2016-02-17 09:00:40
Maintainer
Sylvain Schmitt <sylvain.schmitt@agroparistech.fr>
License
GPL (>= 3) | file LICENSE
Version
0.1.1

View on CRAN

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
gui
SSDM package Global User Interface
load.model
Function to load ensemble SDMs and SSDMs
load_occ
Load occurrence data
load_var
Load environmental variables
modelling
Build an SDM using a single algorithm
Occurrences
Plant occurrence 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

Files in this package

SSDM
SSDM/inst
SSDM/inst/shiny
SSDM/inst/shiny/gui
SSDM/inst/shiny/gui/ui.R
SSDM/inst/shiny/gui/server.R
SSDM/NAMESPACE
SSDM/NEWS
SSDM/data
SSDM/data/Env.rda
SSDM/data/Occurrences.rda
SSDM/R
SSDM/R/plot.model.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/Ensemble.SDM.R
SSDM/R/update.stack.R
SSDM/R/save.model.R
SSDM/R/load_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/zzz.R
SSDM/R/stack_modelling.R
SSDM/MD5
SSDM/DESCRIPTION
SSDM/man
SSDM/man/plot.model.Rd
SSDM/man/save.model.Rd
SSDM/man/Occurrences.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/load_var.Rd
SSDM/man/Env.Rd
SSDM/man/modelling.Rd
SSDM/man/SSDM.Rd
SSDM/man/load.model.Rd
SSDM/LICENSE