sdm: Species Distribution Modelling

An extensible R framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time.

Author
Babak Naimi, Miguel B. Araujo
Date of publication
2016-10-17 00:46:24
Maintainer
Babak Naimi <naimi.b@gmail.com>
License
GPL (>= 3)
Version
1.0-28
URLs

View on CRAN

Man pages

add
add a new method to the package
as.data.frame
Get a data.frame with record id values (rID)
boxplot
boxplot
calibration
Calibration
coordinates
get or set spatial coordinates of species data
density
density
ensemble
Ensemble Forecasting of SDMs
evaluates
evaluate for accuracy
extractIndex
Indexing to extract records of a sdmdata object
featuresFrame-class
featureFrame class
getModelInfo
get info out of a sdmModels objects
gui
Graphical User Interface
installAll
install all packages that may be required by the package
names
Names of species
predict
sdm model prediction
read.sdm
read/write sdm* object from/to a file
roc
plot ROC curves
sdm
Fit and evaluate species distribution models
sdmCorrelativeMethod-class
sdmCorrelativeMethod class
sdmData
creating sdm Data object
sdmdata-class
An S4 class representing sdm dataset
sdmModel-class
sdmModels classes
sdmSetting
creating sdmSetting object
subset
Subset models in a sdmModels object
varImportance
variable importance

Files in this package

sdm
sdm/inst
sdm/inst/shinyApps
sdm/inst/shinyApps/css.rds
sdm/inst/shinyApps/sdmgui
sdm/inst/shinyApps/sdmgui/ui.R
sdm/inst/shinyApps/sdmgui/server.R
sdm/inst/shinyApps/sdmgui/www
sdm/inst/shinyApps/sdmgui/www/bootstrap.min.css
sdm/inst/shinyApps/sdmgui/www/sdm_design.png
sdm/inst/CITATION
sdm/inst/methods
sdm/inst/methods/sdm
sdm/inst/methods/sdm/rpart.R
sdm/inst/methods/sdm/maxent.R
sdm/inst/methods/sdm/glm.R
sdm/inst/methods/sdm/glmnet.R
sdm/inst/methods/sdm/brt.R
sdm/inst/methods/sdm/gam.R
sdm/inst/methods/sdm/mda.R
sdm/inst/methods/sdm/mars.R
sdm/inst/methods/sdm/maxlike.R
sdm/inst/methods/sdm/rf.R
sdm/inst/methods/sdm/svm.R
sdm/inst/methods/sdm/fda.R
sdm/inst/methods/sdm/cart.R
sdm/inst/test
sdm/inst/test/pca.R
sdm/inst/test/sdmgui.R
sdm/inst/doc
sdm/inst/doc/quick_sdm.Rmd
sdm/inst/doc/quick_sdm.html
sdm/inst/external
sdm/inst/external/predictors.grd
sdm/inst/external/species.shp
sdm/inst/external/temperature.asc
sdm/inst/external/model.sdm
sdm/inst/external/po_spatial_points.shx
sdm/inst/external/po_spatial_points.dbf
sdm/inst/external/vegetation.asc
sdm/inst/external/po_spatial_points.shp
sdm/inst/external/pa_spatial_points.shx
sdm/inst/external/precipitation.asc
sdm/inst/external/species.prj
sdm/inst/external/pa_spatial_points.dbf
sdm/inst/external/pa_df.csv
sdm/inst/external/species.shx
sdm/inst/external/po_xy.shp
sdm/inst/external/multi_pa_df.csv
sdm/inst/external/pa_df_with_xy.csv
sdm/inst/external/predictors.gri
sdm/inst/external/species.dbf
sdm/inst/external/elevation.asc
sdm/inst/external/data.sdd
sdm/inst/external/pa_spatial_points.shp
sdm/NAMESPACE
sdm/R
sdm/R/sdmMethods.R
sdm/R/varImp.R
sdm/R/write.R
sdm/R/sdmFormula.R
sdm/R/subset.R
sdm/R/replicate.R
sdm/R/modelFrame.R
sdm/R/plot.R
sdm/R/maxent.R
sdm/R/predict.R
sdm/R/show.R
sdm/R/methods.R
sdm/R/density.R
sdm/R/coordinates.R
sdm/R/gui.R
sdm/R/calibration.R
sdm/R/maxlike.R
sdm/R/ensemble.R
sdm/R/names.R
sdm/R/evaluates.R
sdm/R/roc.R
sdm/R/getData.R
sdm/R/isntallAll.R
sdm/R/AAAClasses.R
sdm/R/sdm.R
sdm/R/sdmData.R
sdm/R/zzz.R
sdm/vignettes
sdm/vignettes/quick_sdm.Rmd
sdm/MD5
sdm/build
sdm/build/vignette.rds
sdm/DESCRIPTION
sdm/man
sdm/man/add.Rd
sdm/man/names.Rd
sdm/man/as.data.frame.Rd
sdm/man/varImportance.Rd
sdm/man/installAll.Rd
sdm/man/getModelInfo.Rd
sdm/man/calibration.Rd
sdm/man/gui.Rd
sdm/man/sdmdata-class.Rd
sdm/man/sdm.Rd
sdm/man/predict.Rd
sdm/man/read.sdm.Rd
sdm/man/sdmData.Rd
sdm/man/sdmSetting.Rd
sdm/man/coordinates.Rd
sdm/man/sdmCorrelativeMethod-class.Rd
sdm/man/boxplot.Rd
sdm/man/sdmModel-class.Rd
sdm/man/ensemble.Rd
sdm/man/featuresFrame-class.Rd
sdm/man/roc.Rd
sdm/man/extractIndex.Rd
sdm/man/subset.Rd
sdm/man/density.Rd
sdm/man/evaluates.Rd