sdm: Species Distribution Modelling
Version 1.0-32

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.

Browse man pages Browse package API and functions Browse package files

AuthorBabak Naimi, Miguel B. Araujo
Date of publication2016-12-01 19:11:57
MaintainerBabak Naimi <naimi.b@gmail.com>
LicenseGPL (>= 3)
Version1.0-32
URL http://biogeoinformatics.org
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sdm", repos="http://R-Forge.R-project.org")

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

Functions

CRSorNULL-class Man page
D Source code
D2 Source code
Extract Source code
Jackard Source code
[,sdmdata,ANY,ANY-method Man page
[,sdmdata,missing,missing-method Man page
[[ Man page
[[,sdmModels,ANY,ANY-method Man page
add Man page
add,list,character-method Man page
addLHSformula Source code
addMethods Source code
agrep Source code
as.data.frame Man page
as.data.frame,sdmdata-method Man page
auc Source code
bin Source code
bioclimDismo Source code
bioclimFit Source code
boxplot Man page
boxplot,sdmEvaluate-method Man page
calibration Man page
calibration,sdmEvaluate,missing-method Man page
calibration,vector,vector-method Man page
char2time Source code
characterORmissing-class Man page
characterORnull-class Man page
checkFactor Source code
cmx Source code
colNumber Source code
coordinates Man page
coordinates,sdmModels-method Man page
coordinates,sdmdata-method Man page
coordinates<- Man page
coordinates<-,sdmdata-method Man page
cor Source code
create.sdmCorrelativeMethod Source code
createSdmdata Source code
cutx Source code
data.frameORnull-class Man page
dataClean Source code
deleteRecords Source code
density Man page
density,sdmEvaluate-method Man page
detachPackage Source code
deviance_binomial Source code
deviance_gaussian Source code
deviance_laplace Source code
deviance_poisson Source code
domClass Source code
ensemble Man page
ensemble,sdmModels,Raster-method Man page
ensemble,sdmModels-method Man page
environmentORnull-class Man page
eqFactLevel Source code
evaluate.binomial Source code
evaluate.cmx Source code
evaluate.numerical Source code
evaluates Man page
evaluates,vector,vector-method Man page
exCoords Source code
exFormula Source code
exFunc Source code
exGroup Source code
exInfo Source code
exProduct Source code
exTime Source code
excludeVector Source code
extractEvaluation Source code
factorFix Source code
factorFix.bm Source code
factorFixW Source code
featuresFrame-class Man page
fixFormula Source code
formulaORnull-class Man page
functionORcharacter-class Man page
functionORnull-class Man page
gauss Source code
generateName Source code
generateWL Source code
generateWLP Source code
getData.sdmMatrix Source code
getData.sdmY Source code
getDataFame Source code
getEvalTable Source code
getEvalThresholds Source code
getEvaluation Man page
getEvaluation,sdmModels-method Man page
getFeature Source code
getFeature.cubic Source code
getFeature.hinge Source code
getFeature.linear Source code
getFeature.poly Source code
getFeature.product Source code
getFeature.quad Source code
getFeature.threshold Source code
getFeatureNamesTypes Source code
getFeatureRecords Source code
getFeaturetype Source code
getFormula Source code
getFormula.gammgcv Source code
getFormula.gammgcv.rhs Source code
getFormula.rhs Source code
getGroupIndex Source code
getGroupLevels Source code
getGroupNames Source code
getHingeParams Source code
getIndex Source code
getModel.info Source code
getModel.info2 Source code
getModelFrame Source code
getModelInfo Man page
getModelInfo,sdmModels-method Man page
getPackageList Source code
getPerformance Source code
getRecordID Source code
getRhsFromFormula Source code
getRoc Man page Source code
getRoc,sdmModels,ANY-method Man page
getRoc,vector,vector-method Man page
getRunID Source code
getSdmDataFrame Source code
getSingleFeatureFrame Source code
getSpecies Source code
getSpeciesDF Source code
getSpeciesDistribution Source code
getSpeciesIndex Source code
getSpeciesNames Source code
getSpeciesRecords Source code
getThresholdParams Source code
getTimeIndex Source code
getTotal.object.size Source code
getVarImp Man page
getVarImp,sdmModels-method Man page
getVarImpObject Source code
getlevels Source code
getmethod Man page
getmethod,character-method Man page
getmethodNames Man page
getmethodNames,ANY-method Man page
gui Man page
gui,sdmModels-method Man page
gui.sdm Source code
hinge Source code
hingeNull_binomial Source code
installAll Man page
installAll,ANY-method Man page
listORcharacter-class Man page
listORnull-class Man page
loadLib Source code
mae Source code
mahal Source code
matrixORnull-class Man page
maxent Source code
maxlike Source code
methodFix Source code
movEnv Source code
movEnv2sdm Source code
names Man page
names,sdmdata-method Man page
names<- Man page
names<-,sdmdata-method Man page
nested_terms Source code
newFormulaFunction Source code
newGroup Source code
newMetadata Source code
newMethod Source code
newgroup Source code
normalize Source code
nt.to.numeric Source code
numericORnull-class Man page
nvhinge Source code
nvthresh Source code
occurrence Source code
onAttach Source code
onUnload Source code
plot.roc Source code
pmatch Source code
pmatch2 Source code
predict Man page
predict,.maxlikeModel-method Man page
predict,sdmModels-method Man page
pseudo Source code
pseudo_eDist Source code
pseudo_eRandom Source code
pseudo_gDist Source code
pseudo_gRandom Source code
raster2df Source code
read.sdm Man page
read.sdm,character-method Man page
replicate.methodFix Source code
rmse Source code
roc Man page Source code
roc,sdmModels,ANY-method Man page
roc,sdmModels-method Man page
roc,vector,vector-method Man page
s.installed Source code
s.windows Source code
sBinomial Source code
sdm Man page
sdm,formula,sdmdata,character-method Man page
sdmCorrelativeMethod-class Man page
sdmData Man page
sdmData,ANY,SpatialPoints,ANY,Raster-method Man page
sdmData,ANY,SpatialPoints,ANY,missing-method Man page
sdmData,ANY,data.frame,ANY,missing-method Man page
sdmData,ANY,data.frame,missing,missing-method Man page
sdmData,data.frame,formula,ANY,missing-method Man page
sdmData,data.frame,missing,ANY,missing-method Man page
sdmEvaluate-class Man page
sdmFormula-class Man page
sdmModels-class Man page
sdmSetting Man page
sdmSetting,ANY,sdmdata,character-method Man page
sdmdata-class Man page
select.terms Source code
show,sdmModels-method Man page
show,sdmSetting-method Man page
show,sdmdata-method Man page
speciesDetect Source code
speciesType Source code
split.formula Source code
statFix Source code
subset Man page
subset,sdmModels-method Man page
subsetRecords Source code
templateMatch Source code
term Source code
thresh Source code
threshold Source code
trim Source code
update.sdmCorrelativeMethod Source code
updateGroup Source code
varExist Source code
varImp Source code
wellP Source code
where Source code
which.is.coords Source code
write.sdm Man page
write.sdm,.sdmCorSetting,character-method Man page
write.sdm,sdmModels,character-method Man page
write.sdm,sdmdata,character-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AAAClasses.R
R/bioclim.R
R/calibration.R
R/coordinates.R
R/density.R
R/ensemble.R
R/evaluates.R
R/getData.R
R/gui.R
R/isntallAll.R
R/maxent.R
R/maxlike.R
R/methods.R
R/modelFrame.R
R/names.R
R/plot.R
R/predict.R
R/replicate.R
R/roc.R
R/sdm.R
R/sdmData.R
R/sdmFormula.R
R/sdmMethods.R
R/show.R
R/subset.R
R/varImp.R
R/write.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/quick_sdm.Rmd
inst/doc/quick_sdm.html
inst/external
inst/external/data.sdd
inst/external/elevation.asc
inst/external/model.sdm
inst/external/multi_pa_df.csv
inst/external/pa_df.csv
inst/external/pa_df_with_xy.csv
inst/external/pa_spatial_points.dbf
inst/external/pa_spatial_points.shp
inst/external/pa_spatial_points.shx
inst/external/po_spatial_points.dbf
inst/external/po_spatial_points.shp
inst/external/po_spatial_points.shx
inst/external/po_xy.shp
inst/external/precipitation.asc
inst/external/predictors.grd
inst/external/predictors.gri
inst/external/species.dbf
inst/external/species.prj
inst/external/species.shp
inst/external/species.shx
inst/external/temperature.asc
inst/external/vegetation.asc
inst/methods
inst/methods/sdm
inst/methods/sdm/bioclim.R
inst/methods/sdm/bioclimDismo.R
inst/methods/sdm/brt.R
inst/methods/sdm/cart.R
inst/methods/sdm/fda.R
inst/methods/sdm/gam.R
inst/methods/sdm/glm.R
inst/methods/sdm/glmnet.R
inst/methods/sdm/mars.R
inst/methods/sdm/maxent.R
inst/methods/sdm/maxlike.R
inst/methods/sdm/mda.R
inst/methods/sdm/rf.R
inst/methods/sdm/rpart.R
inst/methods/sdm/svm.R
inst/shinyApps
inst/shinyApps/css.rds
inst/shinyApps/sdmgui
inst/shinyApps/sdmgui/server.R
inst/shinyApps/sdmgui/ui.R
inst/shinyApps/sdmgui/www
inst/shinyApps/sdmgui/www/bootstrap.min.css
inst/shinyApps/sdmgui/www/sdm_design.png
inst/test
inst/test/pca.R
inst/test/sdmgui.R
man
man/add.Rd
man/as.data.frame.Rd
man/boxplot.Rd
man/calibration.Rd
man/coordinates.Rd
man/density.Rd
man/ensemble.Rd
man/evaluates.Rd
man/extractIndex.Rd
man/featuresFrame-class.Rd
man/getModelInfo.Rd
man/gui.Rd
man/installAll.Rd
man/names.Rd
man/predict.Rd
man/read.sdm.Rd
man/roc.Rd
man/sdm.Rd
man/sdmCorrelativeMethod-class.Rd
man/sdmData.Rd
man/sdmModel-class.Rd
man/sdmSetting.Rd
man/sdmdata-class.Rd
man/subset.Rd
man/varImportance.Rd
vignettes
vignettes/quick_sdm.Rmd
sdm documentation built on May 21, 2017, 12:43 a.m.