Species Distribution Modelling

Documentation for package ‘sdm’ version 1.2-46

Help Pages

-- A --

add	add a new method to the package
add-method	add a new method to the package
Arith-methods	Combine (merge) two sdmModels into a single object
as.data.frame	Get a data.frame with record id values (rID)
as.data.frame-method	Get a data.frame with record id values (rID)

-- B --

background	Generate background (pseudo-absence) records
background-method	Generate background (pseudo-absence) records
boxplot	boxplot
boxplot-method	boxplot

-- C --

calibration	Calibration
calibration-method	Calibration
characterORmissing-class	sdmModels classes
characterORnull-class	sdmModels classes
coords	get or set spatial coordinates of species data
coords-method	get or set spatial coordinates of species data
coords<-	get or set spatial coordinates of species data
coords<--method	get or set spatial coordinates of species data
CRSorNULL-class	sdmModels classes

-- D --

-- E --

ensemble	Ensemble Forecasting of SDMs
ensemble-method	Ensemble Forecasting of SDMs
environmentORnull-class	sdmModels classes
evaluates	evaluate for accuracy
evaluates-method	evaluate for accuracy
expressionORnull-class	sdmModels classes

-- F --

-- G --

getEvaluation	evaluate for accuracy
getEvaluation-method	evaluate for accuracy
getmethod	add a new method to the package
getmethod-method	add a new method to the package
getmethodNames	add a new method to the package
getmethodNames-method	add a new method to the package
getModelId	Get information/modelIDs relevant to fitted models in a sdmModels object
getModelId-method	Get information/modelIDs relevant to fitted models in a sdmModels object
getModelInfo	Get information/modelIDs relevant to fitted models in a sdmModels object
getModelInfo-method	Get information/modelIDs relevant to fitted models in a sdmModels object
getModelObject	Get information/modelIDs relevant to fitted models in a sdmModels object
getModelObject-method	Get information/modelIDs relevant to fitted models in a sdmModels object
getReplication	evaluate for accuracy
getReplication-method	evaluate for accuracy
getResponseCurve	Generate and plot response curves
getResponseCurve-method	Generate and plot response curves
getRoc	plot ROC curves
getRoc-method	plot ROC curves
getVarImp	variable importance
getVarImp-method	variable importance
gui	Graphical User Interface
gui-method	Graphical User Interface

-- I --

installAll	install all packages that may be required by the package
installAll-method	install all packages that may be required by the package
integerORnull-class	sdmModels classes

-- L --

listORcharacter-class	sdmModels classes
listORnull-class	sdmModels classes

-- M --

sdmModels classes

-- N --

names	Names of species
names-method	Names of species
names<-	Names of species
names<--method	Names of species
niche	Generate and plot Ecological Niche
niche-method	Generate and plot Ecological Niche
nicheSimilarity	Niche Similarity
nicheSimilarity-method	Niche Similarity
numericORnull-class	sdmModels classes

-- P --

pa	Converting probability of occurrence to Presence-absence
pa-method	Converting probability of occurrence to Presence-absence
pca	Principle Component Analysis
pca-method	Principle Component Analysis
plot-method	Generate and plot Ecological Niche
plot-method	Generate and plot response curves
predict	sdm model prediction
predict-method	sdm model prediction
princomp-class	Principle Component Analysis

-- R --

rcurve	Generate and plot response curves
rcurve-method	Generate and plot response curves
read.sdm	read/write sdm* object from/to a file
read.sdm-method	read/write sdm* object from/to a file
roc	plot ROC curves
roc-method	plot ROC curves

-- S --

sdm	Fit and evaluate species distribution models
sdm-method	Fit and evaluate species distribution models
sdmAdapt	Adapting sdm* objects in the new version
sdmAdapt-method	Adapting sdm* objects in the new version
sdmCorrelativeMethod-class	sdmCorrelativeMethod class
sdmData	creating sdm Data object
sdmdata-class	An S4 class representing sdm dataset
sdmData-method	creating sdm Data object
sdmEvaluate-class	sdmModels classes
sdmFormula-class	sdmModels classes
sdmModels-class	sdmModels classes
sdmSetting	creating sdmSetting object
sdmSetting-method	creating sdmSetting object
show-method	sdmModels classes
show-method	creating sdmSetting object
show-method	An S4 class representing sdm dataset
subset	Subset models in a sdmModels object
subset-method	Subset models in a sdmModels object

-- W --

write.sdm	read/write sdm* object from/to a file
write.sdm-method	read/write sdm* object from/to a file

-- misc --

+-method	Combine (merge) two sdmModels into a single object
.pcaObject-class	sdmModels classes
[-method	Indexing to extract records of a sdmdata object
[[-method	Subset models in a sdmModels object