# Species Distribution Modelling

## Documentation for package ‘sdm’ version 1.2-55

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I L M N P R S T W misc

## -- A --

add | add a new method to the package
add-method | add a new method to the package
aoa | Area of Applicability
aoa-method | Area of Applicability
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 --

data.frameORmatrix-class | sdmModels classes
data.frameORnull-class | sdmModels classes
density | density
density-method | density

## -- 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 --

featuresFrame-class | featureFrame class
formulaORnull-class | sdmModels classes
functionORcharacter-class | sdmModels classes
functionORnull-class | sdmModels classes

## -- 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
getThreshold | Identifying/extracting the best threshold to convert probabilities to Presence/Absences
getThreshold-method | Identifying/extracting the best threshold to convert probabilities to Presence/Absences
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 --

matrixORnull-class | 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 | evaluate for accuracy
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

## -- T --

threshold | Identifying/extracting the best threshold to convert probabilities to Presence/Absences
threshold-method | Identifying/extracting the best threshold to convert probabilities to Presence/Absences

## -- 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