Package: sdm 1.2-52

sdm: Species Distribution Modelling

An extensible 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. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.

Authors:Babak Naimi, Miguel B. Araujo

sdm_1.2-52.tar.gz
sdm_1.2-52.zip(r-4.5)sdm_1.2-52.zip(r-4.4)sdm_1.2-52.zip(r-4.3)
sdm_1.2-52.tgz(r-4.4-any)sdm_1.2-52.tgz(r-4.3-any)
sdm_1.2-52.tar.gz(r-4.5-noble)sdm_1.2-52.tar.gz(r-4.4-noble)
sdm_1.2-52.tgz(r-4.4-emscripten)sdm_1.2-52.tgz(r-4.3-emscripten)
sdm.pdf |sdm.html✨
sdm/json (API)

# Install 'sdm' in R:
install.packages('sdm', repos = c('https://babaknaimi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/babaknaimi/sdm/issues

On CRAN:

9.29 score 21 stars 1 packages 300 scripts 1.4k downloads 26 mentions 34 exports 5 dependencies

Last updated 14 days agofrom:2f63976069. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winWARNINGNov 08 2024
R-4.5-linuxWARNINGNov 08 2024
R-4.4-winWARNINGNov 08 2024
R-4.4-macWARNINGNov 08 2024
R-4.3-winWARNINGNov 08 2024
R-4.3-macWARNINGNov 08 2024

Exports:addaoabackgroundcalibrationcoordscoords<-ensembleevaluatesgetEvaluationgetmethodgetmethodNamesgetModelIdgetModelInfogetModelObjectgetReplicationgetResponseCurvegetRocgetThresholdgetVarImpguiinstallAllnichenicheSimilaritypapcarcurveread.sdmrocsdmsdmAdaptsdmDatasdmSettingthresholdwrite.sdm

Dependencies:latticerasterRcppspterra

sdm

Rendered fromquick_sdm.pdf.asisusingR.rsp::asison Nov 08 2024.

Last update: 2018-04-05
Started: 2018-04-05

Readme and manuals

Help Manual

Help pageTopics
add a new method to the packageadd add,list,character-method getmethod getmethod,character-method getmethodNames getmethodNames,ANY-method
Area of Applicabilityaoa aoa,SpatRaster,sdmdata-method aoa,SpatRaster,sdmModels-method
Combine (merge) two sdmModels into a single object+,sdmModels,sdmModels-method Arith-methods
Get a data.frame with record id values (rID)as.data.frame as.data.frame,sdmdata-method
Generate background (pseudo-absence) recordsbackground background,Raster-method background,SpatRaster-method
boxplotboxplot boxplot,sdmEvaluate-method
Calibrationcalibration calibration,sdmEvaluate,missing-method calibration,vector,vector-method
get or set spatial coordinates of species datacoords coords,sdmdata-method coords,sdmModels-method coords<- coords<-,sdmdata-method
densitydensity density,sdmEvaluate-method
Ensemble Forecasting of SDMsensemble ensemble,sdmModels,data.frame-method ensemble,sdmModels,Raster-method ensemble,sdmModels,SpatRaster-method ensemble,sdmModels-method
evaluate for accuracyevaluates evaluates,sdmdata,RasterLayer-method evaluates,sdmdata,SpatRaster-method evaluates,vector,vector-method getEvaluation getEvaluation,sdmModels-method getReplication getReplication,sdmModels-method
Indexing to extract records of a sdmdata object[,sdmdata,ANY,ANY-method [,sdmdata,missing,missing-method
featureFrame classfeaturesFrame-class
Get information/modelIDs relevant to fitted models in a sdmModels objectgetModelId getModelId,sdmModels-method getModelInfo getModelInfo,sdmModels-method getModelObject getModelObject,sdmModels-method
variable importancegetVarImp getVarImp,sdmModels-method
Graphical User Interfacegui gui,sdmModels-method
install all packages that may be required by the packageinstallAll installAll,ANY-method
Names of speciesnames names,sdmdata-method names<- names<-,sdmdata-method
Generate and plot Ecological Nicheniche niche,RasterStackBrick,RasterLayer-method niche,RasterStackBrick,sdmdata-method niche,RasterStackBrick,SpatialPoints-method niche,sdmdata,ANY-method niche,SpatRaster,sdmdata-method niche,SpatRaster,SpatRaster-method niche,SpatRaster,SpatVector-method plot,.nicheRaster-method plot,.nicheSpatRaster-method
Niche SimilaritynicheSimilarity nicheSimilarity,.nicheSpatRaster,.nicheSpatRaster-method nicheSimilarity,SpatRaster,missing-method nicheSimilarity,SpatRaster,SpatRaster-method
Converting probability of occurrence to Presence-absencepa pa,SpatRaster,numeric-method pa,SpatRaster,sdmModels-method
Principle Component Analysispca pca,data.frame-method pca,RasterStackBrick-method pca,sdmdata-method pca,SpatRaster-method princomp-class
sdm model predictionpredict predict,.maxlikeModel-method predict,sdmModels-method
Generate and plot response curvesgetResponseCurve getResponseCurve,sdmModels-method plot,.responseCurve-method rcurve rcurve,.responseCurve-method rcurve,sdmModels-method
read/write sdm* object from/to a fileread.sdm read.sdm,character-method write.sdm write.sdm,.sdmCorSetting,character-method write.sdm,sdmdata,character-method write.sdm,sdmModels,character-method
plot ROC curvesgetRoc getRoc,sdmModels,ANY-method getRoc,vector,vector-method roc roc,sdmModels,ANY-method roc,sdmModels-method roc,vector,vector-method
Fit and evaluate species distribution modelssdm sdm,ANY,sdmdata,.sdmCorSetting-method sdm,ANY,sdmdata,character-method sdm,sdmdata,.sdmCorSetting,ANY-method
Adapting sdm* objects in the new versionsdmAdapt sdmAdapt,sdmdata-method sdmAdapt,sdmModels-method
sdmCorrelativeMethod classsdmCorrelativeMethod-class
creating sdm Data objectsdmData sdmData,ANY,data.frame,missing,missing-method sdmData,ANY,data.frame,missing-method sdmData,ANY,data.frame,SpatRaster-method sdmData,ANY,SpatialPoints,missing-method sdmData,ANY,SpatialPoints,Raster-method sdmData,ANY,SpatVector,SpatRaster-method sdmData,data.frame,formula,missing-method sdmData,data.frame,missing,missing-method
An S4 class representing sdm datasetsdmdata-class show,sdmdata-method
sdmModels classes.pcaObject-class characterORmissing-class characterORnull-class CRSorNULL-class data.frameORmatrix-class data.frameORnull-class environmentORnull-class expressionORnull-class formulaORnull-class functionORcharacter-class functionORnull-class integerORnull-class listORcharacter-class listORnull-class matrixORnull-class numericORnull-class sdmEvaluate-class sdmFormula-class sdmModels-class show,sdmModels-method
creating sdmSetting objectsdmSetting sdmSetting,ANY,sdmdata,character-method show,sdmSetting-method
Subset models in a sdmModels objectsubset subset,sdmModels-method [[,sdmModels,ANY,ANY-method
Identifying/extracting the best threshold to convert probabilities to Presence/AbsencesgetThreshold getThreshold,sdmModels,character-method getThreshold,sdmModels,numeric-method threshold,sdmModels,character-method threshold,sdmModels,numeric-method