Package: sdm 1.2-46
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:
sdm_1.2-46.tar.gz
sdm_1.2-46.zip(r-4.5)sdm_1.2-46.zip(r-4.4)sdm_1.2-46.zip(r-4.3)
sdm_1.2-46.tgz(r-4.4-any)sdm_1.2-46.tgz(r-4.3-any)
sdm_1.2-46.tar.gz(r-4.5-noble)sdm_1.2-46.tar.gz(r-4.4-noble)
sdm_1.2-46.tgz(r-4.4-emscripten)sdm_1.2-46.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')) |
Bug tracker:https://github.com/babaknaimi/sdm/issues
Last updated 2 months agofrom:e5bd4514a4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 15 2024 |
| R-4.5-win | NOTE | Sep 15 2024 |
| R-4.5-linux | NOTE | Sep 15 2024 |
| R-4.4-win | NOTE | Sep 15 2024 |
| R-4.4-mac | NOTE | Sep 15 2024 |
| R-4.3-win | NOTE | Sep 15 2024 |
| R-4.3-mac | NOTE | Sep 15 2024 |
Exports:addbackgroundcalibrationcoordscoords<-ensembleevaluatesgetEvaluationgetmethodgetmethodNamesgetModelIdgetModelInfogetModelObjectgetReplicationgetResponseCurvegetRocgetVarImpguiinstallAllnichenicheSimilaritypapcarcurveread.sdmrocsdmsdmAdaptsdmDatasdmSettingwrite.sdm
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add a new method to the package | add add,list,character-method getmethod getmethod,character-method getmethodNames getmethodNames,ANY-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) records | background background,Raster-method background,SpatRaster-method |
| boxplot | boxplot boxplot,sdmEvaluate-method |
| Calibration | calibration calibration,sdmEvaluate,missing-method calibration,vector,vector-method |
| get or set spatial coordinates of species data | coords coords,sdmdata-method coords,sdmModels-method coords<- coords<-,sdmdata-method |
| density | density density,sdmEvaluate-method |
| Ensemble Forecasting of SDMs | ensemble ensemble,sdmModels,data.frame-method ensemble,sdmModels,Raster-method ensemble,sdmModels,SpatRaster-method ensemble,sdmModels-method |
| evaluate for accuracy | evaluates 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 class | featuresFrame-class |
| Get information/modelIDs relevant to fitted models in a sdmModels object | getModelId getModelId,sdmModels-method getModelInfo getModelInfo,sdmModels-method getModelObject getModelObject,sdmModels-method |
| variable importance | getVarImp getVarImp,sdmModels-method |
| Graphical User Interface | gui gui,sdmModels-method |
| install all packages that may be required by the package | installAll installAll,ANY-method |
| Names of species | names names,sdmdata-method names<- names<-,sdmdata-method |
| Generate and plot Ecological Niche | niche 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 Similarity | nicheSimilarity nicheSimilarity,.nicheSpatRaster,.nicheSpatRaster-method nicheSimilarity,SpatRaster,missing-method nicheSimilarity,SpatRaster,SpatRaster-method |
| Converting probability of occurrence to Presence-absence | pa pa,SpatRaster,numeric-method pa,SpatRaster,sdmModels-method |
| Principle Component Analysis | pca pca,data.frame-method pca,RasterStackBrick-method pca,sdmdata-method pca,SpatRaster-method princomp-class |
| sdm model prediction | predict predict,.maxlikeModel-method predict,sdmModels-method |
| Generate and plot response curves | getResponseCurve getResponseCurve,sdmModels-method plot,.responseCurve-method rcurve rcurve,.responseCurve-method rcurve,sdmModels-method |
| read/write sdm* object from/to a file | read.sdm read.sdm,character-method write.sdm write.sdm,.sdmCorSetting,character-method write.sdm,sdmdata,character-method write.sdm,sdmModels,character-method |
| plot ROC curves | getRoc 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 models | sdm sdm,ANY,sdmdata,.sdmCorSetting-method sdm,ANY,sdmdata,character-method sdm,sdmdata,.sdmCorSetting,ANY-method |
| Adapting sdm* objects in the new version | sdmAdapt sdmAdapt,sdmdata-method sdmAdapt,sdmModels-method |
| sdmCorrelativeMethod class | sdmCorrelativeMethod-class |
| creating sdm Data object | sdmData 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 dataset | sdmdata-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 object | sdmSetting sdmSetting,ANY,sdmdata,character-method show,sdmSetting-method |
| Subset models in a sdmModels object | subset subset,sdmModels-method [[,sdmModels,ANY,ANY-method |
