Package: sdm 1.2-67

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 [aut, cre], Miguel B. Araujo [aut]

sdm_1.2-67.tar.gz
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sdm_1.2-67.tgz(r-4.6-any)sdm_1.2-67.tgz(r-4.5-any)
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sdm_1.2-67.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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

On CRAN:

9.33 score 27 stars 2 packages 439 scripts 988 downloads 26 mentions 34 exports 5 dependencies

Last updated from:a3c956f3b9. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	279
source / vignettes	OK	266
linux-release-x86_64	WARNING	275
macos-release-arm64	WARNING	173
macos-oldrel-arm64	WARNING	153
windows-devel	WARNING	232
windows-release	WARNING	247
windows-oldrel	WARNING	248
wasm-release	OK	161

Exports:add aoa background calibration coords coords<-ensemble evaluates getEvaluation getmethod getmethodNames getModelId getModelInfo getModelObject getReplication getResponseCurve getRoc getThreshold getVarImp gui installAll niche nicheSimilarity pa pca rcurve read.sdm roc sdm sdmAdapt sdmData sdmSetting threshold write.sdm

Dependencies:lattice raster Rcpp sp terra

sdm

Rendered fromquick_sdm.pdf.asisusingR.rsp::asis

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

Citation

Development and contributors

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
Area of Applicability	aoa 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
Generates 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,sdmModels,missing-method evaluates,sdmModels,SpatRaster-method evaluates,vector,vector-method getEvaluation getEvaluation,sdmModels-method getReplication getReplication,sdmModels-method show,sdmEvaluate-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,sdmdata-method pa,SpatRaster,sdmModels-method
Principle Components 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 sdmdata 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
Identifying/extracting the best threshold to convert probabilities to presence-absence	getThreshold getThreshold,sdmModels,character-method getThreshold,sdmModels,numeric-method threshold threshold,sdmModels,character-method threshold,sdmModels,numeric-method