sdmo: Species Distribution Modelling (old version)
Version 0.0-12

sdm is an extendable framework to develop species distributions models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time.

AuthorBabak Naimi, Miguel B. Araujo
Date of publication2016-03-31 06:40:30
MaintainerBabak Naimi <naimi.b@gmail.com>
LicenseGPL (>= 3)
Version0.0-12
URL http://biogeoinformatics.org
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sdmo", repos="http://R-Forge.R-project.org")

Popular man pages

ensemble: Ensemble Forecasting of SDMs
names: Names of species
pca: Principle Component Analysis
predict: sdm model prediction
roc: plot ROC curves
sdmSetting: creating sdm Data object
write.sdm: Write an sdm Object to a file
See all...

All man pages Function index File listing

Man pages

ensemble: Ensemble Forecasting of SDMs
evaluates: evaluate for accuracy
gui: Graphical User Interface
names: Names of species
pca: Principle Component Analysis
predict: sdm model prediction
read.sdm: Read sdmModel from a file
roc: plot ROC curves
sdm: fit sdm models
sdmData: creating sdm Data object
sdmModel-class: sdm classes
sdmSetting: creating sdm Data object
write.sdm: Write an sdm Object to a file

Functions

CRSorNULL-class Man page
Extract Source code
SpeciesDataList-class Man page
auc Source code
brtFit Source code
brtPredict Source code
catReport Source code
characterORmissing-class Man page
characterORnull-class Man page
checkFactor Source code
cmx Source code
cor Source code
createModelSetting Source code
createMultipleSpecies Source code
createSModels Source code
createSingleSpecies Source code
createSpeciesDataList Source code
create_multipleSpeciesData Source code
create_singleSpeciesData Source code
create_speciesDatalist Source code
cv.folds Source code
dataClean Source code
df2list Source code
dummy Source code
ensemble Man page
ensemble,sdmModel-method Man page
eqFactLevel Source code
evaluate Source code
evaluate.cmx Source code
evaluates Man page
evaluates,vector,vector-method Man page
excludeVector Source code
exformula Source code
factorFix Source code
featExt Source code
filebase Source code
fixFormula Source code
formulaORnull-class Man page
ftype_names Source code
gamFit Source code
gamPredict Source code
genFormula Source code
generateName Source code
getBasicSetting Source code
getEvalThresholds Source code
getFormula Source code
getGamFormula Source code
getParams Source code
getPerformance Source code
getPerformanceStat Source code
getPredictParams Source code
getRoc Man page
getRoc,vector,vector-method Man page
getRunIndex Source code
getSpeciesIndex Source code
getTestIndex Source code
getlevels Source code
glmFit Source code
glmPredict Source code
glmSetting Man page
glmSetting,ANY-method Man page
gui Man page
gui,ANY-method Man page
labels,speciesData-method Man page
listORnull-class Man page
loadLib Source code
mahal Source code
methodFix Source code
model.frame Source code
multipleSpecies-class Man page
names Man page
names,SpeciesDataList-method Man page
names,multipleSpecies-method Man page
names,singleSpecies-method Man page
names,speciesData-method Man page
names<- Man page
names<-,speciesData,character-method Man page
names<-,speciesData-method Man page
nt.to.numeric Source code
nteraction.generate Source code
occurrence Source code
paramCheck Source code
paramFix Source code
pca Man page
pca,RasterStackBrick-method Man page
pca,multipleSpecies-method Man page
pca,singleSpecies-method Man page
plot.roc Source code
predict Man page
predict,sdmModel-method Man page
pseudo Source code
pseudo_df Source code
raster2df Source code
read.sdm Man page
read.sdm,character-method Man page
replicate Source code
rfFit Source code
rfPredict Source code
roc Man page Source code
roc,sdmModel-method Man page
runScenarios Source code
s.empty Source code
sBinomial Source code
sMethodAvailable Source code
scenarioMatch Source code
sdm Man page
sdm,ANY,singleSpecies,sdmSettings-method Man page
sdm,formula,singleSpecies,character-method Man page
sdmData Man page
sdmData,SpatialPoints,Raster,ANY-method Man page
sdmData,SpatialPointsDataFrame,Raster,ANY-method Man page
sdmData,SpatialPointsDataFrame,missing,ANY-method Man page
sdmData,data.frame,missing,formula-method Man page Man page
sdmData,data.frame,missing,missing-method Man page
sdmEvaluate-class Man page Man page
sdmEvaluates-class Man page
sdmFit Source code
sdmModel-class Man page
sdmSetting Man page
sdmSetting,formula,speciesData,character-method Man page
sdmSetting,missing,speciesData,character-method Man page
sdmSetting<- Man page
sdmSetting<-,ANY-method Man page
sdmSettings-class Man page
show,SpeciesDataList-method Man page
show,multipleSpecies-method Man page
show,sdmModel-method Man page
show,singleSpecies-method Man page
showScenarios Source code
simpleFormula Source code
singleORmulti Source code
singleSpecies-class Man page
species2df Source code
speciesData-class Man page
splitFormula Source code
statFix Source code
statFix2 Source code
statFixname Source code
strIdentical Source code
svmFit Source code
svmPredict Source code
threshold Source code
vectorORnull-class Man page
where Source code
write.sdm Man page
write.sdm,sdmData,character-method Man page
write.sdm,sdmModel,character-method Man page
write.sdm,sdmSettings,character-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AAAClasses.R
R/dataframe.R
R/ensemble.R
R/evaluates.R
R/gui.R
R/names.R
R/pca.R
R/plot.R
R/predict.R
R/sdm.R
R/sdmData.R
R/show.R
R/thresholds.R
R/write.R
inst
inst/external
inst/external/preds.grd
inst/external/preds.gri
inst/external/species.dbf
inst/external/species.shp
inst/external/species.shx
inst/shinyApps
inst/shinyApps/sdm_base
inst/shinyApps/sdm_base/server.R
inst/shinyApps/sdm_base/ui.R
inst/shinyApps/sdm_base/www
inst/shinyApps/sdm_base/www/r_terminal_sdm.png
man
man/ensemble.Rd
man/evaluates.Rd
man/gui.Rd
man/names.Rd
man/pca.Rd
man/predict.Rd
man/read.sdm.Rd
man/roc.Rd
man/sdm.Rd
man/sdmData.Rd
man/sdmModel-class.Rd
man/sdmSetting.Rd
man/write.sdm.Rd
sdmo documentation built on May 21, 2017, 1:54 a.m.

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