MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MLInterfaces")
AuthorVince Carey <stvjc@channing.harvard.edu>, Robert Gentleman, Jess Mar, and contributions from Jason Vertrees <jv@cs.dartmouth.edu> and Laurent Gatto <lg390@cam.ac.uk>
Bioconductor views Classification Clustering
Date of publicationNone
MaintainerV. Carey <stvjc@channing.harvard.edu>
LicenseLGPL
Version1.54.0

View on Bioconductor

Functions

acc Man page
acc,table-method Man page
adaI Man page
baggingI Man page
balKfold.xvspec Man page
BgbmI Man page
blackboostI Man page
classifierOutput-class Man page
classifOutput Man page
clusteringOutput-class Man page
clustOutput Man page
confuMat Man page
confuMat,classifierOutput,character-method Man page
confuMat,classifierOutput-method Man page
confuMat,classifierOutput,missing-method Man page
confuMat,classifierOutput,numeric-method Man page
confuMat-methods Man page
confuTab Man page
DAB Man page
daboostCont-class Man page
dlda Man page
dlda2 Man page
dldaI Man page
F1 Man page
F1,table-method Man page
fn Man page
fn,table-method Man page
fp Man page
fp,table-method Man page
fs.absT Man page
fsHistory Man page
fsHistory,classifierOutput-method Man page
fs.probT Man page
fs.topVariance Man page
gbm2 Man page
getConverter Man page
getConverter,clusteringSchema-method Man page
getDist Man page
getDist,clusteringSchema-method Man page
getGrid Man page
getGrid,data.frame-method Man page
getGrid,ExpressionSet-method Man page
getVarImp Man page
getVarImp,classifierOutput,logical-method Man page
getVarImp,classifierOutput,missing-method Man page
getVarImp,classifOutput,logical-method Man page
glmI.logistic Man page
groupIndex Man page
hclustI Man page
hclustWidget Man page
kmeansI Man page
knn2 Man page
knn.cv2 Man page
knn.cvI Man page
knnI Man page
ksvm2 Man page
ksvmI Man page
ldaI Man page
ldaI.predParms Man page
learnerIn3D Man page
learnerIn3D,projectedLearner-method Man page
learnerSchema-class Man page
lvq Man page
lvqI Man page
macroF1 Man page
macroF1,classifierOutput,character-method Man page
macroF1,classifierOutput,missing-method Man page
macroF1,classifierOutput,numeric-method Man page
macroF1-methods Man page
macroF1,numeric,numeric-method Man page
macroF1,table,missing-method Man page
makeLearnerSchema Man page
membMat Man page
mkfmla Man page
MLearn Man page
MLearn,formula,data.frame,clusteringSchema,ANY-method Man page
MLearn,formula,data.frame,learnerSchema,numeric-method Man page
MLearn,formula,data.frame,learnerSchema,xvalSpec-method Man page
MLearn,formula,ExpressionSet,character,numeric-method Man page
MLearn,formula,ExpressionSet,learnerSchema,numeric-method Man page
MLearn,formula,ExpressionSet,learnerSchema,xvalSpec-method Man page
MLearn_new Man page
mlearnWidget Man page
MLLabel Man page
MLOutput Man page
MLScore Man page
naiveBayesI Man page
nnetI Man page
nonstandardLearnerSchema-class Man page
pamI Man page
planarPlot Man page
planarPlot,classifierOutput,data.frame,character-method Man page
planarPlot,classifierOutput,ExpressionSet,character-method Man page
planarPlot-methods Man page
plot Man page
plot,clusteringOutput,ANY-method Man page
plotOne Man page
plotOne,projectedLearner-method Man page
plot,projectedLearner,ANY-method Man page
plot,varImpStruct,ANY-method Man page
plot,varImpStruct-method Man page
plotXvalRDA Man page
plsda2 Man page
plsdaI Man page
plspinHcube Man page
precision Man page
precision,classifierOutput,character-method Man page
precision,classifierOutput,missing-method Man page
precision,classifierOutput,numeric-method Man page
precision-methods Man page
precision,table,missing-method Man page
Predict Man page
predict.classifierOutput Man page
Predict,daboostCont-method Man page
predictions Man page
predictions,classifierOutput-method Man page
Predict,raboostCont-method Man page
predScore Man page
predScore,classifierOutput-method Man page
predScores Man page
predScores,classifierOutput-method Man page
probArray Man page
probMat Man page
projectedLearner-class Man page
projectLearnerToGrid Man page
qdaI Man page
qualScore Man page
rab Man page
RAB Man page
RAB4es Man page
RABI Man page
raboostCont-class Man page
randomForestI Man page
rdacvI Man page
rdacvML Man page
rdaI Man page
rdaML Man page
recall Man page
recall,classifierOutput,character-method Man page
recall,classifierOutput,missing-method Man page
recall,classifierOutput,numeric-method Man page
recall-methods Man page
recall,table,missing-method Man page
report Man page
report,varImpStruct-method Man page
RObject Man page
RObject,classifierOutput-method Man page
RObject,clusteringOutput-method Man page
rpartI Man page
sensitivity Man page
sensitivity,classifierOutput,character-method Man page
sensitivity,classifierOutput,missing-method Man page
sensitivity,classifierOutput,numeric-method Man page
sensitivity-methods Man page
sensitivity,table,missing-method Man page
show,classifierOutput-method Man page
show,clusteringOutput-method Man page
show,clusteringSchema-method Man page
show,learnerSchema-method Man page
show,projectedLearner-method Man page
show,raboostCont-method Man page
show,varImpStruct-method Man page
silhouetteVec Man page
sldaI Man page
SOMBout Man page
somout Man page
specificity Man page
specificity,table-method Man page
standardMLIConverter Man page
svm2 Man page
svmI Man page
testPredictions Man page
testPredictions,classifierOutput-method Man page
testScores Man page
testScores,classifierOutput-method Man page
tn Man page
tn,table-method Man page
tonp Man page
tp Man page
tp,table-method Man page
trainInd Man page
trainInd,classifierOutput-method Man page
trainPredictions Man page
trainPredictions,classifierOutput-method Man page
trainScores Man page
trainScores,classifierOutput-method Man page
varImpStruct-class Man page
xvalLoop Man page
xvalSpec Man page
xvalSpec-class Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/MLIConverters.R R/MLIPredicters.R R/MLearn.R R/RAB.R R/clDesign.R R/featSel.R R/hcw.R R/localBridge.R R/methods-classifierOutput.R R/methods-clusteringOutput.R R/methods-learnerSchema.R R/mlw.R R/partPlot.R R/performance-analytics.R R/plsdaI.R R/plspinHcube.R R/pplot.R R/pv.R R/schemaInterfaces.R R/varImp.R R/xval.R
README.txt
build
build/vignette.rds
inst
inst/MLIschema
inst/MLIschema/notes.txt
inst/doc
inst/doc/MLInterfaces.R
inst/doc/MLInterfaces.Rnw
inst/doc/MLInterfaces.pdf
inst/doc/MLint_devel.R
inst/doc/MLint_devel.Rnw
inst/doc/MLint_devel.pdf
inst/doc/MLprac2_2.R
inst/doc/MLprac2_2.Rnw
inst/doc/MLprac2_2.pdf
inst/doc/xvalComputerClusters.R
inst/doc/xvalComputerClusters.Rnw
inst/doc/xvalComputerClusters.pdf
inst/extras
inst/extras/mlint08.Rnw
inst/formula
inst/formula/code.R
inst/formula/notes.txt
inst/formula/test.R
inst/oldFiles
inst/oldFiles/INIT.R inst/oldFiles/MASSInterfaces.R inst/oldFiles/classInterfaces.R inst/oldFiles/clusterInterfaces.R inst/oldFiles/cvB.R inst/oldFiles/e1071Interfaces.R inst/oldFiles/gbmB.R inst/oldFiles/ipredInterfaces.R inst/oldFiles/nnetInterfaces.R
inst/oldFiles/nonsyn.Rnw
inst/oldFiles/pamrInterfaces.R inst/oldFiles/randTrain.R inst/oldFiles/randomForestInterfaces.R inst/oldFiles/rpartInterfaces.R inst/oldFiles/silhouetteInterface.R inst/oldFiles/smaInterfaces.R inst/oldFiles/somInterfaces.R inst/oldFiles/statsInterfaces.R
inst/unitTests
inst/unitTests/test_performance-analytics.R
man
man/MLIntInternals.Rd man/MLearn-new.Rd man/RAB.Rd man/balKfold.xvspec.Rd man/classifierOutput-class.Rd man/clusteringOutput-class.Rd man/confuMat-methods.Rd man/confuTab.Rd man/fs.absT.Rd man/fsHistory.Rd man/hclustWidget.Rd man/learnerSchema-class.Rd man/performance-analytics.Rd man/planarPlot-methods.Rd man/plspinHcube.Rd man/predict.classifierOutput.Rd man/projectLearnerToGrid.Rd man/projectedLearner-class.Rd man/raboostCont-class.Rd man/varImpStruct-class.Rd man/xvalLoop.Rd man/xvalSpec.Rd
tests
tests/runTests.R
vignettes
vignettes/MLInterfaces.Rnw
vignettes/MLint_devel.Rnw
vignettes/MLprac2_2.Rnw
vignettes/doc.notes
vignettes/fuskmap.png
vignettes/xvalComputerClusters.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.