MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Version 1.56.0

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

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
Version1.56.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MLInterfaces")

Popular man pages

fsHistory: extract history of feature selection for a cross-validated...
learnerSchema-class: Class "learnerSchema" - convey information on a machine...
MLearn-new: revised MLearn interface for machine learning
MLIntInternals: MLInterfaces infrastructure
planarPlot-methods: Methods for Function planarPlot in Package 'MLInterfaces'
RAB: real adaboost (Friedman et al)
xvalSpec: container for information specifying a cross-validated...
See all...

All man pages Function index File listing

Man pages

balKfold.xvspec: generate a partition function for cross-validation, where the...
classifierOutput-class: Class "classifierOutput"
clusteringOutput-class: container for clustering outputs in uniform structure
confuMat-methods: Compute the confusion matrix for a classifier.
confuTab: Compute confusion tables for a confusion matrix.
fs.absT: support for feature selection in cross-validation
fsHistory: extract history of feature selection for a cross-validated...
hclustWidget: shiny-oriented GUI for cluster or classifier exploration
learnerSchema-class: Class "learnerSchema" - convey information on a machine...
MLearn-new: revised MLearn interface for machine learning
MLIntInternals: MLInterfaces infrastructure
performance-analytics: Assessing classifier performance
planarPlot-methods: Methods for Function planarPlot in Package 'MLInterfaces'
plspinHcube: shiny app for interactive 3D visualization of mlbench...
predict.classifierOutput: Predict method for 'classifierOutput' objects
projectedLearner-class: Class '"projectedLearner"'
projectLearnerToGrid: create learned tesselation of feature space after PC...
RAB: real adaboost (Friedman et al)
raboostCont-class: Class "raboostCont" ~~~
varImpStruct-class: Class "varImpStruct" - collect data on variable importance...
xvalLoop: Cross-validation in clustered computing environments
xvalSpec: container for information specifying a cross-validated...

Functions

BgbmI Man page Source code
DAB Man page Source code
F1 Man page Source code
F1,table-method Man page
MLIConverter.Bgbm Source code
MLIConverter.RAB Source code
MLIConverter.blackboost Source code
MLIConverter.dlda Source code
MLIConverter.knn Source code
MLIConverter.knncv Source code
MLIConverter.ksvm Source code
MLIConverter.ldaPredMeth Source code
MLIConverter.logistic Source code
MLIConverter.naiveBayes Source code
MLIConverter.nnet Source code
MLIConverter.plsda Source code
MLIConverter.randomForest Source code
MLIConverter.rpart Source code
MLIConverter.selftesting Source code
MLIConverter.slda Source code
MLIConverter.svm Source code
MLIConverterListEl.class Source code
MLIConverterPredType.class Source code
MLIPredicter.knn Source code
MLIPredicter.ksvm Source code
MLIPredicter.naiveBayes Source code
MLIPredicter.nnet Source code
MLIPredicter.plsda Source code
MLIPredicter.randomForest Source code
MLIPredicter.svm Source code
MLLabel Man page
MLOutput Man page
MLScore Man page
MLearn 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,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_new Man page
Predict Man page
Predict,daboostCont-method Man page
Predict,raboostCont-method Man page
RAB Man page Source code
RAB4es Man page Source code
RABI Man page
RObject Man page
RObject,classifierOutput-method Man page
RObject,clusteringOutput-method Man page
SOMBout Man page
acc Man page
acc,table-method Man page
accuracy Source code
adaI Man page
baggingI Man page
balKfold.xvspec Man page Source code
blackboostI Man page
classifOutput Man page
classifierOutput-class Man page
clustOutput Man page
clusteringOutput-class Man page
confuMat Man page
confuMat,classifierOutput,character-method Man page
confuMat,classifierOutput,missing-method Man page
confuMat,classifierOutput,numeric-method Man page
confuMat,classifierOutput-method Man page Man page
confuMat-methods Man page
confuTab Man page Source code
cverrs Source code
daboostCont-class Man page
dlda Man page
dlda2 Man page Source code
dldaI Man page
es2df Source code
fn Man page Source code
fn,table-method Man page
fp Man page Source code
fp,table-method Man page
fs.absT Man page Source code
fs.probT Man page Source code
fs.topVariance Man page Source code
fsHistory Man page Man page
fsHistory,classifierOutput-method Man page
gbm2 Man page Source code
getConverter Man page
getConverter,clusteringSchema-method Man page
getDist Man page
getDist,clusteringSchema-method Man page
getGrid Man page
getGrid,ExpressionSet-method Man page
getGrid,data.frame-method Man page
getVarImp Man page
getVarImp,classifOutput,logical-method Man page
getVarImp,classifierOutput,logical-method Man page
getVarImp,classifierOutput,missing-method Man page
glmI.logistic Man page Source code
groupIndex Man page
hclustConverter Source code
hclustI Man page Source code
hclustWidget Man page Source code
kmeansConverter Source code
kmeansI Man page
knn.cv2 Man page Source code
knn.cvI Man page Source code
knn2 Man page Source code
knnI Man page Source code
ksvm2 Man page Source code
ksvmI Man page
ldaI Man page
ldaI.predParms Man page Source code
learnerIn3D Man page
learnerIn3D,projectedLearner-method Man page
learnerSchema-class Man page
lvq Man page Source code
lvqI Man page
macroF1 Man page Source code
macroF1,classifierOutput,character-method Man page
macroF1,classifierOutput,missing-method Man page
macroF1,classifierOutput,numeric-method Man page
macroF1,numeric,numeric-method Man page
macroF1,table,missing-method Man page
macroF1-methods Man page
makeClusteringSchema Source code
makeConfuMat Source code
makeLearnerSchema Man page Source code
mapPSvec Source code
membMat Man page
mkfmla Man page Source code
mlearnWidget Man page Source code
naAs0 Source code
naiveBayesI Man page
nnetI Man page
nonstandardLearnerSchema-class Man page
pamConverter Source code
pamI Man page Source code
partPlot Source code
planarPlot Man page
planarPlot,classifierOutput,ExpressionSet,character-method Man page
planarPlot,classifierOutput,data.frame,character-method Man page
planarPlot-methods Man page
planarPlot2 Source code
plot Man page
plot,clusteringOutput,ANY-method Man page
plot,projectedLearner,ANY-method Man page
plot,varImpStruct,ANY-method Man page
plot,varImpStruct-method Man page
plotOne Man page
plotOne,projectedLearner-method Man page
plotXvalRDA Man page Source code
plsda2 Man page Source code
plsdaI Man page
plspinDF Source code
plspinHcube Man page Source code
precision Man page Source code
precision,classifierOutput,character-method Man page
precision,classifierOutput,missing-method Man page
precision,classifierOutput,numeric-method Man page
precision,table,missing-method Man page
precision-methods Man page
predScore Man page
predScore,classifierOutput-method Man page
predScores Man page
predScores,classifierOutput-method Man page
predict.RAB Source code
predict.classifierOutput Man page Source code
predict.dlda2 Source code
predict.gbm2 Source code
predict.knn.cv2 Source code
predict.knn2 Source code
predict.lvq Source code
predict.rdaML Source code
predict.rdacvML Source code
predictions Man page
predictions,classifierOutput-method Man page
print.rdaML Source code
print.rdacvML Source code
probArray Man page
probMat Man page
projectLearnerToGrid Man page Source code
projectedLearner-class Man page
qdaI Man page
qualScore Man page
rab Man page Source code
raboostCont-class Man page
randomForestI Man page
rda.xvalAns Source code
rdaCV Source code
rdaFixed Source code
rdaI Man page
rdaML Man page Source code
rdacvI Man page
rdacvML Man page Source code
recall Man page Source code
recall,classifierOutput,character-method Man page
recall,classifierOutput,missing-method Man page
recall,classifierOutput,numeric-method Man page
recall,table,missing-method Man page
recall-methods Man page
report Man page
report,varImpStruct-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,table,missing-method Man page
sensitivity-methods 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
somout Man page
specificity Man page Source code
specificity,table-method Man page
standardMLIConverter Man page Source code
svm2 Man page Source code
svmI Man page
testPredictions Man page Man page
testPredictions,classifierOutput-method Man page
testScores Man page
testScores,classifierOutput-method Man page
tn Man page Source code
tn,table-method Man page
tonp Man page Source code
tp Man page Source code
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 Source code
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
MLInterfaces documentation built on May 20, 2017, 10:12 p.m.

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

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

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