FRESA.CAD: Feature Selection Algorithms for Computer Aided Diagnosis

Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.

AuthorJose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Date of publication2016-09-10 18:02:27
MaintainerJose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
LicenseLGPL (>= 2)
Version2.2.1

View on CRAN

Man pages

backVarElimination.Bin: IDI/NRI-based backwards variable elimination

backVarElimination.Res: NeRI-based backwards variable elimination

baggedModel: Get the bagged model from a list of forward models

bootstrapValidation.Bin: Bootstrap validation of binary classification models

bootstrapValidation.Res: Bootstrap validation of regression models

bootstrapVarElimination.Bin: IDI/NRI-based backwards variable elimination with...

bootstrapVarElimination.Res: NeRI-based backwards variable elimination with bootstrapping

CancerVarNames: Data frame used in several examples of this package

crossValidationFeatureSelection.Bin: IDI/NRI-based selection of a linear, logistic, or Cox...

crossValidationFeatureSelection.Res: NeRI-based selection of a linear, logistic, or Cox...

featureAdjustment: Adjust each listed variable to the provided set of covariates

ForwardModel.Bin: IDI/NRI-based feature selection procedure for linear,...

ForwardModel.Res: NeRI-based feature selection procedure for linear, logistic,...

FRESA.CAD-package: FeatuRE Selection Algorithms for Computer-Aided Diagnosis...

FRESA.Model: Automated model selection

getKNNpredictionFromFormula: Predict classification using KNN

getVar.Bin: Analysis of the effect of each term of a binary...

getVar.Res: Analysis of the effect of each term of a linear regression...

heatMaps: Plot a heat map of selected variables

improvedResiduals: Estimate the significance of the reduction of predicted...

listTopCorrelatedVariables: List the variables that are highly correlated with each other

medianPredict: The median prediction from a list of models

modelFitting: Fit a model to the data

plot.bootstrapValidation.Bin: Plot ROC curves of bootstrap results

plot.bootstrapValidation.Res: Plot ROC curves of bootstrap results

plotModels.ROC: Plot test ROC curves of each cross-validation model

predictForFresa: Linear or probabilistic prediction

rankInverseNormalDataFrame: Perform a z-transformation of the data using the rank-based...

reportEquivalentVariables: Report the set of variables that will perform an equivalent...

residualForFRESA: Return residuals from prediction

summary.bootstrapValidation: Generate a report of the results obtained using the...

summaryReport: Report the univariate analysis, the cross-validation analysis...

timeSeriesAnalysis: Fit the listed time series variables to a given model

uniRankVar: Univariate analysis of features (additional values returned)

univariateRankVariables: Univariate analysis of features

updateModel.Bin: Update the IDI/NRI-based model using new data or new...

updateModel.Res: Update the NeRI-based model using new data or new threshold...

update.uniRankVar: Update the univariate analysis using new data

Functions

backVarElimination_Bin Man page
backVarElimination_Res Man page
baggedModel Man page
bootstrapValidation_Bin Man page
bootstrapValidation_Res Man page
bootstrapVarElimination_Bin Man page
bootstrapVarElimination_Res Man page
cancerVarNames Man page
crossValidationFeatureSelection_Bin Man page
crossValidationFeatureSelection_Res Man page
featureAdjustment Man page
ForwardSelection.Model.Bin Man page
ForwardSelection.Model.Res Man page
FRESA.CAD Man page
FRESA.CAD-package Man page
FRESA.Model Man page
getKNNpredictionFromFormula Man page
getVar.Bin Man page
getVar.Res Man page
heatMaps Man page
improvedResiduals Man page
listTopCorrelatedVariables Man page
medianPredict Man page
modelFitting Man page
plot Man page
plot.bootstrapValidation_Bin Man page
plot.bootstrapValidation_Res Man page
plotModels.ROC Man page
predictForFresa Man page
rankInverseNormalDataFrame Man page
reportEquivalentVariables Man page
residualForFRESA Man page
summary Man page
summary.bootstrapValidation_Bin Man page
summaryReport Man page
timeSerieAnalysis Man page
uniRankVar Man page
univariateRankVariables Man page
update Man page
updateModel.Bin Man page
updateModel.Res Man page
update.uniRankVar Man page

Files

FRESA.CAD
FRESA.CAD/src
FRESA.CAD/src/FRESAcommons.cpp
FRESA.CAD/src/Makevars
FRESA.CAD/src/FRESAcommons.h
FRESA.CAD/src/rankInverseNormalCpp.cpp
FRESA.CAD/src/regresionFeatureSelectionCpp.cpp
FRESA.CAD/src/Makevars.win
FRESA.CAD/src/binaryFeatureSelectionCpp.cpp
FRESA.CAD/NAMESPACE
FRESA.CAD/NEWS
FRESA.CAD/data
FRESA.CAD/data/cancerVarNames.rda
FRESA.CAD/R
FRESA.CAD/R/update.uniRankVar.R FRESA.CAD/R/getVar.Res.R FRESA.CAD/R/medianPredict.R FRESA.CAD/R/ForwardSelection.Model.Bin.R FRESA.CAD/R/plotModels.ROC.R FRESA.CAD/R/crossValidationFeatureSelection.Res.R FRESA.CAD/R/getVar.Bin.R FRESA.CAD/R/featureAdjustment.R FRESA.CAD/R/bootstrapVarElimination.Bin.R FRESA.CAD/R/heatMaps.R FRESA.CAD/R/improvedResiduals.R FRESA.CAD/R/timeSerieAnalysis.R FRESA.CAD/R/plot.bootstrapValidation.Res.R FRESA.CAD/R/FRESA.Model.R FRESA.CAD/R/backVarElimination.Bin.R FRESA.CAD/R/reportEquivalentVariables.R FRESA.CAD/R/ForwardSelection.Model.Res.R FRESA.CAD/R/predictForFresa.R FRESA.CAD/R/summary.bootstrapValidation.R FRESA.CAD/R/updateModel.Bin.R FRESA.CAD/R/modelFitting.R FRESA.CAD/R/rankInverseNormalDataFrame.R FRESA.CAD/R/backVarElimination.Res.R FRESA.CAD/R/updateModel.Res.R FRESA.CAD/R/bootstrapValidation.Res.R FRESA.CAD/R/bootstrapValidation.Bin.R FRESA.CAD/R/uniRankVar.R FRESA.CAD/R/listTopCorrelatedVariables.R FRESA.CAD/R/univariateRankVariables.R FRESA.CAD/R/getKNNpredictionFromFormula.R FRESA.CAD/R/crossValidationFeatureSelection.Bin.R FRESA.CAD/R/summaryReport.R FRESA.CAD/R/plot.bootstrapValidation.Bin.R FRESA.CAD/R/residualtForFRESA.R FRESA.CAD/R/bootstrapVarElimination.Res.R FRESA.CAD/R/baggedModel.R
FRESA.CAD/MD5
FRESA.CAD/DESCRIPTION
FRESA.CAD/man
FRESA.CAD/man/summary.bootstrapValidation.Rd FRESA.CAD/man/crossValidationFeatureSelection.Bin.Rd FRESA.CAD/man/ForwardModel.Res.Rd FRESA.CAD/man/FRESA.CAD-package.Rd FRESA.CAD/man/CancerVarNames.Rd FRESA.CAD/man/bootstrapValidation.Bin.Rd FRESA.CAD/man/bootstrapVarElimination.Bin.Rd FRESA.CAD/man/backVarElimination.Res.Rd FRESA.CAD/man/modelFitting.Rd FRESA.CAD/man/updateModel.Res.Rd FRESA.CAD/man/bootstrapValidation.Res.Rd FRESA.CAD/man/summaryReport.Rd FRESA.CAD/man/timeSeriesAnalysis.Rd FRESA.CAD/man/plot.bootstrapValidation.Bin.Rd FRESA.CAD/man/baggedModel.Rd FRESA.CAD/man/ForwardModel.Bin.Rd FRESA.CAD/man/improvedResiduals.Rd FRESA.CAD/man/medianPredict.Rd FRESA.CAD/man/plotModels.ROC.Rd FRESA.CAD/man/backVarElimination.Bin.Rd FRESA.CAD/man/plot.bootstrapValidation.Res.Rd FRESA.CAD/man/listTopCorrelatedVariables.Rd FRESA.CAD/man/update.uniRankVar.Rd FRESA.CAD/man/bootstrapVarElimination.Res.Rd FRESA.CAD/man/heatMaps.Rd FRESA.CAD/man/FRESA.Model.Rd FRESA.CAD/man/univariateRankVariables.Rd FRESA.CAD/man/uniRankVar.Rd FRESA.CAD/man/getVar.Res.Rd FRESA.CAD/man/getKNNpredictionFromFormula.Rd FRESA.CAD/man/residualForFRESA.Rd FRESA.CAD/man/updateModel.Bin.Rd FRESA.CAD/man/featureAdjustment.Rd FRESA.CAD/man/crossValidationFeatureSelection.Res.Rd FRESA.CAD/man/predictForFresa.Rd FRESA.CAD/man/reportEquivalentVariables.Rd FRESA.CAD/man/getVar.Bin.Rd FRESA.CAD/man/rankInverseNormalDataFrame.Rd

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

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