FRESA.CAD: Feature Selection Algorithms for Computer Aided Diagnosis

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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.

Author
Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Date of publication
2016-09-10 18:02:27
Maintainer
Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
License
LGPL (>= 2)
Version
2.2.1

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

Files in this package

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