EMLasso: Fit (logistic) LASSO when there is missing data in the predictors

Fit (logistic) LASSO when there is missing data in the predictors/covariates

AuthorNick Sabbe <nick.sabbe@ugent.be>
Date of publication2013-06-16 13:30:06
MaintainerNick Sabbe <nick.sabbe@ugent.be>
LicenseGPL (>= 2)
Version2.0.9

View on R-Forge

Man pages

checkConvergence.glmnet: Check whether convergence has occurred in the zeroness of...

collectImputationModels: Collect data from a model, needed for multiple imputation...

convergenceDiagnostics: Diagnose convergence of EMLasso.lognet objects

crossValidate: Crossvalidate a model

EMLasso: Fit EMLasso to a complete dataset, creating a GLoMo for each...

EMLasso.1l: Fit EMLasso for 1 lambda

EMLasso.1l.param: Collect parameters to EMLasso.1l into one list

EMLassoFromDir: Get EMLasso from the save files in a folder

EMLasso-package: EM (logistic) LASSO

findReasonableLambdaHelper: Function to run on a dataset with not too much missing data...

fit.glmnet: Tailormade weighted fitting of logistic glmnet

fit.lognet: Tailormade weighted fitting of logistic glmnet

fit.logreg: Fit logistic regression by using logistic LASSO with lambda=0

getMinMaxPosLikeGlmnet: Find a region of interest in a set of lambdas given criteria...

imputeDs2FitDs: Reusable information to convert an imputed dataset to fitting...

lognetProbabilityReusable: Function to help calculate predicted probability of a lognet...

marginalCompleter: Wrapper to complete a dataset based on (univariate) marginal...

outcomeModelValidationReusables: Create reusable part of validation (for rejection sampling)

plotCoefConvergence: Plot coefficient evolution of EMLasso.lognet objects

postProcessEMLasso: Postprocess EMLasso (e.g. add extra members or change class)

postProcessEMLasso1l: Postprocess EMLasso for 1 lambda result (e.g. add extra...

predictorModelSamplingReusables: Create reusable part of prediction for repeated sampling

predictProb: predict probabilities

retrieveLambdas: Retrieve lambdas

sampleConditional: Complete a dataset conditional on a model and the outcomes

setDebugmodeEMLasso: Set tracing of all calls on/off

simplyValidate: Validate a model (to its original data)

thresHolding: Simple threshold selection for some sets of variables...

validateFunction.lognet: validation function for use in...

Functions

acceptOrRejectFunction Man page
acceptOrRejectFunction.default Man page
acceptOrRejectFunction.lognet Man page
checkConvergence.glmnet Man page
collectImputationModels Man page
collectImputationModels.EMLassoGLoMo Man page
completeMarginal Man page
completeMarginal.default Man page
completeMarginal.function Man page
constButWarnFunction Man page
convergenceCheckCreator Man page
convergenceDiagnostics Man page
crossValidate Man page
crossValidate.EMLassoGLoMo Man page
cv.EMLassoGLoMo-class Man page
cv.EMLasso.lognet Man page
cv.MI.logreg Man page
cv.MI.logreg-class Man page
EMLasso Man page
EMLasso1l Man page
EMLasso.1l Man page
EMLasso1l-class Man page
[.EMLasso.1l.param Man page
EMLasso.1l.param Man page
EMLasso-class Man page
EMLassoFromDir Man page
EMLasso.glmnet Man page
EMLasso.glmnet-class Man page
EMLassoGLoMo Man page
EMLassoGLoMo-class Man page
EMLassoGLoMoImputationData Man page
EMLassoGLoMoImputationData-class Man page
EMLasso.lognet Man page
EMLasso.lognet-class Man page
EMLasso-package Man page
findReasonableLambdaHelper Man page
fit.glmnet Man page
fit.lognet Man page
fit.logreg Man page
getLambdas Man page
getLambdas.LambdaHelper Man page
getLambdas.lambdaregion Man page
getMinMaxPosLikeGlmnet Man page
getMinMaxPosLikeGlmnet.cv.glmnet Man page
getMinMaxPosLikeGlmnet.default Man page
getSafeFunction Man page
getSafeFunction.default Man page
getSafeFunction.unsafefunction Man page
getUnsafeFunction Man page
getUnsafeFunction.default Man page
getUnsafeFunction.unsafefunction Man page
illegals2Null Man page
illegalsCalculatedConstCountered Man page
illegalsCountered Man page
illegalToSmryLegalFunction Man page
imputeDs2FitDs Man page
imputeDs2FitDs.default Man page
imputeDs2FitDs.dfrConversionProps Man page
imputeDs2FitDs.dfrConversionPropsEx Man page
imputeDs2FitDsProps Man page
imputeDs2FitDsProps.default Man page
imputeDs2FitDsProps.normalImputationConversion Man page
interactionAdderAllNonSelf Man page
isIllegal Man page
[.LambdaHelper Man page
length.EMLasso.1l.param Man page
lognetProbabilityReusable Man page
logregLikeGlmnet Man page
marginalCompleted Man page
marginalCompleted-class Man page
marginalCompleter Man page
newIllegals Man page
normalImputationConversion Man page
normalImputationConversion-class Man page
outcomeModelValidationReusables Man page
outcomeModelValidationReusables.default Man page
outcomeModelValidationReusables.lognet Man page
plotCoefConvergence Man page
postProcessEMLasso Man page
postProcessEMLasso1l Man page
postProcessEMLasso1l.default Man page
postProcessEMLasso1l.lognet Man page
postProcessEMLasso.default Man page
postProcessEMLasso.GLoMo Man page
predict.EMLassoGLoMoImputationData Man page
predictorModelSamplingReusables Man page
predictorModelSamplingReusables.GLoMo Man page
predictProb Man page
predictProb.lognetProbabilityReusable Man page
print.unsafefunction Man page
removeIllegals Man page
removeScaling Man page
removeScaling.default Man page
removeScaling.dfrConversionPropsEx Man page
repeatedlyPredictOut Man page
repeatedPredictedProbAUC Man page
retrieveLambdas Man page
retrieveLambdas.default Man page
retrieveLambdas.smartLambdaRetriever Man page
sampleConditional Man page
sampleConditional.GLoMo Man page
sampledConditionally Man page
sampledConditionally-class Man page
sampledConditionallyGLomo Man page
sampledConditionallyGLomo-class Man page
SamplingReusablesGLoMo Man page
SamplingReusablesGLoMo-class Man page
setDebugmodeEMLasso Man page
simplyValidate Man page
simplyValidate.EMLassoGLoMo Man page
smartLambdaRetriever Man page
smartLambdaRetriever-class Man page
specialLegalX Man page
sv.EMLassoGLoMo-class Man page
sv.EMLasso.lognet Man page
thresHolding Man page
typicalScaleAndCenter Man page
typicalTransformations Man page
unsafefunction Man page
unsafefunction-class Man page
validateFunction.lognet Man page

Files

EMLasso/DESCRIPTION
EMLasso/NAMESPACE
EMLasso/R
EMLasso/R/EMLasso-package.R EMLasso/R/EMLasso.1l.R EMLasso/R/EMLasso.1l.param.R EMLasso/R/EMLasso.R EMLasso/R/EMLassoFromDir.R EMLasso/R/checkConvergence.glmnet.R EMLasso/R/collectImputationModels.R EMLasso/R/convergenceDiagnostics.R EMLasso/R/crossValidate.R EMLasso/R/findReasonableLambdaHelper.R EMLasso/R/fit.glmnet.R EMLasso/R/fit.lognet.R EMLasso/R/fit.logreg.R EMLasso/R/getMinMaxPosLikeGlmnet.R EMLasso/R/imputeDs2FitDs.R EMLasso/R/lognetProbabilityReusable.R EMLasso/R/marginalCompleter.R EMLasso/R/outcomeModelValidationReusables.R EMLasso/R/plotCoefConvergence.R EMLasso/R/postProcessEMLasso.R EMLasso/R/postProcessEMLasso1l.R EMLasso/R/predictProb.R EMLasso/R/predictorModelSamplingReusables.R EMLasso/R/retrieveLambdas.R EMLasso/R/sampleConditional.R EMLasso/R/setDebugmodeEMLasso.R EMLasso/R/simplyValidate.R EMLasso/R/thresHolding.R EMLasso/R/validateFunction.lognet.R
EMLasso/man
EMLasso/man/EMLasso-package.Rd EMLasso/man/EMLasso.1l.Rd EMLasso/man/EMLasso.1l.param.Rd EMLasso/man/EMLasso.Rd EMLasso/man/EMLassoFromDir.Rd EMLasso/man/checkConvergence.glmnet.Rd EMLasso/man/collectImputationModels.Rd EMLasso/man/convergenceDiagnostics.Rd EMLasso/man/crossValidate.Rd EMLasso/man/findReasonableLambdaHelper.Rd EMLasso/man/fit.glmnet.Rd EMLasso/man/fit.lognet.Rd EMLasso/man/fit.logreg.Rd EMLasso/man/getMinMaxPosLikeGlmnet.Rd EMLasso/man/imputeDs2FitDs.Rd EMLasso/man/lognetProbabilityReusable.Rd EMLasso/man/marginalCompleter.Rd EMLasso/man/outcomeModelValidationReusables.Rd EMLasso/man/plotCoefConvergence.Rd EMLasso/man/postProcessEMLasso.Rd EMLasso/man/postProcessEMLasso1l.Rd EMLasso/man/predictProb.Rd EMLasso/man/predictorModelSamplingReusables.Rd EMLasso/man/retrieveLambdas.Rd EMLasso/man/sampleConditional.Rd EMLasso/man/setDebugmodeEMLasso.Rd EMLasso/man/simplyValidate.Rd EMLasso/man/thresHolding.Rd EMLasso/man/validateFunction.lognet.Rd

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