Sepsis.test             Sepsis Trial testing dataset
Sepsis.train            Sepsis Trial training dataset
SubgrpID                Exploratory Subgroup Identification main
                        function
SubgrpID-package        Patient subgroup identification for clinical
                        drug development
aim.batting             The main AIM-BATTing function
aim.batting.wrapper     Wrapper function for cv.aim.batting to be
                        passed to kfold.cv.
aim.rule.batting        The main AIM-Rule-BATTing function
aim.rule.batting.wrapper
                        Wrapper function for aim.rule.batting, to be
                        passed to kfold.cv
aim.score.pred          Find score of cutoff (returned by
                        aim.find.cutoff.pred) for predictive case.
aim.score.prog          Find score of cutoff (returned by
                        aim.find.cutoff.pred) for prognostic case.
backfit.cox.interaction
                        An internal function used in cox.interaction
balanced.folds          Create balanced folds for cross-validation.
batting.pred            Main predictive BATTing function
batting.prog            Main prognostic BATTing function
binary.stats            A function for binary statistics
combine.condition       Internal function
cox.interaction         Interaction Cox AIM
create.training.dataset.index
                        create training/testing dataset indexes.
cv.aim.batting          The function for CV in aim.batting
cv.aim.rule.batting     The function for CV in aim.rule.batting
cv.cox.interaction      A function for CV in Cox AIM with interaction.
cv.cox.main             A function for the number of binary rules in
                        the main effect AIM with time to event outcome
cv.folds                Cross-validation folds.
cv.lm.interaction       A function for CV in linear AIM with
                        interaction.
cv.lm.main              A function for the number of binary rules in
                        the main effect AIM with continuous outcome
cv.logistic.interaction
                        A function for CV in logistic AIM with
                        interaction.
cv.logistic.main        A function for the number of binary rules in
                        the main effect AIM with binary outcome
cv.pval                 p-value calculation for each iteration of cross
                        validation.
cv.seqlr.batting        Cross Validation for Sequential BATTing
evaluate.cv.results     Cross-validation Performance Evaluation
evaluate.results        Get statistics for a single set of predictions.
filter                  Filter function for predictive/prognostic
                        biomarker candidates for signature development
filter.glmnet           Flitering using MC glmnet
filter.unicart          rpart filtering (only for prognostic case)
filter.univariate       Univariate Filtering
find.pred.stats         Find predictive stats from response and
                        prediction vector
find.prog.stats         Find prognostic stats from response and
                        prediction vector
get.var.counts.aim      Get counts of signature variables from output
                        of cv.aim.batting.
get.var.counts.seq      Get signature variables from output of
                        seqlr.batting.
interaction.plot        A function for interaction plot
kfold.cv                Perform k-fold cross-validation of a model.
make.arg.list           Create a list of variables corresponding to the
                        arguments of the function func.name and assigns
                        values.
one.dropping            Perform dropping one time in predictive case.
one.dropping.prog       Perform dropping one time in prognostic case.
one.pasting             Perform pasting one time in predictive case.
one.pasting.prog        Perform pasting one time in prognostic case.
one.peeling             Perform peeling one time in predictive case.
one.peeling.prog        Perform peeling one time in prognostic case.
permute.rows            Ramdomly permute the rows of a matrix.
permute.vector          Randomly permute the entries of a vector.
pred.aim                Make predictions for data given prediction rule
                        in predict.rule.
pred.aim.cv             Make predictions for data given prediction rule
                        in predict.rule
pred.prim               Prediction function for PRIM
pred.prim.cv            Prediction function for PRIM CV
pred.seqlr              Prediction function for Sequential BATTing
pred.seqlr.cv           Prediction function for CV Sequential BATTing
prim.cv                 Cross-validation for PRIM
prim.train              The main PRIM function
prim.train.pred.once    Apply PRIM one time on the training data for a
                        fixed value of alpha in predictive case
prim.train.prog.once    Apply PRIM one time on the training data for a
                        fixed value of alpha (in prognostic case)
prim.train.wrapper      Wrapper function for PRIM CV
pval.cal                Calculate p-value for treatment in each
                        subgroup in predictive case
pval.cal.prog           Calculate p-value for treatment in each
                        subgroup in prognostic case
query.data              internal function used in seqlr.batting
query.from.condition    An internal function inside one.pasting.
resample                Creates a permutation of given size.
seqlr.batting           Perform sequential BATTing method.
seqlr.batting.wrapper   Wrapper function for seqlr.batting, to be
                        passed to kfold.cv.
seqlr.find.cutoff.pred
                        Find cutoff for predictive case.
seqlr.find.cutoff.prog
                        Find cutoff for prognostic case.
seqlr.score.pred        Compute score of cutoff for predictive case
seqlr.score.prog        Compute score of cutoff for prognostic case
summarize.cv.stats      Calculate summary statistics from raw
                        statistics returned by evaluate.cv.results.
