DREAM                   FIMM-UTU DREAM winning implementation of an
                        ensemble of Penalized Cox Regression models for
                        mCPRC research (ePCR)
NelsonAalen             Cox-Oakes extension of the Nelson-Aalen
                        estimates for a Cox model
PEP-class               Penalized Ensemble Predictor (PEP) S4-class
                        ensemble consisting of individual PSP-members
PEP-methods             PEP-methods
PSP-class               Penalized Single Predictor (PSP) S4-class as a
                        member of PEP-ensembles
PSP-methods             PSP-methods
TYKS                    ePCR model fitted to the Turku University
                        Hospital cohorts (all features)
TYKSSIMU                TYKSSIMU - simulated data matrices and survival
                        responses from Turku University Hospital
TYKS_reduced            ePCR model fitted to the Turku University
                        Hospital cohorts (features derived from text
                        mining only)
TimeSurvProb            Predict cumulative survival probabilities for
                        new data at given time points
bootstrapRegCoefs       Bootstrapped testing of regression coefficients
                        in a penalized model
conforminput            Conform the dimensions of a new input data
                        matrix to a readily fitted PEP or PSP object
cv                      Function that creates customized
                        cross-validation folds
cv.alpha                Cross-validation runs for risk predition at a
                        single value of alpha
cv.grid                 Cross-validation runs for risk predition for a
                        grid of predetermined alpha values and their
                        conditional lambda values
ePCR                    Ensemble Penalized Cox Regression Modeling for
                        Overall Survival and Time-to-Event Prediction
                        in Advanced Prostate Cancer
heatcv                  Plot a heatmap of the prediction performance
                        statistic as a function of lambda and alpha
                        combinations
integrateRegCurve       Integrate the area over/under the
                        regularization path of a penalized regression
                        model
interact.all            Compute all pairwise interactions between the
                        columns of a data matrix
interact.part           Compute a chosen set of pairwise interactions
                        between two sets of columns in a data matrix
meanrank                Compute mean of predicted risk ranks for an
                        ePCR ensemble
normriskrank            Normalize ensemble risk scores to ranks and
                        then to uniform range
score.cindex            Scoring function for evaluating survival
                        prediction through concordance index (c-index)
score.iAUC              Scoring function for evaluating survival
                        prediction by time-wise integrated AUC
zt                      Extended function for z-transformation, filling
                        non-finite values and changes column names at
                        will
