# Ensemble Penalized Cox Regression for Survival Prediction

## Documentation for package ‘ePCR’ version 0.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bootstrapRegCoefs | Bootstrapped testing of regression coefficients in a penalized model
coef-method | PSP-methods
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
DREAM | FIMM-UTU DREAM winning implementation of an ensemble of Penalized Cox Regression models for mCPRC research (ePCR)
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
NelsonAalen | Cox-Oakes extension of the Nelson-Aalen estimates for a Cox model
normriskrank | Normalize ensemble risk scores to ranks and then to uniform range
PEP-class | Penalized Ensemble Predictor (PEP) S4-class ensemble consisting of individual PSP-members
PEP-methods | PEP-methods
plot | PSP-methods
plot-method | PSP-methods
predict-method | PEP-methods
predict-method | PSP-methods
print-method | PEP-methods
print-method | PSP-methods
PSP-class | Penalized Single Predictor (PSP) S4-class as a member of PEP-ensembles
PSP-methods | PSP-methods
PSP.BOX | PSP-methods
PSP.BOX-method | PSP-methods
PSP.CSP | PSP-methods
PSP.CSP-method | PSP-methods
PSP.KM | PSP-methods
PSP.KM-method | PSP-methods
PSP.NA | PSP-methods
PSP.NA-method | PSP-methods
PSP.PCA | PSP-methods
PSP.PCA-method | PSP-methods
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
TimeSurvProb | Predict cumulative survival probabilities for new data at given time points
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)
xMEDISIMU | TYKSSIMU - simulated data matrices and survival responses from Turku University Hospital
xTEXTSIMU | TYKSSIMU - simulated data matrices and survival responses from Turku University Hospital
yMEDISIMU | TYKSSIMU - simulated data matrices and survival responses from Turku University Hospital
yTEXTSIMU | TYKSSIMU - simulated data matrices and survival responses from Turku University Hospital
zt | Extended function for z-transformation, filling non-finite values and changes column names at will