| ePCR-package | Ensemble Penalized Cox Regression Modeling for Overall Survival and Time-to-Event Prediction in Advanced Prostate Cancer |
| 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 |