Ensemble Penalized Cox Regression for Survival Prediction

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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