A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

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Documentation for package ‘RCASPAR’ version 1.51.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

RCASPAR-package	A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
Bergamaschi	Gene expression data of 82 patients with 10 genes as covariates
deriv_weight_estimator_BLH	A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms.
deriv_weight_estimator_BLH_noprior	A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms without including the prior on the regression coefficients.
kmplt	Plot Kaplan Meier curve
kmplt_svrl	A function that plots the KM curves of $2-3$ patient sets in one graph.
logrnk	Performs Log Rank test on the long and short patient sets
pltgamma	Plotting the gamma distribution of shape parameter
pltprior	A function to visualize the shape of the prior on the weights with the chosen q and s parameters.
RCASPAR	A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
simpson	A function that calculates the area under a curve based on the Simposon algorithm
STpredictor_BLH	Predicts the survival times of the validation set based on the regression coefficients and baseline hazards determined according to the Piecewise baseline hazard Cox regression model.
STpredictor_xvBLH	This function performs a cross validation on the full data set to help predict the survival times of the patients using the piecewise baseline hazard PH Cox model.
survData	Survial data of 82 patients
survivAURC	A function that calculates the area under a curve constructed from plotting the area under a ROC curve at the corresponding time point at which it was generated.
survivROC	Generates the ROC curve at a given time point given the observed and predicted survival data in the presence of censored subjects.
trapezoid	A function that calculates the area under a curve based on the Simposon algorithm
weights_BLH	Optimization for the regression coefficients and baseline hazards that maximize the partial likelihood in our PW Cox PH regression model.
weights_xvBLH	A special version of STpredictor.BLH used within k-xv to predict the survival times of the kth validation group in the cross validation step.
weight_estimator_BLH	Returns the value of the objective function used for optimizing for the regression parameters and baseline hazards in the model.
weight_estimator_BLH_noprior	Returns the value of the objective function used for optimizing for the regression parameters and baseline hazards in the model, without including the prior on the regression coefficients.