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. |