deriv_weight_estimator_BLH: A function that gives the derivative of the objective...
In RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

Description Usage Arguments Value Note Author(s) References See Also Examples

Given the necessary data, this function calculates the derivative of the objective function without a w.r.t. the baseline hazards and weights(regression coefficients) in the model to be used in gradient-based optimization algorithms.

1	deriv_weight_estimator_BLH(geDataT, survDataT, weights_baselineH, q, s, a, b, groups)

`geDataT`	The co-variate data (gene expression or aCGH, etc...) of the patient set passed on by the user. It is a matrix with the co-variates in the columns and the subjects in the rows. Each cell corresponds to that rowth subject's columnth co-variate's value.
`survDataT`	The survival data of the patient set passed on by the user. It takes on the form of a data frame with at least have the following columns “True_STs” and “censored”, corresponding to the observed survival times and the censoring status of the subjects consecutively. Censored patients are assigned a “1” while patients who experience an event are assigned “1”.
`weights_baselineH`	A single vector with the initial values of the baseline hazards followed by the weights(regression coefficients) for the co-variates.
`q`	One of the two parameters on the prior distribution used on the weights (regression coefficients) in the model.
`s`	The second of the two parameters on the prior distribution used on the weights (regression coefficients) in the model.
`a`	The shape parameter for the gamma distribution used as a prior on the baseline hazards.
`b`	The scale parameter for the gamma distribution used as a prior on the baseline hazards.
`groups`	The number of partitions along the time axis for which a different baseline hazard is to be assigned. This number should be the same as the number of initial values passed for the baseline hazards in the beginning of the “weights\_baselineH” argument.

A vector of the same length as the “weights\_baselineH” argument corresponding to the calculated derivatives of the objective with respect to every component of “weights\_baselineH”.

This function is in itself not ver useful to the user, but is used within the function weights\_BLH

Douaa Mugahid

The basic model is based on the Cox regression model as first introduced by Sir David Cox in: Cox,D.(1972).Regression models & life tables. Journal of the Royal Society of Statistics, 34(2), 187-220. The extension of the Cox model to its stepwise form was adapted from: Ibrahim, J.G, Chen, M.-H. & Sinha, D. (2005). Bayesian Survival Analysis (second ed.). NY: Springer. as well as Kaderali, Lars.(2006) A Hierarchial Bayesian Approach to Regression and its Application to Predicting Survival Times in Cancer Patients. Aachen: Shaker The prior on the regression coefficients was adopted from: Mazur, J., Ritter,D.,Reinelt, G. & Kaderali, L. (2009). Reconstructing Non-Linear dynamic Models of Gene Regulation using Stochastic Sampling. BMC Bioinformatics, 10(448).

weight_estimator_BLH, codederiv_weight_estimator_BLH_noprior

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data(Bergamaschi)
data(survData)        
deriv_weight_estimator_BLH(survDataT=survData[1:10, 9:10], geDataT=Bergamaschi[1:10, 1:2], weights_baselineH=c(0.1,0.2,0.3,rep(0,2)), q=1, s=1, a=1.5, b=0.3, groups=3)