decomposeSurv {coxphf}R Documentation

Decompose A Survival Formula

Description

Decompose a Surv formula which can have time-dependent effects and return the model matrix and the time function matrix.

Usage

decomposeSurv(formula, data, sort)

Arguments

formula A formula with Surv on the left-handed side and an arbitrary part on the right-handed side, including possibly time-dependent effects, e.g. Surv(time, event) ~ x1 * x2 + I(x3^2) + x1 * log(time).
data The data.frame with the columns needed to extract the formula.
sort If TRUE, the returned model matrizes are sorted by stoptime and event.

Details

This function is mainly a helper function for coxphf, coxphftest and coxphfplot.

Value

NTDE The number of time dependent effects.
fac The factor matrix, see the value of terms.
resp N x 3 - response matrix, see model.extract with parameter response.
mm1 Model matrix without time effects.
timedata Matrix with time functions as columns.
timeind Indicator of time-dependent effect: the i-th column of timedata interacts with the timeind[i]-th column of mm1.
covnames The names of the covariates.
ind An indicator vector. Elements with FALSE mean that these covnames are not part of the formula, but are needed to span a coherent model frame.

Author(s)

Meinhard Ploner, Georg Heinze

References

Heinze, G. and Schemper, M. (2001). A Solution to the Problem of Monotone Likelihood in Cox Regression. Biometrics 57/1, 114-119.

Heinze, G. (1999). Technical Report 10/1999: The application of Firth's procedure to Cox and logistic regression. Section of Clinical Biometrics, Department of Medical Computer Sciences, University of Vienna, Vienna.

Ploner, M. and Heinze, G. (2001). Technical Report 1/2001: An SPLUS library to perform Cox regression without convergence problems. Section of Clinical Biometrics, Department of Medical Computer Sciences, University of Vienna, Vienna.

Heinze, G. and Ploner, M. (2002). SAS and SPLUS programs to perform Cox regression without convergence problems. Computer Methods and Programs in Biomedicine 67, 217-223.

Examples

## prepares matrices for a model with time-dependent effects 
test3 <- data.frame(list(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8),
                         stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17),
                         event=c(1, 0, 0, 1, 0, 1, 1, 0, 0, 0),
                         x    =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) ))
                         
decomposeSurv(Surv(start,stop,event) ~ x + x * log(stop), data=test3)

[Package coxphf version 1.0-2 Index]