parseCoxph {gmvjoint}

Parsing the survival formula and constructing all survival-related data objects.

Description

Creates a set of survival data and fits a coxph model using a survival formula and a data set.

Usage

parseCoxph(surv.formula, data, center = TRUE)

Arguments

surv.formula

A formula readable by 'coxph'.

data

a set of data containing covariate information for variables named by ‘surv.formula'. Can be of any ’completeness', as the function returns a reduced set.

center

Should the covariate matrices be mean-centered before being returned? defaults to center = TRUE.

Value

A list with class parseCoxph containing:

survdata

reduced version of data, with only one row per subject, with covariates specified by surv.formula along with survival time and failure status.

Smat

matrix containing all requisite survival covariates (one row per subject).

ph

the model fit from coxph.

Delta

list of failure indicators for each of the unique subjects.

n

number of unique subjects.

ft

vector of unique failure times.

nev

vector containing number of failures at each failure time ft.

survtime

the name of the time variable in surv.formula.

status

the name of the event variable in surv.formula.

Examples

data = simData()$data
parseCoxph(Surv(survtime, status) ~ bin, data = data)