pcoxsurvfit.pcoxtime: Compute survival curve and cumulative hazard from a pcoxtime...

In pcoxtime: Penalized Cox Proportional Hazard Model for Time-Dependent Covariates

Compute survival curve and cumulative hazard from a pcoxtime model

Description

Compute the predicted survivor and cumulative hazard function for a penalized Cox proportional hazard model.

Usage

## S3 method for class 'pcoxtime'
pcoxsurvfit(fit, newdata, ...)

## S3 method for class 'pcoxtime'
pcoxbasehaz(fit, centered = TRUE)

Arguments

fit	fitted pcoxtime object
newdata	a data frame containing the variables appearing on the right hand side of pcoxtime formula.
...	for future implementations
centered	if TRUE (default), return data from a predicted survival function at the mean values of the predictors, if FALSE returns prediction for all predictors equal to zero (baseline hazard).

Details

pcoxsurvfit and pcoxbasehaz functions produce survival curves and estimated cumulative hazard, respectively, for the fitted pcoxtime model. They both return the estimated survival probability and the estimated cumulative hazard, which are both Breslow estimate.

The pcoxbasehaz is an alias for pcoxsurvfit which simply computed the predicted survival estimates (baseline).

If the newdata argument is missing, the "average" survival or cumulative hazard estimates are produced with the predictor values equal to means of the data set. See survfit.coxph for warning against this. If the newdata is specified, then the returned object will contain a matrix of both survival and cumulative hazard estimates with each column for each row in the newdata.

Value

pcoxsurvfit and pcoxbasehaz return S3 objects of class pcoxsurvfit.pcoxtime and pcoxbasehaz.pcoxtime, respectively:

n	number of observations used in the fit.
events	total number of events of interest in the fit.
time	time points defined by the risk set.
n.risk	the number of individuals at risk at time t.
n.event	the number of events that occur at time t.
n.censor	the number of subjects who exit the risk set, without an event, at time t.
surv	a vector or a matrix of estimated survival function.
cumhaz, hazard	a vector or a matrix of estimated cumulative hazard.
call	the call that produced the object.

See Also

pcoxtime, plot.pcoxsurvfit

Examples

data(heart, package="survival")
lam <- 0.1
alp <- 0.8
pfit <- pcoxtime(Surv(start, stop, event) ~ age + year + surgery + transplant
	, data = heart
	, lambda = lam
	, alpha = alp
)

# Survival estimate
psurv <- pcoxsurvfit(pfit)
print(psurv)

# Baseline survival estimate
bsurv <- pcoxbasehaz(pfit, centered = FALSE)

pcoxtime documentation built on May 13, 2022, 1:05 a.m.