phreg {eha}R Documentation

Parametric Proportional Hazards Regression

Description

Proportional hazards model with parametric baseline hazard(s). Allows for stratification with different scale and shape in each stratum, and left truncated and right censored data.

Usage

phreg(formula = formula(data), data = parent.frame(),
na.action = getOption("na.action"), dist = "weibull", init, shape = 0,
control = list(eps = 1e-08, maxiter = 20, trace = FALSE),
singular.ok = TRUE, model = FALSE, x = FALSE, y = TRUE, center = TRUE)

Arguments

formula a formula object, with the response on the left of a ~ operator, and the terms on the right. The response must be a survival object as returned by the Surv function.
data a data.frame in which to interpret the variables named in the formula.
na.action a missing-data filter function, applied to the model.frame, after any subset argument has been used. Default is options()$na.action.
dist Which distributin? Default is "weibull", with the alternatives "loglogistic" and "lognormal".
init vector of initial values of the iteration. Default initial value is zero for all variables.
shape If positive, the shape parameter is fixed at that value (in each stratum). If zero or negative, the shape parameter is estimated. If more than one stratum is present in data, each stratum gets its own estimate.
control a list with components eps (convergence criterion), maxiter (maximum number of iterations), and silent (logical, controlling amount of output). You can change any component without mention the other(s).
singular.ok Not used.
model Not used.
x Return the design matrix in the model object?
y Return the response in the model object?
center Should the covariates be centered? Default is TRUE. No correction in parameter estimates is made if centering.

Details

The parameterization is the same as in coxreg and coxph, but different from the one used by survreg. The model is

S(t; a, b, beta, z) = S0((t/b)^a)^exp(z beta)

where S0 is some standardized survivor function.

Value

A list of class c("phreg", "coxreg", "coxph") with components

coefficients Fitted parameter estimates.
var Covariance matrix of the estimates.
loglik Vector of length two; first component is the value at the initial parameter values, the second componet is the maximized value.
score The score test statistic (at the initial value).
linear.predictors The estimated linear predictors.
means Means of the columns of the design matrix.
w.means Weighted (against exposure time) means of covariates; weighted relative frequencies of levels of factors.
n Number of spells in indata (possibly after removal of cases with NA's).
events Number of events in data.
terms Used by extractor functions.
assign Used by extractor functions.
y The Surv vector.
isF Logical vector indicating the covariates that are factors.
covars The covariates.
ttr Total Time at Risk.
levels List of levels of factors.
formula The calling formula.
call The call.
method The method.
convergence Did the optimization converge?
fail Did the optimization fail? (Is NULL if not).
pfixed TRUE if shape was fixed in the estimation.

Warning

The print method print.phreg doesn't work if threeway or higher order interactions are present. Use print.coxph in that case.

Note further that covariates are internally centered, if center = TRUE, by this function, and this is not corrected for in the output. This affects the estimate of \log(scale), but nothing else. If you don't like this, set center = FALSE.

Author(s)

Göran Broström

See Also

coxreg, check.dist, \code{link{aftreg}}.

Examples

data(male.mortality)
fit <- phreg(Surv(enter, exit, event) ~ ses, data = male.mortality)
fit
plot(fit)
fit.cr <- coxreg(Surv(enter, exit, event) ~ ses, data = male.mortality)
check.dist(fit.cr, fit)

[Package eha version 1.2-4 Index]