survival: agreg.fit – R documentation

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agreg.fit

Cox model fitting functions

Description

These are the the functions called by coxph that do the actual computation. In certain situations, e.g. a simulation, it may be advantageous to call these directly rather than the usual coxph call using a model formula.

Usage

agreg.fit(x, y, strata, offset, init, control, weights, method,
rownames, resid=TRUE, nocenter=NULL)
coxph.fit(x, y, strata, offset, init, control, weights, method,
rownames, resid=TRUE, nocenter=NULL)

Arguments

`x`	Matix of predictors. This should not include an intercept.
`y`	a `Surv` object containing either 2 columns (coxph.fit) or 3 columns (agreg.fit).
`strata`	a vector containing the stratification, or NULL
`offset`	optional offset vector
`init`	initial values for the coefficients
`control`	the result of a call to `coxph.control`
`weights`	optional vector of weights
`method`	method for hanling ties, one of "breslow" or "efron"
`rownames`	this is only needed for a NULL model, in which case it contains the rownames (if any) of the original data.
`resid`	compute and return residuals.
`nocenter`	an optional list of values. Any column of the X matrix whose values lie strictly within that set will not be recentered. Note that the coxph function has (-1, 0, 1) as the default.

Details

This routine does no checking that arguments are the proper length or type. Only use it if you know what you are doing!

The resid and concordance arguments will save some compute time for calling routines that only need the likelihood, the generation of a permutation distribution for instance.

Value

a list containing results of the fit

Author(s)

Terry Therneau