R: A direct interface to the 'computational engine' of...

coxsurv.fit {survival} | R Documentation

## A direct interface to the ‘computational engine’ of survfit.coxph

### Description

This program is mainly supplied to allow other packages to invoke the survfit.coxph function at a ‘data’ level rather than a ‘user’ level. It does no checks on the input data that is provided, which can lead to unexpected errors if that data is wrong.

### Usage

    coxsurv.fit(ctype, stype, se.fit, varmat, cluster,
                y, x, wt, risk, position, strata, oldid,
                y2, x2, risk2, strata2, id2, unlist=TRUE)

### Arguments

`stype` | survival curve computation: 1=direct, 2=exp(-cumulative hazard)
`ctype` | cumulative hazard computation: 1=Breslow, 2=Efron
`se.fit` | if TRUE, compute standard errors
`varmat` | the variance matrix of the coefficients
`cluster` | vector to control robust variance
`y` | the response variable used in the Cox model. (Missing values removed of course.)
`x` | covariate matrix used in the Cox model
`wt` | weight vector for the Cox model. If the model was unweighted use a vector of 1s.
`risk` | the risk score exp(X beta + offset) from the fitted Cox model.
`position` | optional argument controlling what is counted as 'censored'. Due to time dependent covariates, for instance, a subject might have start, stop times of (1,5)(5,30)(30,100). Times 5 and 30 are not 'real' censorings. Position is 1 for a real start, 2 for an actual end, 3 for both, 0 for neither.
`strata` | strata variable used in the Cox model. This will be a factor.
`oldid` | identifier for subjects with multiple rows in the original data.
`y2, x2, risk2, strata2` | variables for the hypothetical subjects, for which prediction is desired
`id2` | optional; if present and not NULL this should be a vector of identifiers of length `nrow(x2)`. A non-null value signifies that `x2` contains time dependent covariates, in which case this identifies which rows of `x2` go with each subject.
`unlist` | if `FALSE` the result will be a list with one element for each strata. Otherwise the strata are “unpacked” into the form found in a `survfit` object.

### Value

a list containing nearly all the components of a `survfit` object. All that is missing is to add the confidence intervals, the type of the original model's response (as in a coxph object), and the class.

### Note

The source code for for both this function and `survfit.coxph` is written using noweb. For complete documentation see the `inst/sourcecode.pdf` file.

### Author(s)

Terry Therneau

### See Also

`survfit.coxph`

[Package survival version 3.2-7 Index]