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

survfitcoxph.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

    survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype,
    vartype, varmat, id, y2, strata2, unlist=TRUE)

### Arguments

`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.
`x2` | matrix describing the hypothetical subjects for which a curve is desired. Must have the same number of columns as `x`.
`risk` | the risk score exp(X beta) from the fitted Cox model. If the model had an offset, include it in the argument to exp.
`newrisk` | risk scores for the hypothetical subjects
`strata` | strata variable used in the Cox model. This will be a factor.
`se.fit` | if `TRUE` the standard errors of the curve(s) are returned
`survtype` | 1=Kalbfleisch-Prentice, 2=Nelson-Aalen, 3=Efron. It is usual to match this to the approximation for ties used in the `coxph` model: KP for ‘exact’, N-A for ‘breslow’ and Efron for ‘efron’.
`vartype` | 1=Greenwood, 2=Aalen, 3=Efron
`varmat` | the variance matrix of the coefficients
`id` | optional; if present and not NULL this should be a vector of identifiers of length `nrow(x2)`. A mon-null value signifies that `x2` contains time dependent covariates, in which case this identifies which rows of `x2` go with each subject.
`y2` | survival times, for time dependent prediction. It gives the time range (time1,time2] for each row of `x2`. Note: this must be a Surv object and thus contains a status indicator, which is never used in the routine, however.
`strata2` | vector of strata indicators for `x2`. This must be a factor.
`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]