R: Methods for Surv objects

Surv-methods {survival} | R Documentation

## Methods for Surv objects

### Description

The list of methods that apply to `Surv` objects

### Usage

        ## S3 method for class 'Surv'
    anyDuplicated(x, ...)
        ## S3 method for class 'Surv'
    as.character(x, ...)
        ## S3 method for class 'Surv'
    as.data.frame(x, ...)
        ## S3 method for class 'Surv'
    as.integer(x, ...)
        ## S3 method for class 'Surv'
    as.matrix(x, ...)
        ## S3 method for class 'Surv'
    as.numeric(x, ...)
        ## S3 method for class 'Surv'
    c(...)
        ## S3 method for class 'Surv'
    duplicated(x, ...)
        ## S3 method for class 'Surv'
    format(x, ...)
        ## S3 method for class 'Surv'
    head(x, ...)
        ## S3 method for class 'Surv'
    is.na(x)
        ## S3 method for class 'Surv'
    length(x)
        ## S3 method for class 'Surv'
    mean(x, ...)
        ## S3 method for class 'Surv'
    median(x, ...)
        ## S3 method for class 'Surv'
    names(x)
        ## S3 replacement method for class 'Surv'
    names(x) <- value
        ## S3 method for class 'Surv'
    quantile(x, probs, na.rm=FALSE, ...)
        ## S3 method for class 'Surv'
    plot(x, ...)
        ## S3 method for class 'Surv'
    rep(x, ...)
        ## S3 method for class 'Surv'
    rep.int(x, ...)
        ## S3 method for class 'Surv'
    rep_len(x, ...)
        ## S3 method for class 'Surv'
    rev(x)
        ## S3 method for class 'Surv'
    t(x)
        ## S3 method for class 'Surv'
    tail(x, ...)
        ## S3 method for class 'Surv'
    unique(x, ...)

### Arguments

`x` | a `Surv` object
`probs` | a vector of probabilities
`na.rm` | remove missing values from the calculation
`value` | a character vector of up to the same length as `x`, or `NULL`
`...` | other arguments to the method

### Details

These functions extend the standard methods to `Surv` objects. The arguments and results from these are mostly as expected, with the following further details:

- The `as.character` function uses "5+" for right censored at time 5, "5-" for left censored at time 5, "[2,7]" for an observation that was interval censored between 2 and 7, "(1,6]" for a counting process data denoting an observation which was at risk from time 1 to 6, with an event at time 6, and "(1,6+]" for an observation over the same interval but not ending with and event. For a multi-state survival object the type of event is appended to the event time using ":type".

- The `print` and `format` methods make use of `as.character`.

- The `as.numeric` and `as.integer` methods perform these actions on the survival times, but do not affect the censoring indicator.

- The `as.matrix` and `t` methods return a matrix

- The `length` of a `Surv` object is the number of survival times it contains, not the number of items required to encode it, e.g., `x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x)` has a value of 4. Likewise `names(x)` will be NULL or a vector of length 4. (For technical reasons, any names are actually stored in the `rownames` attribute of the object.)

- For a multi-state survival object `levels` returns the names of the endpoints, otherwise it is NULL.

- The `median`, `quantile` and `plot` methods first construct a survival curve using `survfit`, then apply the appropriate method to that curve.

- The concatonation method `c()` is asymmetric, its first argument determines the exection path. For instance `c(Surv(1:4), Surv(5:6))` will concatonate the two objects, `c(Surv(1:4), 5:6)` will give an error, and `c(5:6, Surv(1:4))` is equivalent to `c(5:6, as.vector(Surv(1:4)))`.

### See Also

`Surv`

[Package survival version 3.2-7 Index]