survival: Survmethods – R documentation

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survival

Survmethods

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))).