Survmethods: Methods for Surv objects

In survival: Survival Analysis

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.matrix(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, na.rm=FALSE, ...)
    ## 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. (There is no central index of R methods, so there may well be useful candidates that the author has missed.) 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 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, 5:8, 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 xtfrm method, which underlies sort and order, sorts by time, with censored after uncensored within a tied time. For an interval censored observation the midpoint is used. For (time1, time2) counting process data, sorting is by time2, censoring, and then time1.

• The unique method treats censored and uncensored observations at the same time as distinct, it returns a Surv object.

• The concatonation method c() is asymmetric, its first argument determines the execution path. For instance c(Surv(1:4), Surv(5:6)) will return a Surv object of length 6, 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))) which is a numeric of length 10.

See Also

Surv

survival documentation built on June 22, 2024, 10:49 a.m.