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

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