Surv {survival}R Documentation

Create a Survival Object

Description

Create a survival object, usually used as a response variable in a model formula. Argument matching is special for this function, see Details below.

Usage

Surv(time, time2, event,
    type=c('right', 'left', 'interval', 'counting', 'interval2', 'mstate'),
    origin=0)
is.Surv(x)

Arguments

time

for right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.

event

The status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death). For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored. For multiple endpoint data the event variable will be a factor, whose first level is treated as censoring. Although unusual, the event indicator can be omitted, in which case all subjects are assumed to have an event.

time2

ending time of the interval for interval censored or counting process data only. Intervals are assumed to be open on the left and closed on the right, (start, end]. For counting process data, event indicates whether an event occurred at the end of the interval.

type

character string specifying the type of censoring. Possible values are "right", "left", "counting", "interval", "interval2" or "mstate".

origin

for counting process data, the hazard function origin. This option was intended to be used in conjunction with a model containing time dependent strata in order to align the subjects properly when they cross over from one strata to another, but it has rarely proven useful.

x

any R object.

Details

When the type argument is missing the code assumes a type based on the following rules:

As a consequence the type argument will normally be omitted.

When the survival type is "mstate" then the status variable will be treated as a factor. The first level of the factor is taken to represent censoring and remaining ones a transition to the given state. (If the status variable is a factor then mstate is assumed.)

Interval censored data can be represented in two ways. For the first use type = "interval" and the codes shown above. In that usage the value of the time2 argument is ignored unless event=3. The second approach is to think of each observation as a time interval with (-infinity, t2) for left censored, (t1, infinity) for right censored, (t,t) for exact and (t1, t2) for an interval. This is the approach used for type = interval2. Infinite values can be represented either by actual infinity (Inf) or NA. The second form has proven to be the more useful one.

Presently, the only methods allowing interval censored data are the parametric models computed by survreg and survival curves computed by survfit; for both of these, the distinction between open and closed intervals is unimportant. The distinction is important for counting process data and the Cox model.

The function tries to distinguish between the use of 0/1 and 1/2 coding for censored data via the condition if (max(status)==2). If 1/2 coding is used and all the subjects are censored, it will guess wrong. In any questionable case it is safer to use logical coding, e.g., Surv(time, status==3) would indicate that '3' is the code for an event. For multi-state survival the status variable will be a factor, whose first level is assumed to correspond to censoring.

Surv objects can be subscripted either as a vector, e.g. x[1:3] using a single subscript, in which case the drop argument is ignored and the result will be a survival object; or as a matrix by using two subscripts. If the second subscript is missing and drop=F (the default), the result of the subscripting will be a Surv object, e.g., x[1:3,,drop=F], otherwise the result will be a matrix (or vector), in accordance with the default behavior for subscripting matrices.

Value

An object of class Surv. There are methods for print, is.na, and subscripting survival objects. Surv objects are implemented as a matrix of 2 or 3 columns that has further attributes. These include the type (left censored, right censored, counting process, etc.) and labels for the states for multi-state objects. Any attributes of the input arguments are also preserved in inputAttributes. This may be useful for other packages that have attached further information to data items such as labels; none of the routines in the survival package make use of these values, however.

In the case of is.Surv, a logical value TRUE if x inherits from class "Surv", otherwise an FALSE.

Note

The use of 1/2 coding for status is an interesting historical artifact. For data contained on punch cards, IBM 360 Fortran treated blank as a zero, which led to a policy within the Mayo Clinic section of Biostatistics to never use "0" as a data value since one could not distinguish it from a missing value. Policy became habit, as is often the case, and the use of 1/2 coding for alive/dead endured long after the demise of the punch cards that had sired the practice. At the time Surv was written many Mayo data sets still used this obsolete convention, e.g., the lung data set found in the package.

See Also

coxph, survfit, survreg, lung.

Examples

with(aml, Surv(time, status))
survfit(Surv(time, status) ~ ph.ecog, data=lung)
Surv(heart$start, heart$stop, heart$event)
[Package survival version 3.8-3 Index]