Surv {survival} | R Documentation |
Create a survival object, usually used as a response variable in a model formula. Argument matching is special for this function, see Details below.
Surv(time, time2, event, type=c('right', 'left', 'interval', 'counting', 'interval2', 'mstate'), origin=0) is.Surv(x)
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
|
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, |
type |
character string specifying the type of censoring. Possible values
are |
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. |
When the type
argument is missing the code assumes a type based
on the following rules:
If there are two unnamed arguments, they will match time
and
event
in that order. If there are three unnamed arguments
they match time
, time2
and event
.
If the event variable is a factor then type mstate
is
assumed. Otherwise type right
if there is no time2
argumement, and type counting
if there is.
As a consequence the type
argument can usually 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.
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, t) for left censored, (t, infinity) for right censored, (t,t) for exact and (t1, t2) for an interval. This is the approach used for type = interval2, with NA taking the place of infinity. It has proven to be the more useful.
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
left and right censored data using
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 a 3
is
the code for an event.
For multi-state survival (type= "mstate") the status variable can have multiple levels. The first of these will stand for censoring, and the others for various event types, e.g., causes of death.
Surv objects can be subscripted either as an object, e.g.
x[1:3]
using a single subscript;
in which case the drop
argument is ignored;
or as a matrix, using two arguments.
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.
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.
In the case of is.Surv
, a logical value TRUE
if x
inherits from class "Surv"
, otherwise an FALSE
.
with(lung, Surv(time, status)) Surv(heart$start, heart$stop, heart$event)