| 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'),
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
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.
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", or "interval2". The default is
"right" or "counting" depending on whether the
time2 argument is absent or present, respectively.
|
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. |
Typical usages are
Surv(time, event) Surv(time, time2, event, type= )The
time,time2 and event arguments are matched by
position, not by name, so use, eg, Surv(time, dead) rather than
Surv(time, event=dead)
In theory it is possible to represent interval censored data without a third column containing the explicit status. Exact, right censored, left censored and interval censored observation would be represented as intervals of [a,a], (a, infinity), (-infinity,b), and [a,b] respectively; each interval is a pair of time points within which the event is known to have occurred.
If type="interval2" then the representation given above is
assumed, with NA taking the place of infinity.
If type="interval" then event must be given.
If event is 0, 1, or 2,
the relevant
information is assumed to be contained in time,
the value in time2 is ignored,
and the second column of the internal representation contains a
placeholder value.
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.
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)