Computes the predicted survivor function for a Cox proportional hazards model.
# S3 method for coxph
survfit(formula, newdata,
se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,
conf.type=c("log","log-log","plain","none", "logit", "arcsin"),
censor=TRUE, start.time, id, influence=FALSE,
na.action=na.pass, type, ...)A coxph object.
a data frame with the same variable names as those that appear
in the coxph formula. It is also valid to use a vector, if
the data frame would consist of a single row.
The curve(s) produced will be representative of a cohort whose
covariates correspond to the values in newdata.
Default is the mean of the covariates used in the
coxph fit.
a logical value indicating whether standard errors should be
computed. Default is TRUE.
the level for a two-sided confidence interval on the survival curve(s). Default is 0.95.
depricated argument, replaced by the general
id
computation of the survival curve, 1=direct, 2= exponenial of the cumulative hazard.
whether the cumulative hazard computation should have a correction for ties, 1=no, 2=yes.
One of "none", "plain", "log" (the default),
"log-log" or "logit". Only
enough of the string to uniquely identify it is necessary.
The first option causes confidence intervals not to be
generated. The second causes the standard intervals
curve +- k *se(curve), where k is determined from
conf.int. The log option calculates intervals based on the
cumulative hazard or log(survival). The log-log option uses
the log hazard or log(-log(survival)), and the logit
log(survival/(1-survival)).
if FALSE time points at which there are no events (only censoring) are not included in the result.
optional variable name of subject identifiers. If this is
present, it will be search for in the newdata data frame.
Each group of rows in newdata with the same subject id represents
the covariate path through time of a single subject, and the result
will contain one curve per subject. If the coxph fit had
strata then that must also be specified in newdata.
If newid is not present, then each
individual row of newdata is presumed to represent a distinct
subject.
optional starting time, a single numeric value.
If present the returned curve contains survival after
start.time conditional on surviving to start.time.
option to return the influence values
the na.action to be used on the newdata argument
older argument that encompassed stype and
ctype, now depricated
for future methods
an object of class "survfit".
See survfit.object for
details. Methods defined for survfit objects are
print, plot,
lines, and points.
If the following pair of lines is used inside of another function then
the model=TRUE argument must be added to the coxph call:
fit <- coxph(...); survfit(fit).
This is a consequence of the non-standard evaluation process used by the
model.frame function when a formula is involved.
This routine produces Pr(state) curves based on a coxph
model fit. For single state models it produces the single curve for
S(t) = Pr(remain in initial state at time t), known as the survival
curve; for multi-state models a matrix giving probabilities for all states.
The stype argument states the type of estimate, and defaults
to the exponential of the cumulative hazard, better known as the Breslow
estimate. For a multi-state Cox model this involves the exponential
of a matrix.
The argument stype=1 uses a non-exponential or `direct'
estimate. For a single endpoint coxph model the code evaluates the
Kalbfleich-Prentice estimate, and for a multi-state model it uses an
analog of the Aalen-Johansen estimator. The latter approach is the
default in the mstate package.
The ctype option affects the estimated cumulative hazard, and
if stype=2 the estimated P(state) curves as well. If not
present it is chosen so as to be concordant with the
ties option in the coxph call. (For multistate
coxphms objects only ctype=1 is currently implemented.)
Likewise
the choice between a model based and robust variance estimate for the
curve will mirror the choice made in the coxph call,
any clustering is also inherited from the parent model.
If the newdata argument is missing, then a curve is produced
for a single "pseudo" subject with
covariate values equal to the means of the data set.
The resulting curve(s) almost never make sense, but
The default remains due to an unwarranted attachment to the option shown by
some users and by other packages. Two particularly egregious examples
are factor variables and interactions. Suppose one were studying
interspecies transmission of a virus, and the data set has a factor
variable with levels ("pig", "chicken") and about equal numbers of
observations for each. The ``mean'' covariate level will be 0.5 --
is this a flying pig? As to interactions assume data with sex coded as 0/1,
ages ranging from 50 to 80, and a model with age*sex. The ``mean''
value for the age:sex interaction term will be about 30, a value
that does not occur in the data.
Users are strongly advised to use the newdata argument.
For these reasons predictions from a multistate coxph model require
the newdata argument.
When the original model contains time-dependent covariates, then the
path of that covariate through time needs to be specified in order to
obtain a predicted curve. This requires newdata to contain
multiple lines for each hypothetical subject which gives the covariate
values, time interval, and strata for each line (a subject can change
strata), along with an id variable
which demarks which rows belong to each subject.
The time interval must have the same (start, stop, status)
variables as the original model: although the status variable is not
used and thus can be set to a dummy value of 0 or 1, it is necessary for
the response to be recognized as a Surv object.
Last, although predictions with a time-dependent covariate path can be
useful, it is very easy to create a prediction that is senseless. Users
are encouraged to seek out a text that discusses the issue in detail.
When a model contains strata but no time-dependent covariates the user of this routine has a choice. If newdata argument does not contain strata variables then the returned object will be a matrix of survival curves with one row for each strata in the model and one column for each row in newdata. (This is the historical behavior of the routine.) If newdata does contain strata variables, then the result will contain one curve per row of newdata, based on the indicated stratum of the original model. In the rare case of a model with strata by covariate interactions the strata variable must be included in newdata, the routine does not allow it to be omitted (predictions become too confusing). (Note that the model Surv(time, status) ~ age*strata(sex) expands internally to strata(sex) + age:sex; the sex variable is needed for the second term of the model.)
See survfit for more details about the counts (number of
events, number at risk, etc.)
Fleming, T. H. and Harrington, D. P. (1984). Nonparametric estimation of the survival distribution in censored data. Comm. in Statistics 13, 2469-86.
Kalbfleisch, J. D. and Prentice, R. L. (1980). The Statistical Analysis of Failure Time Data. New York:Wiley.
Link, C. L. (1984). Confidence intervals for the survival function using Cox's proportional hazards model with covariates. Biometrics 40, 601-610.
Therneau T and Grambsch P (2000), Modeling Survival Data: Extending the Cox Model, Springer-Verlag.
Tsiatis, A. (1981). A large sample study of the estimate for the integrated hazard function in Cox's regression model for survival data. Annals of Statistics 9, 93-108.
print.survfit,
plot.survfit,
lines.survfit,
coxph,
Surv,
strata.