estimate_KM {visR} | R Documentation |
Wrapper for Kaplan-Meier Time-to-Event analysis
Description
This function is a wrapper around survival::survfit.formula()
to perform a Kaplan-Meier analysis, assuming right-censored data.
The result is an object of class survfit
which can be used in
downstream functions and methods that rely on the survfit
class.
The function can leverage the conventions and controlled vocabulary from
CDISC ADaM ADTTE data model,
and also works with standard, non-CDISC datasets through the formula
argument.
Usage
estimate_KM(
data = NULL,
strata = NULL,
CNSR = "CNSR",
AVAL = "AVAL",
formula = NULL,
...
)
Arguments
Value
survfit object ready for downstream processing in estimation or visualization functions and methods.
Estimation of 'survfit' object
The estimate_KM()
function utilizes the defaults in survival::survfit()
:
The Kaplan Meier estimate is estimated directly (stype = 1).
The cumulative hazard is estimated using the Nelson-Aalen estimator (ctype = 1): H.tilde = cumsum(x$n.event/x$n.risk). The MLE (H.hat(t) = -log(S.hat(t))) can't be requested.
A two-sided pointwise 0.95 confidence interval is estimated using a log transformation (conf.type = "log").
When strata are present, the returned survfit object is supplemented with the a named list of the stratum and associated label. To support full traceability, the data set name is captured in the named list and the call is captured within its corresponding environment.
PARAM/PARAMCD and CDISC
If the data frame includes columns PARAM/PARAMCD (part of the CDISC format), the function expects the data has been filtered on the parameter of interest.
References
https://github.com/therneau/survival
See Also
Examples
## No stratification
visR::estimate_KM(data = adtte)
## Stratified Kaplan-Meier analysis by `TRTP`
visR::estimate_KM(data = adtte, strata = "TRTP")
## Stratified Kaplan-Meier analysis by `TRTP` and `SEX`
visR::estimate_KM(data = adtte, strata = c("TRTP", "SEX"))
## Stratification with one level
visR::estimate_KM(data = adtte, strata = "PARAMCD")
## Analysis on subset of adtte
visR::estimate_KM(data = adtte[adtte$SEX == "F", ])
## Modify the default analysis by using the ellipsis
visR::estimate_KM(
data = adtte, strata = NULL,
type = "kaplan-meier", conf.int = FALSE, timefix = TRUE
)
## Example working with non CDISC data
head(survival::veteran[c("time", "status", "trt")])
# Using non-CDSIC data
visR::estimate_KM(data = survival::veteran, formula = Surv(time, status) ~ trt)