Cuminc {mstate} | R Documentation |
This function computes nonparametric cumulative incidence functions and associated standard errors for each value of a group variable.
Cuminc(time, status, data, group, failcodes, na.status=c("remove","extra"), variance=TRUE) ## S3 method for class 'Cuminc' print(x, ...) ## S3 method for class 'Cuminc' plot(x, ...) ## S3 method for class 'Cuminc' summary(object, ...)
time |
Either 1) a numeric vector containing the failure times or 2) a string containing the column name indicating these failure times |
status |
Either 1) a numeric, factor or character vector containing the failure codes or 2) a string containing the column name indicating these failure codes |
data |
When appropriate, a data frame containing |
group |
Optionally, name of column in data indicating a
grouping variable; cumulative incidence functions are calculated
for each value or level of |
failcodes |
A vector indicating which values of |
na.status |
One of |
variance |
Logical value, indicating whether the standard errors
of the cumulative incidences should be output ( |
x |
Object of class |
object |
Object of class |
... |
Further arguments to plot or print method |
The estimated cumulative incidences are as described in Putter, Fiocco & Geskus (2007); the standard errors are the square roots of the Greenwood variance estimators, see eg. Andersen, Borgan, Gill & Keiding (1993), de Wreede, Fiocco & Putter (2009), and they correspond to the variances in eg. Marubini & Valsecchi (1995). In case of no censoring, the estimated cumulative incidences and variances reduce to simple binomial frequencies and their variances.
An object of class "Cuminc"
, which is a data frame
containing the estimated failure-free
probabilities and cumulative incidences and their standard errors.
The names of the dataframe are time
, Surv
,
seSurv
, and cuminc
and secuminc
followed by
the values or levels of the failcodes
. If group
was
specified, a group
variable is included with the same name and
values/levels as the original grouping variable, and with estimated
cumulative incidences (SE) for each value/level of group
.
Cuminc is now simply a wrapper around survfit of the survival package
with type="mstate"
, only maintained for backward compatibility.
The survfit object is kept as attribute (attr("survfit")
), and
the print, plot and summary functions are simply print, plot and
summary applied to the survfit object. Subsetting the "Cuminc"
object results in subsetting the data frame, not in subsetting the
survfit object.
Hein Putter H.Putter@lumc.nl
Andersen PK, Borgan O, Gill RD, Keiding N (1993). Statistical Models Based on Counting Processes. Springer, New York.
Marubini E, Valsecchi MG (1995). Analysing Survival Data from Clinical Trials and Observational Studies. Wiley, New York.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
de Wreede L, Fiocco M, Putter H (2009). The mstate package for estimation and prediction in non- and semi-parametric multi-state models. Submitted. www.msbi.nl/multistate.
### These data were used in Putter, Fiocco & Geskus (2007) data(aidssi) ci <- Cuminc(time=aidssi$time, status=aidssi$status) head(ci); tail(ci) ci <- Cuminc(time="time", status="status", data=aidssi, group="ccr5") head(ci); tail(ci) ### Some fake data fake <- data.frame(surv=c(seq(2,10,by=2),seq(1,13,by=3),seq(1,9,by=2),seq(1,13,by=3)), stat=rep(0:3,5),Tstage=c(1:4,rep(1:4,rep(4,4)))) fake$stat[fake$stat==0 & fake$Tstage==2] <- 3 fake$stat[fake$stat==3 & fake$Tstage==1] <- 2 fake Cuminc(time="surv", status="stat", data=fake) # If we remove all entries with status=0, # we should get binomial sample probabilities and corresponding SEs fake0 <- fake[fake$stat!=0,] Cuminc(time="surv", status="stat", data=fake0)