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)
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 time ,
status and/or group variables |
group |
Optionally, name of column in data indicating a
grouping variable; cumulative incidence functions are calculated
for each value or level of group . If missing no groups are
considered |
failcodes |
A vector indicating which values of status are
considered as different causes of failure; other values of status
are considered as censorings. If missing and status is numeric,
it is assumed that 0 is censoring and all other values indicate failcodes;
if missing and status is character or factor, then it is assumed
that each of the levels/values of status is a cause of failure |
na.status |
One of "remove" (default) or "extra" ,
indicating whether subjects with missing cause of failure should be
removed or whether missing cause of failure should be treated as a
separate cause of failure |
variance |
Logical value, indicating whether the standard errors
of the cumulative incidences should be output (TRUE , the default)
or not |
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 (1997). In case of no censoring, the estimated cumulative incidences and variances reduce to simple binomial frequencies and their variances.
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
.
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$stat!=0,] Cuminc(time="surv", status="stat", data=fake0) # Use failcodes Cuminc(time="surv", status="stat", data=fake, failcodes=c(1,3)) # Make grouping variable and status variable a factor fake$Tstage <- factor(fake$Tstage,labels=c("T1","T2","T3","T4")) fake$stat <- factor(fake$stat,levels=0:3, labels=c("eventfree","event1","event2","event3")) Cuminc(time="surv", status="stat", data=fake, group="Tstage") # (The warnings are a result of the fact that some failure causes # do not occur for some values/levels of the grouping variable) # The previous command didn't do what we wanted because we didn't # tell Cuminc that eventfree is not an event Cuminc(time="surv", status="stat", data=fake, group="Tstage", failcodes=c("event1","event2","event3"))