Hist {prodlim} | R Documentation |
Functionality for managing censored
event history response data. The function can be used as
the left hand side of a formula:
Hist
serves prodlim
in a similar way as Surv
from the survival package
serves `survfit'.
Hist
provides the suitable extensions for dealing with right
censored and interval censored
data from competing risks and
other multi state models. Objects generated with Hist
have a print and a plot
method.
Hist(time, event, id = NULL, cens.code = "0")
time |
for right censored data a numeric vector of event times –
for interval censored data a list or a data.frame providing two
numeric vectors the left and right endpoints of the intervals.
See Details .
|
event |
A vector or a factor that
specifies the events that occurred
at the corresponding value of time . Numeric,
character and logical values are recognized.
It can also be a list or a data.frame for the longitudinal
form of storing the data of a multi state model – see
Details .
|
id |
Identifies the subjects to which multiple events belong
for the longitudinal
form of storing the data of a multi state model – see
Details .
|
cens.code |
A character or numeric vector to identify the right censored
observations in the
values of event .
Defaults to "0" which is equivalent to 0.
|
*Specification of the event times*
If time
is a numeric vector then the values are interpreted as
right censored event times, ie as the
minimum of the event times and the censoring times.
If time
is
a list with two elements or data frame with two numeric columns
The first element (column) is used as the left
endpoints of interval censored
observations and the second as the corresponding right endpoints.
When the two endpoints are equal, then this observation is treated as
an exact uncensored observation of
the event time.
If the value of the right interval endpoint is
either NA
or Inf
, then this observation is treated as a right
censored observation. Right censored observations can also be specified
by setting the value of event
to cens.code
.
This latter specification of right censored event times overwrites
the former: if event
equals cens.code
the observation
is treated as right censored no matter what the value of the right
interval endpoint is.
*Specification of the events*
If event
is a numeric, character or logical vector then
the order of the attribute "state" given to the value
of
Hist
is
determined by the order in which the values appear.
If it is a factor then the order
from the levels of the factor is used instead.
**Normal form of a multi state model**
If event
is a list or a data.frame
with exactly two elements,
then these describe the transitions in a multi state model
that occurred at the corresponding time
as follows:
The values of the first element are interpreted as the
from
states of the transition and values of the second
as the corresponding to
states.
**Longitudinal form of a multi state model**
If id
is given then event
must be a vector. In this
case two subsequent values of event
belonging to the same
value of id
are treated as the from
and to
states of the transitions.
An object of class Hist
for which there are print and plot methods.
The object's internal is a matrix with some of the following columns:
time |
the right censored times |
L |
the left endpoints of internal censored event times |
R |
the right endpoints of internal censored event times |
status |
0 for right censored, 1 for exact, and 2 for interval censored event times. |
event |
an integer valued numeric vector that codes the events. |
from |
an integer valued numeric vector that codes the from states of a transition in a multi state model. |
to |
an integer valued numeric vector that codes the to states of a transition in a multi state model. |
Further information is stored in attributes
.
The key to the official names given to the events and the from and to states
is stored in an attribute "states".
Thomas A. Gerds tag@biostat.ku.dk
plot.Hist
, summary.Hist
, prodlim
## Right censored responses of a two state model ## --------------------------------------------- Hist(time=1:10,event=c(0,1,0,0,0,1,0,1,0,0)) ## change the code for events and censored observations Hist(time=1:10,event=c(99,"event",99,99,99,"event",99,"event",99,99),cens.code=99) TwoStateFrame <- data.frame(time=rlnorm(100),status=rbinom(100,1,.5)) SurvHist <- with(TwoStateFrame,Hist(time,status)) summary(SurvHist) plot(SurvHist) ## Right censored data from a competing risk model ## -------------------------------------------------- CompRiskFrame <- data.frame(time=1:10,event=c(1,2,0,3,0,1,2,1,2,1)) CRHist <- with(CompRiskFrame,Hist(time,event)) summary(CRHist) plot(CRHist) ## Interval censored data from a survival model icensFrame <- data.frame(L=c(1,1,3,4,6),R=c(2,NA,3,6,9),event=c(1,1,1,2,2)) with(icensFrame,Hist(time=list(L,R))) ## Interval censored data from a competing risk model with(icensFrame,Hist(time=list(L,R),event)) ## Multi state model MultiStateFrame <- data.frame(time=1:10, from=c(1,1,3,1,2,4,1,1,2,1), to=c(2,3,1,2,4,2,3,2,4,4)) with(MultiStateFrame,Hist(time,event=list(from,to))) ## MultiState with right censored observations MultiStateFrame1 <- data.frame(time=1:10, from=c(1,1,3,2,1,4,1,1,3,1), to=c(2,3,1,0,2,2,3,2,0,4)) with(MultiStateFrame1,Hist(time,event=list(from,to))) ## Using the longitudinal input method MultiStateFrame2 <- data.frame(time=rep(1,10), event=c(1,2,3,0,1,2,4,2,1,2), id=c(1,1,1,1,2,2,2,2,3,3)) with(MultiStateFrame2,Hist(time,event,id))