Hist  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,
entry = NULL,
id = NULL,
cens.code = "0",
addInitialState = FALSE
)
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 
event 
A vector or a factor that specifies the events that occurred at
the corresponding value of 
entry 
Vector of delayed entry times (lefttruncation) or list of two times when the entry time is interval censored. 
id 
Identifies the subjects to which multiple events belong for the
longitudinal form of storing the data of a multi state model – see

cens.code 
A character or numeric vector to identify the right
censored observations in the values of 
addInitialState 
If TRUE, an initial state is added to all ids for the longitudinal input form of a multistate model. 
*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 

event 
an integer valued numeric vector that codes the events. 
from 
an integer
valued numeric vector that codes the 
to 
an integer valued numeric vector that codes
the 
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, Arthur Allignol arthur.allignol@fdm.unifreiburg.de
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 < SimSurv(10)
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=c(0,1,2,3,4,0,1,2,0,1),
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=event,id=id))
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