Cut follow-up at a specified date for each person.
Follow-up intervals in a Lexis object are divided into two sub-intervals: one before and one after an intermediate event. The intermediate event may denote a change of state, in which case the entry and exit status variables in the split Lexis object are modified.
cutLexis( data, cut, timescale = 1,
new.state = nlevels(data$lex.Cst)+1,
new.scale = FALSE,
split.states = FALSE,
progressive = FALSE,
precursor.states = transient(data),
count = FALSE )
countLexis( data, cut, timescale = 1 )data |
A |
cut |
A numeric vector with the times of the intermediate event.
If a time is missing ( |
timescale |
The timescale that |
new.state |
The state to which a transition occur at time
|
new.scale |
Name of the timescale defined as "time since entry to
new.state". If |
split.states |
Should states that are not precursor states be split according to whether the intermediate event has occurred. |
progressive |
a logical flag that determines the changes to exit status. See details. |
precursor.states |
an optional vector of states to be considered
as "less severe" than |
count |
logical indicating whether the |
The cutLexis function allows a number of different ways
of specifying the cutpoints and of modifying the status variable.
If the cut argument is a dataframe it must have columns lex.id,
cut and new.state. The values of lex.id must be unique.
In this case it is assumed that each row represents a cutpoint (on the
timescale indicated in the argument timescale). This cutpoint will
be applied to all records in data with the corresponding lex.id.
This makes it possible to apply cutLexis to a split Lexis object.
If a new.state argument is supplied, the status variable is
only modified at the time of the cut point. However, it is often
useful to modify the status variable after the cutpoint when an
important event occurs. There are three distinct ways of doing this.
If the progressive=TRUE argument is given, then a "progressive"
model is assumed, in which the status can either remain the same or
increase during follow-up, but never decrease. This assumes that the
state variables lex.Cst and lex.Xst are either numeric or
ordered factors. In this case, if
new.state=X, then any exit status with a value less than
X is replaced with X. The Lexis object
must already be progressive, so that there are no rows for which the
exit status is less than the entry status. If lex.Cst and
lex.Xst are factors they must be ordered factors if
progressive=TRUE is given.
As an alternative to the progressive argument, an explicit
vector of precursor states, that are considered less severe than the
new state, may be given. If new.state=X and
precursor.states=c(Y,Z) then any exit status of Y or
Z in the second interval is replaced with X and all
other values for the exit status are retained.
The countLexis function is a variant of cutLexis when
the cutpoint marks a recurrent event, and the status variable is used
to count the number of events that have occurred. Times given in cut
represent times of new events. Splitting with
countLexis increases the status variable by 1. If the current
status is X and the exit status is Y before cutting,
then after cutting the entry status is X, X+1 for
the first and second intervals, respectively, and the exit status is
X+1, Y+1 respectively. Moreover the values of the status
is increased by 1 for all intervals for all intervals after the cut
for the person in question. Hence, a call to countLexis is
needed for as many times as the person with most events. But also it
is immaterial in what order the cutpoints are entered.
A Lexis object, for which each follow-up interval containing
the cutpoint is split in two: one before and one after the
cutpoint. Any record representing follow up after the cutpoint has its
value of lex.Cst updated to the new state. An extra time-scale
is added; the time since the event at cut. This time scake will
beNA for any follow-up prior to the intermediate event.
The function tsNA20 will replace all missing values in
timescales with 0. This is commonly meeded when timescales defined as
time since entry into an intermediate state are used in modeling. But
you do not want to do that permanently in the cut data frame.
The cutLexis function superficially resembles the
splitLexis function. However, the splitLexis function
splits on a vector of common cut-points for all rows of the Lexis
object, whereas the cutLexis function splits on a single time
point, which may be distinct for each row, modifies the status
variables, adds a new timescale and updates the attribute
"time.since". This attribute is a character vector of the same length
as the "time.scales" attribute, whose value is '""' if the
corresponding timescale is defined for any piece of follow-up, and if
the corresponding time scale is defined by say
cutLexis(obj,new.state="A",new.scale=TRUE), it has the value
"A".
Bendix Carstensen, Steno Diabetes Center, b@bxc.dk, Martyn Plummer, martyn.plummer@r-project.org
# A small artificial example
xx <- Lexis( entry=list(age=c(17,24,33,29),per=c(1920,1933,1930,1929)),
duration=c(23,57,12,15), exit.status=c(1,2,1,2) )
xx
cut <- c(33,47,29,50)
cutLexis(xx, cut, new.state=3, precursor=1)
cutLexis(xx, cut, new.state=3, precursor=2)
cutLexis(xx, cut, new.state=3, precursor=1:2)
# The same as the last example
cutLexis(xx, cut, new.state=3)
# The same example with a factor status variable
yy <- Lexis(entry = list(age=c(17,24,33,29),per=c(1920,1933,1930,1929)),
duration = c(23,57,12,15),
entry.status = factor(rep("alpha",4),
levels=c("alpha","beta","gamma")),
exit.status = factor(c("alpha","beta","alpha","beta"),
levels=c("alpha","beta","gamma")))
cutLexis(yy,c(33,47,29,50),precursor="alpha",new.state="gamma")
cutLexis(yy,c(33,47,29,50),precursor=c("alpha","beta"),new.state="aleph")
## Using a dataframe as cut argument
rl <- data.frame( lex.id=1:3, cut=c(19,53,26), timescale="age", new.state=3 )
rl
cutLexis( xx, rl )
cutLexis( xx, rl, precursor=1 )
cutLexis( xx, rl, precursor=0:2 )
## It is immaterial in what order splitting and cutting is done
xs <- splitLexis( xx, breaks=seq(0,100,10), time.scale="age" )
xs
xsC <- cutLexis(xs, rl, precursor=0 )
xC <- cutLexis( xx, rl, pre=0 )
xC
xCs <- splitLexis( xC, breaks=seq(0,100,10), time.scale="age" )
xCs
str(xCs)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.