Create a data structures suitable for use with packages mstate, etm.

Description

The mstate package requires input in the form of a stacked dataset with specific variable names. This is provided by msdata.Lexis. The resulting dataframe contains the same information as the result of a call to stack.Lexis.

The etm package requires input (almost) in the form of a Lexis object, but with specific column names etc. This is provided by etm.Lexis.

Usage

msdata(obj, ...)
## S3 method for class 'Lexis'
msdata(obj,
                time.scale = timeScales(obj)[1],
                       ... )
## S3 method for class 'Lexis'
etm( obj,
              time.scale = timeScales(obj)[1],
               cens.name = "cens",
                       s = 0,
                       t = "last",
              covariance = TRUE,
                delta.na = TRUE,
                     ... )

Arguments

Value

msdata.Lexis returns a dataframe with the Lexis specific variables stripped, and with the following added: id, Tstart, Tstop, from, to, trans, status, which are used in the mstate package.

etm.Lexis transforms the Lexis object into a dataframe suitable for analysis by the function etm from the etm package, and actually calls this function, so returns an object of class etm.

Author(s)

Bendix Carstensen, bxc@steno.dk, http://BendixCarstensen.com

See Also

stack.Lexis, msdata, etm

Examples

data(DMlate)
str(DMlate)
dml <- Lexis( entry = list(Per=dodm,Age=dodm-dobth,DMdur=0),
               exit = list(Per=dox),
        exit.status = factor(!is.na(dodth),labels=c("DM","Dead")),
               data = DMlate[1:1000,] )
dmi <- cutLexis( dml, cut=dml$doins, new.state="Ins", pre="DM" )
summary( dmi )

# Use the interface to the mstate package
if( require(mstate) )
{
ms.dmi <- msdata.Lexis( dmi )
# Check that all the transitions and person-years got across.
with( ms.dmi, rbind( table(status,trans),
                     tapply(Tstop-Tstart,trans,sum) ) )
}

# Use the etm package directly with a Lexis object
if( require(etm) )
{
dmi <- subset(dmi,lex.id<1000)
etm.D <- etm.Lexis( dmi, time.scale=3 )
plot( etm.D, col=rainbow(5), lwd=2, lty=1, xlab="DM duration" )
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(Epi)

Attaching package: 'Epi'

The following object is masked from 'package:base':

    merge.data.frame

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Epi/foreign.Lexis.Rd_%03d_medium.png", width=480, height=480)
> ### Name: foreign.Lexis
> ### Title: Create a data structures suitable for use with packages mstate,
> ###   etm.
> ### Aliases: msdata msdata.Lexis etm etm.Lexis
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(DMlate)
> str(DMlate)
'data.frame':	10000 obs. of  7 variables:
 $ sex  : Factor w/ 2 levels "M","F": 2 1 2 2 1 2 1 1 2 1 ...
 $ dobth: num  1940 1939 1918 1965 1933 ...
 $ dodm : num  1999 2003 2005 2009 2009 ...
 $ dodth: num  NA NA NA NA NA ...
 $ dooad: num  NA 2007 NA NA NA ...
 $ doins: num  NA NA NA NA NA NA NA NA NA NA ...
 $ dox  : num  2010 2010 2010 2010 2010 ...
> dml <- Lexis( entry = list(Per=dodm,Age=dodm-dobth,DMdur=0),
+                exit = list(Per=dox),
+         exit.status = factor(!is.na(dodth),labels=c("DM","Dead")),
+                data = DMlate[1:1000,] )
NOTE: entry.status has been set to "DM" for all.
> dmi <- cutLexis( dml, cut=dml$doins, new.state="Ins", pre="DM" )
> summary( dmi )
     
Transitions:
     To
From   DM Ins Dead  Records:  Events: Risk time:  Persons:
  DM  616 178  195       989      373    4454.40       989
  Ins   0 142   47       189       47     854.16       189
  Sum 616 320  242      1178      420    5308.56      1000
> 
> # Use the interface to the mstate package
> if( require(mstate) )
+ {
+ ms.dmi <- msdata.Lexis( dmi )
+ # Check that all the transitions and person-years got across.
+ with( ms.dmi, rbind( table(status,trans),
+                      tapply(Tstop-Tstart,trans,sum) ) )
+ }
Loading required package: mstate
Loading required package: survival
         1        2        3
0  811.000  794.000 142.0000
1  178.000  195.000  47.0000
  4454.401 4454.401 854.1602
> 
> # Use the etm package directly with a Lexis object
> if( require(etm) )
+ {
+ dmi <- subset(dmi,lex.id<1000)
+ etm.D <- etm.Lexis( dmi, time.scale=3 )
+ plot( etm.D, col=rainbow(5), lwd=2, lty=1, xlab="DM duration" )
+ }
Loading required package: etm

Attaching package: 'etm'

The following object is masked from 'package:Epi':

    etm

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>