R: Summarize transitions and risk time from a Lexis object

summary.Lexis {Epi} | R Documentation

## Summarize transitions and risk time from a Lexis object

### Description

A two-way table of records and transitions classified by states (`lex.Cst` and `lex.Xst`), as well the risk time in each state.

### Usage

      ## S3 method for class 'Lexis'
    summary( object, simplify=TRUE, scale=1, by=NULL,
                               Rates=FALSE, timeScales=FALSE, ... )
      ## S3 method for class 'summary.Lexis'
    print( x, ..., digits=2 )

### Arguments

`object` | A Lexis object.
`simplify` | Should rows with 0 follow-up time be dropped?
`scale` | Scaling factor for the rates. The calculated rates are multiplied by this number.
`by` | Character vector of name(s) of variable(s) in `object`. Used to give a separate summaries for subsets of `object`. If longer than than 1, the interaction between that variables is used to stratify the summary. It is also possible to supply a vector of length `nrow(object)`, and the distinct values of this will be used to stratify the summary.
`Rates` | Should a component with transition rates be returned (and printed) too?
`timeScales` | Should the names of the timescales and the indication of since which entry also be given?
`x` | A `summary.Lexis` object.
`digits` | How many digits should be used for printing?
`...` | Other parameters - ignored

### Value

An object of class `summary.Lexis`, a list with two components, `Transitions` and `Rates`, each one a matrix with rows classified by states where persons spent time, and columns classified by states to which persons transit. The `Transitions` contains number of transitions and has 4 extra columns with number of records, total number of events, total risk time and number of person contributing attached. The `Rates` contains the transitions rates.

If the argument `Rates` is FALSE (the default), then only the first component of the list is returned.

### Author(s)

Bendix Carstensen, http://BendixCarstensen.com

### Examples

    data( nickel )
    # Lung cancer deaths and other deaths are coded 1 and 2
    nic <- Lexis( data=nickel,
                 entry=list(age=agein),
                  exit=list(age=ageout,cal=ageout+dob,tfh=ageout-age1st),
           exit.status=factor( (icd > 0) + (icd %in% c(162,163)),
                               labels=c("Alive","Other","Lung") ) )
    str( nic )
    head( nic )
    summary( nic )
    # More detailed summary, by exposure level
    summary( nic, by=nic$exposure>5, Rates=TRUE, scale=100 )

[Package Epi version 2.40 Index]