Epi: summary.Lexis – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

summary.Lexis

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 )

Epi

Statistical Analysis in Epidemiology

v2.44

GPL-2

Authors

Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]

Initial release

2021-02-28