R: Plot a Lexis diagram

Lexis.diagram {Epi} | R Documentation

## Plot a Lexis diagram

### Description

Draws a Lexis diagram, optionally with life lines from a cohort, and with lifelines of a cohort if supplied. Intended for presentation purposes.

### Usage

    Lexis.diagram( age = c( 0, 60),
                  alab = "Age",
                  date = c( 1940, 2000 ),
                  dlab = "Calendar time",
                   int = 5,
               lab.int = 2*int,
              col.life = "black",
              lwd.life = 2,
              age.grid = TRUE,
             date.grid = TRUE,
              coh.grid = FALSE,
              col.grid = gray(0.7),
              lwd.grid = 1,
                   las = 1,
            entry.date = NA,
             entry.age = NA,
             exit.date = NA,
              exit.age = NA,
             risk.time = NA,
            birth.date = NA,
                  fail = NA,
              cex.fail = 1.1,
              pch.fail = c(NA,16),
              col.fail = rep( col.life, 2 ),
                  data = NULL, ... )

### Arguments

`age` | Numerical vector of length 2, giving the age-range for the diagram
`alab` | Label on the age-axis.
`date` | Numerical vector of length 2, giving the calendar time-range for the diagram
`dlab` | label on the calendar time axis.
`int` | The interval between grid lines in the diagram. If a vector of length two is given, the first value will be used for spacing of age-grid and the second for spacing of the date grid.
`lab.int` | The interval between labelling of the grids.
`col.life` | Colour of the life lines.
`lwd.life` | Width of the life lines.
`age.grid` | Should grid lines be drawn for age?
`date.grid` | Should grid lines be drawn for date?
`coh.grid` | Should grid lines be drawn for birth cohorts (diagonals)?
`col.grid` | Colour of the grid lines.
`lwd.grid` | Width of the grid lines.
`las` | How are the axis labels plotted?
`entry.date, entry.age, exit.date, exit.age, risk.time, birth.date` | Numerical vectors defining lifelines to be plotted in the diagram. At least three must be given to produce lines. Not all subsets of three will suffice, the given subset has to define life lines. If insufficient data is given, no life lines are produced.
`fail` | Logical of event status at exit for the persons whose life lines are plotted.
`pch.fail` | Symbols at the end of the life lines for censorings (`fail==0`) and failures (`fail != 0`).
`cex.fail` | Expansion of the status marks at the end of life lines.
`col.fail` | Character vector of length 2 giving the colour of the failure marks for censorings and failures respectively.
`data` | Dataframe in which to interpret the arguments.
`...` | Arguments to be passed on to the initial call to plot.

### Details

The default unit for supplied variables are (calendar) years. If any of the variables `entry.date`, `exit.date` or `birth.date` are of class "`Date`" or if any of the variables `entry.age`, `exit.age` or `risk.time` are of class "`difftime`", they will be converted to calendar years, and plotted correctly in the diagram. The returned dataframe will then have colums of classes "`Date`" and "`difftime`".

### Value

If sufficient information on lifelines is given, a data frame with one row per person and columns with entry ages and dates, birth date, risk time and status filled in.

Side effect: a plot of a Lexis diagram is produced with the life lines in it is produced. This will be the main reason for using the function. If the primary aim is to illustrate follow-up of a cohort, then it is better to represent the follow-up in a `Lexis` object, and use the generic `plot.Lexis` function.

### Author(s)

Bendix Carstensen, http://bendixcarstensen.com

### See Also

`Life.lines`, `Lexis.lines`

### Examples

    Lexis.diagram( entry.age = c(3,30,45),
                   risk.time = c(25,5,14),
                  birth.date = c(1970,1931,1925.7),
                        fail = c(TRUE,TRUE,FALSE) )
    LL <- Lexis.diagram( entry.age = sample( 0:50, 17, replace=TRUE ),
                         risk.time = sample( 5:40, 17, r=TRUE),
                        birth.date = sample( 1910:1980, 17, r=TRUE ),
              		  fail = sample( 0:1, 17, r=TRUE ),
    	              cex.fail = 1.1,
    	              lwd.life = 2 )
    # Identify the persons' entry and exits
    text( LL$exit.date, LL$exit.age, paste(1:nrow(LL)), col="red", font=2, adj=c(0,1) )
    text( LL$entry.date, LL$entry.age, paste(1:nrow(LL)), col="blue", font=2, adj=c(1,0) )
    data( nickel )
    attach( nickel )
    LL <- Lexis.diagram( age=c(10,100), date=c(1900,1990),
    	             entry.age=age1st, exit.age=ageout, birth.date=dob,
    		     fail=(icd %in% c(162,163)), lwd.life=1,
    		     cex.fail=0.8, col.fail=c("green","red") )
    abline( v=1934, col="blue" )
    nickel[1:10,]
    LL[1:10,]

[Package Epi version 2.47 Index]