rateplot: Functions to plot rates from a table classified by age and...

In Epi: Statistical Analysis in Epidemiology

Functions to plot rates from a table classified by age and calendar time (period)

Description

Produces plots of rates versus age, connected within period or cohort (Aplot), rates versus period connected within age-groups (Pplot) and rates and rates versus date of birth cohort (Cplot). rateplot is a wrapper for these, allowing to produce the four classical displays with a single call.

Usage

rateplot( rates,
          which = c("ap","ac","pa","ca"),
            age = as.numeric( dimnames( rates )[[1]] ),
            per = as.numeric( dimnames( rates )[[2]] ),
           grid = FALSE,
         a.grid = grid,
         p.grid = grid,
         c.grid = grid,
          ygrid = grid,
       col.grid = gray( 0.9 ),
          a.lim = range( age, na.rm=TRUE ) + c(0,diff( range( age ) )/30),
          p.lim = range( per, na.rm=TRUE ) + c(0,diff( range( age ) )/30),
          c.lim = NULL, 
           ylim = range( rates[rates>0], na.rm=TRUE ),
             at = NULL,
         labels = paste( at ),
          a.lab = "Age at diagnosis",
          p.lab = "Date of diagnosis",
          c.lab = "Date of birth",
           ylab = "Rates",
           type = "l",
            lwd = 2,
            lty = 1,
         log.ax = "y",
            las = 1,
            ann = FALSE,
          a.ann = ann,
          p.ann = ann,
          c.ann = ann,
          xannx = 1/20,
        cex.ann = 0.8,
         a.thin = seq( 1, length( age ), 2 ),
         p.thin = seq( 1, length( per ), 2 ),
         c.thin = seq( 2, length( age ) + length( per ) - 1, 2 ),
            col = par( "fg" ),
          a.col = col,
          p.col = col,
          c.col = col,
            ... )

Aplot( rates, age = as.numeric( dimnames( rates )[[1]] ),
       per = as.numeric( dimnames( rates )[[2]] ), grid = FALSE,
       a.grid = grid, ygrid = grid, col.grid = gray( 0.9 ),
       a.lim = range( age, na.rm=TRUE ), ylim = range( rates[rates>0], na.rm=TRUE ),
       at = NULL, labels = paste( at ), a.lab = names( dimnames( rates ) )[1],
       ylab = deparse( substitute( rates ) ), type = "l", lwd = 2, lty = 1,
       col = par( "fg" ), log.ax = "y", las = 1, c.col = col, p.col = col,
       c.ann = FALSE, p.ann = FALSE, xannx = 1/20, cex.ann = 0.8,
       c.thin = seq( 2, length( age ) + length( per ) - 1, 2 ),
       p.thin = seq( 1, length( per ), 2 ), p.lines = TRUE,
       c.lines = !p.lines, ... )

Pplot( rates, age = as.numeric( dimnames( rates )[[1]] ),
       per = as.numeric( dimnames( rates )[[2]] ), grid = FALSE,
       p.grid = grid, ygrid = grid, col.grid = gray( 0.9 ),
       p.lim = range( per, na.rm=TRUE ) + c(0,diff(range(per))/30),
       ylim = range( rates[rates>0], na.rm=TRUE ), p.lab = names( dimnames( rates ) )[2],
       ylab = deparse( substitute( rates ) ), at = NULL, labels = paste( at ),
       type = "l", lwd = 2, lty = 1, col = par( "fg" ), log.ax = "y",
       las = 1, ann = FALSE, cex.ann = 0.8, xannx = 1/20,
       a.thin = seq( 1, length( age ), 2 ), ... )

Cplot( rates, age = as.numeric( rownames( rates ) ),
       per = as.numeric( colnames( rates ) ), grid = FALSE,
       c.grid = grid, ygrid = grid, col.grid = gray( 0.9 ),
       c.lim = NULL, ylim = range( rates[rates>0], na.rm=TRUE ),
       at = NULL, labels = paste( at ), c.lab = names( dimnames( rates ) )[2],
       ylab = deparse( substitute( rates ) ), type = "l", lwd = 2, lty = 1,
       col = par( "fg" ), log.ax = "y", las = 1, xannx = 1/20, ann = FALSE,
       cex.ann = 0.8, a.thin = seq( 1, length( age ), 2 ), ...  )

Arguments

rates	A two-dimensional table (or array) with rates to be plotted. It is assumed that the first dimension is age and the second is period.
which	A character vector with elements from c("ap","ac","apc","pa","ca"), indication which plots should be produced. One plot per element is produced. The first letter indicates the x-axis of the plot, the remaining which groups should be connected, i.e. "pa" will plot rates versus period and connect age-classes, and "apc" will plot rates versus age, and connect both periods and cohorts.
age	Numerical vector giving the means of the age-classes. Defaults to the rownames of rates as numeric.
per	Numerical vector giving the means of the periods. Defaults to the columnnames of rates as numeric.
grid	Logical indicating whether a background grid should be drawn.
a.grid	Logical indicating whether a background grid on the age-axis should be drawn. If numerical it indicates the age-coordinates of the grid.
p.grid	do. for the period.
c.grid	do. for the cohort.
ygrid	do. for the rate-dimension.
col.grid	The colour of the grid.
a.lim	Range for the age-axis.
p.lim	Range for the period-axis.
c.lim	Range for the cohort-axis.
ylim	Range for the y-axis (rates).
at	Position of labels on the y-axis (rates).
labels	Labels to put on the y-axis (rates).
a.lab	Text on the age-axis. Defaults to "Age".
p.lab	Text on the period-axis. Defaults to "Date of diagnosis".
c.lab	Text on the cohort-axis. Defaults to "Date of birth".
ylab	Text on the rate-axis. Defaults to the name of the rate-table.
type	How should the curves be plotted. Defaults to "l".
lwd	Width of the lines. Defaults to 2.
lty	Which type of lines should be used. Defaults to 1, a solid line.
log.ax	Character with letters from "apcyr", indicating which axes should be logarithmic. "y" and "r" both refer to the rate scale. Defaults to "y".
las	see par.
ann	Should the curves be annotated?
a.ann	Logical indicating whether age-curves should be annotated.
p.ann	do. for period-curves.
c.ann	do. for cohort-curves.
xannx	The fraction that the x-axis is expanded when curves are annotated.
cex.ann	Expansion factor for characters annotating curves.
a.thin	Vector of integers indicating which of the age-classes should be labelled.
p.thin	do. for the periods.
c.thin	do. for the cohorts.
col	Colours for the curves.
a.col	Colours for the age-curves.
p.col	do. for the period-curves.
c.col	do. for the cohort-curves.
p.lines	Should rates from the same period be connected?
c.lines	Should rates from the same cohort be connected?
...	Additional arguments pssed on to matlines when plotting the curves.

Details

Zero values of the rates are ignored. They are neiter in the plot nor in the calculation of the axis ranges.

Value

NULL. The function is used for its side-effect, the plot.

Author(s)

Bendix Carstensen, Steno Diabetes Center, http://bendixcarstensen.com

See Also

apc.frame

Examples

data( blcaIT )
attach(blcaIT)

# Table of rates:
bl.rate <- tapply( D, list(age,period), sum ) /
           tapply( Y, list(age,period), sum )
bl.rate

# The four classical plots:
par( mfrow=c(2,2) )
rateplot( bl.rate*10^6 )

# The labels on the vertical axis could be nicer:
rateplot( bl.rate*10^6, at=10^(-1:3), labels=c(0.1,1,10,100,1000) ) 

# More bells an whistles
par( mfrow=c(1,3), mar=c(3,3,1,1), oma=c(0,3,0,0), mgp=c(3,1,0)/1.6 )
rateplot( bl.rate*10^6, ylab="", ann=TRUE, which=c("AC","PA","CA"),
                      at=10^(-1:3), labels=c(0.1,1,10,100,1000),
                      col=topo.colors(11), cex.ann=1.2 ) 

Epi documentation built on Oct. 1, 2024, 5:07 p.m.