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rateplot {Epi}

Functions to plot rates from a table classified by age and calendar time (period)
Package: 
Epi
Version: 
1.1.49

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.

Values

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

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 )

Author(s)

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

Documentation reproduced from package Epi, version 1.1.49. License: GPL-2