Epi: matshade – R documentation

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matshade

Plot confidence intervals as shaded areas around lines.

Description

Uses an x-vector and a matrix of 3*N columns with estimates and ci.s to produce the lines of estimates and confidence intervals as shaded areas in transparent colours around the lines of the estimates.

Usage

matshade( x, y, lty = 1,
          col = 1:(ncol(y)/3), col.shade=col, alpha=0.15,
         plot = dev.cur()==1,
          ... )

Arguments

`x`	Numerical vector. Unlike `matplot` this can only be a vector.
`y`	A matrix with 3*N columns — representing estimates and confidence bounds for N curves. Order of columns are assumed to be (est,lo,hi,est,lo,hi...) (or (est,hi,lo...))
`lty`	Line types for the curves.
`col`	Color(s) of the estimated curves.
`col.shade`	Color(s) of the shaded areas. These are the colors that are made transparent by the `alpha` factor. Defaults to the same colors as the lines.
`alpha`	Number in [0,1] indicating the transparency of the colors for the confidence intervals. Larger values makes the shades darker. Can be a vector which then applies to the curves in turn.
`plot`	Logical. Should a new plot frame be started? If no device is active, the default is to start one, and plot all `y`s versus x in transparent color. On the rare occasion a device is open, but no plot have been called you will get an error telling that plot.new has not been called yet, in which case you should explicitly set `plot` to `TRUE`.
`...`	Arguments passed on to `matplot` (if `plot=TRUE`) and `matlines` for use when plotting the lines. Note that `lwd=0` will cause lines to be omitted and only the shades be plotted.

Details

All shaded areas are plotted first, the curves added afterwards, so that lines are not 'overshadowed'.

If there are NAs in x or y there will be separate shaded areas for each non-NA sequence. Applies separately to each set of confidence bands in y.

Note that if you repeat the same command, you will get the curves and the shaded areas overplotted in the same frame, so the effect is to have the shades darker, because the transparent colors are plotted on top of those from the first command.

Value

NULL. Used for its side effects.

Author(s)

Bendix Carstensen, http://bendixcarstensen.com

Examples

# Follow-up data of Danish DM patients
data( DMlate )
mL <- Lexis( entry=list(age=dodm-dobth,per=dodm),
              exit=list(per=dox),
       exit.status=factor(!is.na(dodth),labels=c("Alive","Dead")),
              data=DMlate )
# Split follow-up and model by splines
sL <- splitLexis( mL, breaks=0:100, time.scale="age")
## Not run: 
# the same thing with popEpi
sL <- splitMulti( mL, age=0:100 )    
        
## End(Not run)
# Mortality rates separately for M and F:
mort <- glm( (lex.Xst=="Dead") ~ sex*Ns(age,knots=c(15,3:8*10)),
             offset = log(lex.dur),
             family = poisson,
               data = sL )
## Not run: 
# The counterpart with gam
library( mgcv )
mort <- gam( (lex.Xst=="Dead") ~ s(age,by=sex) + sex,
             offset = log(lex.dur),
             family = poisson,
               data = sL )
       
## End(Not run)
# predict rates (per 1000 PY) for men and women
ndM <- data.frame( age=10:90, sex="M", lex.dur=1 )
ndF <- data.frame( age=10:90, sex="F", lex.dur=1 )
# gam objects ignores the offset in prediction so
# lex.dur=1000 in prediction frame wll not work.
prM <- ci.pred( mort, ndM )*1000
prF <- ci.pred( mort, ndF )*1000
# predict rate-ratio
MFr <- ci.exp( mort, ctr.mat=list(ndM,ndF) )
# plot lines with shaded confidence limits
# for illustration we make a holes for the RRs:
MFr[40:45,2] <- NA
MFr[44:49,1] <- NA
matshade( ndM$age, cbind( MFr, prF, prM ), col=c(1,2,4), lwd=3,
          log="y", xlab="Age", ylab="Mortality per 1000 PY (and RR)" )
abline( h=1 )

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