Here is an example. It requires a bit of extra work, but that's the beauty of R
-- you can essentially customize a graph to your taste with low-level
functions. I also added the prediction interval using the addcred argument (as
suggested by Michael), since it gives the same information as that fancy normal
distribution at the bottom. Essentially, that distribution is just
window-dressing. I am not sure if I would go as far as calling that
chart-junk, but it's certainly somewhat gratuitous. Well, I hope the code
below gives you enough of an idea so that you can adjust this to your specific
case.
library(metafor)
### load BCG vaccine data
data(dat.bcg)
### meta-analysis of the log relative risks using a random-effects model
res - rma(ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg, measure=RR,
slab=paste(author, year, sep=, ), method=REML)
### forest plot with extra annotations
forest(res, slab=paste(dat.bcg$author, dat.bcg$year, sep=, ),
xlim=c(-16, 6), at=log(c(.05, .25, 1, 4)), atransf=exp,
ilab=cbind(dat.bcg$tpos, dat.bcg$tneg, dat.bcg$cpos, dat.bcg$cneg),
ilab.xpos=c(-9.5,-8,-6,-4.5), cex=.7, ylim=c(-3,16), addcred=TRUE)
text(c(-9.5,-8,-6,-4.5), 15, c(TB+, TB-, TB+, TB-), font=2, cex=.70)
text(c(-8.75,-5.25), 16, c(Vaccinated, Control), font=2, cex=.70)
text(-16,15, Author(s) and Year, pos=4, font=2, cex=.70)
text(6, 15, Relative Risk [95% CI], pos=2, font=2, cex=.70)
text(-16, -2.5, Prediction Distribution, pos=4, cex=.70)
### add prediction distribution
res - predict(res)
pred.m - res$pred
pred.s - (res$cr.ub - res$cr.lb) / (2*1.96)
xs - seq(-2.5,1,.01)
cords.xs - c(-2,xs,-2)
cords.ys - c(0, 1.5*dnorm(xs, pred.m, sd=pred.s), 0) - 3
polygon(cords.xs, cords.ys, col=darkgray, border=NA)
ptext - paste(round(exp(res$pred),2), [ , round(exp(res$cr.lb),2), , ,
round(exp(res$cr.ub),2), ], sep=)
text(6, -2.5, ptext, pos=2, cex=.70)
--
Wolfgang Viechtbauer, Ph.D., Statistician
Department of Psychiatry and Psychology
School for Mental Health and Neuroscience
Faculty of Health, Medicine, and Life Sciences
Maastricht University, P.O. Box 616 (VIJV1)
6200 MD Maastricht, The Netherlands
+31 (43) 368-5248 | http://www.wvbauer.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Michael Dewey
Sent: Monday, December 12, 2011 18:50
To: Frank Peter; r-help@r-project.org
Subject: Re: [R] Overlaying density plot on forest plot
At 15:09 11/12/2011, you wrote:
Dear Michael,
Thanks for the email. This is the kind of forest plot, I want to
replicate
http://www.biomedcentral.com/1471-2334/11/122/figure/F2
It would be helpful to cc to r-help in case someone else there knows
better.
If you follow my suggestion you get a similar plot to sub-plot A in your
example but the credible interval is shown as a dashed line superimposed
on the summary diamond and not as a normal density as shown in sub-plot A.
Whether that is what you want is up to you I think.
Regards
Frank Peter
Original Message
From: Michael Dewey i...@aghmed.fsnet.co.uk
To: Frank Peter frankpe...@safe-mail.net, r-help@r-project.org
Subject: Re: [R] Overlaying density plot on forest plot
Date: Sun, 11 Dec 2011 14:20:13 +
At 07:16 10/12/2011, Frank Peter wrote:
Dear R User,
Please, I am new to R. I want to overlay density plot for
predictive interval pooled result in meta-analysis.
http://addictedtor.free.fr/graphiques/graphcode.php?graph=114
It is hard to be sure from your rather brief question but does the
addcred parameter to forest.rma in package metafor do what you want?
Regards
Frank Peter
Michael Dewey
i...@aghmed.fsnet.co.uk
http://www.aghmed.fsnet.co.uk/home.html
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