I think Michael already gave you some really good hints. To add a bit more
details to this, first of all, I suggest to use:
q2 <- rma(yi, vi, mods=cbind(grupo), data=qim)
forest(q2, transf=transf.ztor, digits=3, alim=c(0,1), refline=.5, addfit=FALSE)
so that the fitted values for that categorical moderator are not actually shown
in the plot yet. Then use:
par("usr")
after you create the forest plot. That will tell you what the xlim values are
that were chosen by default (the first and second value). Start adjusting these
values with the xlim argument to see how that expands and shrinks the
horizontal space.
Next, try the following. Suppose you have k=20 observed correlations in total
that will be shown in the forest plot. Then the default value for ylim (for a
model that does includes a moderator, as you have) will be ylim=c(0.5, 23)
(i.e., the second value is k+3). The first study will be placed in row 20 of
the plot, the second in row 19, and so on, all the way down to row 1 for the
20th study. So, try this:
abline(h=20, lwd=3)
abline(h=1, lwd=3)
which will show you where that first and last study are being placed.
In row 21, the horizontal line is plotted. So try this:
abline(h=20, lwd=3)
which shows you where that line is being placed.
Rows 22 and 23 are for some extra white space at the top of the figure to add
column headings (with the text() function). So try this:
text(par("usr")[1], 22, "Study", pos=4, font=2)
text(par("usr")[2], 22, "Cor [95% CI]", pos=2, font=2)
which will add column headings for the first and last column. Of course, you
can adjust the value 22 to something slightly different (i.e., to adjust the
vertical placement of the headings).
Now try using ylim=c(0.5, 30) in the call to forest(). You will see that a
bunch of extra vertical space is added. The first study is still placed in row
20, going down again to row 1 for the 20th study. Confirm this with:
abline(h=20, lwd=3)
abline(h=1, lwd=3)
Now, you want to use the row argument to actually tell the forest() function
where those studies should be placed. Try rows=c(25:21, 15:1) in the call to
forest(), which will place study 1 in row 25, study 2 in row 24, going down to
study 5 in row 21, and then study 6 in row 15, study 7 in row 14, going down to
study 1 in row 1. Again, you can use something like:
abline(h=25, lwd=3)
abline(h=15, lwd=3)
to check on the vertical placement of the 1st and 6th study.
So now you have full control over the placement of the studies and you can add
space as needed. Then you can use the addpoly() function to add summary
polygons for the various levels of the "grupo" factor. I suggest carefully
going through the last example in:
help(addpoly.default)
to see a detailed example of this.
Finally, to change the axis limits to .5 and 1, just use alim=c(0.5, 1) in the
call to forest().
I hope this helps!
Best,
Wolfgang
--
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) 388-4170 | 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: Wednesday, July 18, 2012 19:16
> To: eeste...@ualg.pt; r-help@r-project.org
> Subject: Re: [R] tweaking forest plot (metafor package)
>
> At 00:10 18/07/2012, eeste...@ualg.pt wrote:
> >Dear All,
> >
> >I'm having trouble tweaking a forest plot made using the R
> >meta-analysis package metafor. I did the analysis based upon the
> >correlation coeff from studies and plotted the corresponding forest
> >plot easily
> >
> >>q2<-rma(yi,vi,mods=cbind(grupo),data=qim)
> >>q2
> >>forest (q2,transf=transf.ztor,digits=3, ... ,alim=c(0,1),refline=.5)
> >>text(-1.55,42,"Espécie [refª]",pos=4,font=2)
>
> Not sure why you use cbind(grupo) but it will not change much.
>
>
> >I'd like to subdivide the "table" by the moderator 'grupo' - i.e.
> >create the necessary spacings in the list of studies to accommodate
> >the moderator statistics (cf.
> >http://rgm2.lab.nig.ac.jp/RGM2/func.php?rd_id=metafor:addpoly.default).
> >
> >My main issue is that I cannot really understand how the function
> >(forest()) really uses space; specifically, how to use the parameters
> >'xlim', 'ylim' and 'rows' in the function? how can I change the scale
> >from 0-1 to 0.5-1?
>
> An example of what went wrong would help but I
> think you will find that the rows argument tells
> forest where to put the results of the individual
> trials so if you give it non-consecutive integers
> you will get gaps in the plot which you can fill
> with addpoly. So if rows does not contain 4 you
> can use addpoly to put something in row 4. As far
> as xlim and ylim are concerned my advice would be
> to try a whole range of values and see what
> happens as this is one of those cases where it is
> easier to experiment than to explain. If all else
> fails either (a) look at the code (b) wait for
> Wolfgang to ell you and me what really happens.
>
> >Hopefully I've made myself (relatively) clear but... Thanks.
> >
> >Eduardo Esteves
> >
> >
>
> Michael Dewey
> i...@aghmed.fsnet.co.uk
> http://www.aghmed.fsnet.co.uk/home.html
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