Thanks again for your help. I'm sorry to bother you but I don't get
how to widen the forest plot; if I try to change the values of xlim or
the ilab.xpos values the width of the forest plot region does not
change, but only moves on the graphs. What I'm I missing?
forest(pc, var, ci95m, ci95p, slab = authoryear, psize=1, subset=(pub==1),
xlim = c(-16, 6),
ilab = data.frame(SIMdv, SIMiv),
ilab.xpos = c(-7.5, -5.5), cex = 0.75)
op <- par(cex=.75, font=2)
text(c(-7.5, -5.5), 54, c("DV", "IV"))
text(-16, 54, "Author(s) and Year", pos=4)
text(6, 54, "Outcome [95% CI]", pos=2)
par(op)
> par("usr")[1:2]
[1] -16 6
On 25 August 2015 at 15:54, Viechtbauer Wolfgang (STAT)
<wolfgang.viechtba...@maastrichtuniversity.nl> wrote:
> Further comments in line as well.
>
>> -----Original Message-----
>> From: Michael Dewey [mailto:li...@dewey.myzen.co.uk]
>> Sent: Tuesday, August 25, 2015 13:23
>> To: Marco Colagrossi; Viechtbauer Wolfgang (STAT)
>> Cc: r-help@r-project.org
>> Subject: Re: [R] Metafor and forest(); not showing 'ilab' and text
>>
>> Hello Marco
>>
>> Comments in line again
>>
>> On 24/08/2015 18:49, Marco Colagrossi wrote:
>> > I tried to upload the file once again. I tweaked it a bit, now my code
>> is:
>> >
>> > forest(pc, var, ci95m, ci95p, slab = authoryear, psize=1,
>> subset=(pub==1),
>> > xlim = c(-16, 6),
>> > ilab = cbind(SIMdv, SIMiv),
>> > ilab.xpos = c(-7.5, -5.5), cex = 0.75)
>> > op <- par(cex=.75, font=2)
>> > text(c(-7.5, -5.5), 54, c("DV", "IV"))
>> > text(-16, 54, "Author(s) and Year", pos=4)
>> > text(6, 54, "Outcome [95% CI]", pos=2)
>> > par(op)
>> >
>> > I managed to show both the Ilab argument and the text above. I still
>> > have 3 issues:
>> > - now the forest plot is too narrow - that is, pretty unreadable;
>>
>> You need to re-read Wolfgang's advice again. The forest function tells
>> you what values of xlim it used and you can then adjust them to suit.
>> This will take a few attempts in my experience.
>>
>> > - I cannot still export it properly, as shown in the enclosed .png
>>
>> It looked correctly exported to me. One comment, do you really need the
>> complete citation of each study? Most of the forest plots I see as a
>> reviewer just use the first author name and the year. This would
>> potentially give you a lot more space.
>
> Also, if you have lots of outcomes, you may need to increase the height of
> the plotting device to make everything fit (or you need to reduce the font
> size even further, but things will become illegible eventually).
>
>> > - SIMdv, SIMiv are shown as number while on mine .csv are actually
>> > text variable.
>
> Those variables are apparently coded as factors, so use data.frame() instead
> of cbind() to avoid the coercion to integer codes.
>
>> > regarding the rma.mv package, I set it up this way (preliminarily)
>> >
>>
>> I will leave this one to Wolfgang to answer.
>>
>> > multi <- rma.mv(pc, var, random = ~ 1 | author, data=codebook)
>> >
>> > I'm trying to compare the results with this equation, which is what -
>> > I think, correct me if I'm wrong - in econometrics we call
>> > author-fixed effect, that is, model which are constant across
>> > individuals (the random\fix notation is a bit tricky):
>> >
>> > author_fix <- rma(pc, var, mods = ~ I(author), data=codebook,
>> method="ML")
>> >
>> > What I was wondering if that the two equation above mentioned also
>> > correct for heteroskedasticity which I need since my studies have
>> > different sample and specifications.
>
> I cannot comment on model choices. But yes, the functions properly account
> for the fact that the sampling variances are heteroskedastic.
>
>> > Thanks for your help, your patience and your time, and many
>> > compliments for the package, is guiding me through the use of R for
>> > the first time - as you might have guessed.
>> >
>> > Marco
>> >
>> >
>> > On 24 August 2015 at 16:50, Viechtbauer Wolfgang (STAT)
>> > <wolfgang.viechtba...@maastrichtuniversity.nl> wrote:
>> >> I cannot reproduce the issue with 'ilab' not being shown when using
>> 'subset'. My guess is that the values for 'ilab.xpos' specified are
>> actually outside of the plotting region. After you have drawn the forest
>> plot, try:
>> >>
>> >> par("usr")[1:2]
>> >>
>> >> to see what the default limits actually are. Then use 'xlim' to adjust
>> the limits to your taste. And then use appropriate values for
>> 'ilab.xpos', so they are inside those limits.
>> >>
>> >>> Moreover, the graph is showed correctly only within the zoom in
>> >>> Rstudio but if I save it it is showed as enclosed.
>> >>
>> >> Nothing was enclosed (or it was stripped).
>> >>
>> >>> Moreover, how would you suggest to handle (graphically) the
>> >>> multiple-cases-per-study thing? It's a 'good' way to average the
>> cases
>> >>> among different studies in the graphs?
>> >>
>> >> Maybe add some space between groupings (i.e., studies). The example
>> given here can provide some clues how one could go about this:
>> http://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups
>> But drawing a plot like this requires a lot of hand-tweaking.
>> >>
>> >> Best,
>> >> Wolfgang
>> >>
>> >> --
>> >> Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry
>> and
>> >> Neuropsychology | 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 [mailto:r-help-boun...@r-project.org] On Behalf Of Marco
>> >>> Colagrossi
>> >>> Sent: Monday, August 24, 2015 16:04
>> >>> To: r-help@r-project.org
>> >>> Subject: [R] Metafor and forest(); not showing 'ilab' and text
>> >>>
>> >>> Hello folks,
>> >>>
>> >>> I have a couple of issues with the metafor package, specifically with
>> >>> the forest graphs.
>> >>> I am currently conducting a Meta-Analysis in economics throughout the
>> >>> metafor package.
>> >>>
>> >>> My meta-analysis has the specific of having different cases from
>> >>> single studies, and this proven to be challenging especially when
>> >>> trying to plot graphically the results I'm obtaining.
>> >>>
>> >>> Here's the code:
>> >>>
>> >>> forest(pc, var, ci95m, ci95p, slab = authoryear, psize=1,
>> >>> subset=(pub==1),
>> >>> ilab = cbind(ys, f_dim, SIMdv, SIMiv),
>> >>> ilab.xpos = c(-9.5, -8, -6, -4.5), cex = 0.75)
>> >>> par(font=2)
>> >>> text(c(-9.5,-8,-6,-4.5), 26, c("Years", "Firm(s) Dimension",
>> "DV",
>> >>> "IV"))
>> >>> text(-16, 26, "Author(s) and Year", pos=4)
>> >>> text(6, 26, "Observed Outcome [95% CI]",
>> pos=2)
>> >>> par(op)
>> >>>
>> >>> 'pc' is the 'effect size', 'var' the variance, 'ci95m & ci95p' the
>> CI,
>> >>> 'pub' if the paper has been published or not. the pub subset was the
>> >>> first idea I had in order to split my sample that otherwise would
>> have
>> >>> been to big. The issue with this solution is that forest() displays
>> >>> only the slap argument and the forest with the confidence interval,
>> >>> completely ignoring the lab argument and the text I'm trying to add.
>> >>> Moreover, the graph is showed correctly only within the zoom in
>> >>> Rstudio but if I save it it is showed as enclosed.
>> >>>
>> >>> What I'm doing wrong? I tried both to look at the package
>> >>> documentation and online but I can't figure it out.
>> >>>
>> >>> Moreover, how would you suggest to handle (graphically) the
>> >>> multiple-cases-per-study thing? It's a 'good' way to average the
>> cases
>> >>> among different studies in the graphs?
>> >>> In my meta-analysis I'm using a multilevel model as shown in
>> >>> Gelman-Hill but graphically (and in tables) I'm struggling.
>> >>>
>> >>> Thanks for your help and patience
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