Viechtbauer Wolfgang (STAT)
2015-Aug-25 13:54 UTC
[R] Metafor and forest(); not showing 'ilab' and text
Further comments in line as well.> -----Original Message----- > From: Michael Dewey [mailto:lists at dewey.myzen.co.uk] > Sent: Tuesday, August 25, 2015 13:23 > To: Marco Colagrossi; Viechtbauer Wolfgang (STAT) > Cc: r-help at 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.viechtbauer at 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-bounces at r-project.org] On Behalf Of Marco > >>> Colagrossi > >>> Sent: Monday, August 24, 2015 16:04 > >>> To: r-help at 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
Marco Colagrossi
2015-Aug-25 15:58 UTC
[R] Metafor and forest(); not showing 'ilab' and text
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.viechtbauer at maastrichtuniversity.nl>
wrote:> Further comments in line as well.
>
>> -----Original Message-----
>> From: Michael Dewey [mailto:lists at dewey.myzen.co.uk]
>> Sent: Tuesday, August 25, 2015 13:23
>> To: Marco Colagrossi; Viechtbauer Wolfgang (STAT)
>> Cc: r-help at 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.viechtbauer at 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-bounces at r-project.org] On
Behalf Of Marco
>> >>> Colagrossi
>> >>> Sent: Monday, August 24, 2015 16:04
>> >>> To: r-help at 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
Viechtbauer Wolfgang (STAT)
2015-Aug-25 16:11 UTC
[R] Metafor and forest(); not showing 'ilab' and text
The 'xlim' argument does not change the actual width of the plotting
device. For that, you need to use the 'width' argument with whatever
device you are actually using. You can then use the 'xlim' argument to
create appropriate spacing to the left/right of the part of the plot that shows
the estimates and their CIs. Within that space, you can then add additional
columns with the 'ilab' argument. It's up to you to find an
appropriate combination of plotting device width, character/symbol expansion
factor ('cex' argument), 'xlim' values, and 'ilab.xpos'
values to create a nice looking plot that has no overlapping text and no
excessive white space. An example is this:
http://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups
Note that it took me dozens of iterations to create that plot. You just have to
start experimenting.
Best,
Wolfgang
> -----Original Message-----
> From: Marco Colagrossi [mailto:marco.colagrossi at gmail.com]
> Sent: Tuesday, August 25, 2015 17:59
> To: Viechtbauer Wolfgang (STAT)
> Cc: r-help at r-project.org; Michael Dewey
> Subject: Re: [R] Metafor and forest(); not showing 'ilab' and text
>
> 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