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Marco Colagrossi

2015-Aug-24 17:49 UTC

[R] Metafor and forest(); not showing 'ilab' and text

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;
- I cannot still export it properly, as shown in the enclosed .png
- SIMdv, SIMiv are shown as number while on mine .csv are actually
text variable.

regarding the rma.mv package, I set it up this way (preliminarily)

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.

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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.-------------- next part --------------
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Michael Dewey

2015-Aug-25 11:23 UTC

head link

[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.
> - SIMdv, SIMiv are shown as number while on mine .csv are actually
> text variable.
>
> 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.
>
> 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
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-
>>> guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
-- 
Michael
http://www.dewey.myzen.co.uk/home.html

Viechtbauer Wolfgang (STAT)

2015-Aug-25 13:54 UTC

head link

[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

R help - Aug 2015 - Metafor and forest(); not showing 'ilab' and text

[R] Metafor and forest(); not showing 'ilab' and text

[R] Metafor and forest(); not showing 'ilab' and text

[R] Metafor and forest(); not showing 'ilab' and text