[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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Re: [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)
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
>> on
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
On 25 August 2015 at 15:54, Viechtbauer Wolfgang (STAT)
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)
>> > 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
Re: [R] Metafor and forest(); not showing 'ilab' and text
Thanks for your help,
I got the mistake I was making and I managed to find a solution
regarding those graphs; I don't want to abuse of your patience but I
have three further questions:
1. Always regarding the forest plots, it is possible to make a
cross-subset? I try to explain my self better; I have one dummy
variable called pub and another variable called SIMiv that can take
the values of "share", "loan", "number" and "duration". How can I
subset my sample so that the forest shows only (for example) studies
when the dummy takes the value of 1 and the SIMiv variable takes the
values of "share" and "loan"?
Something like this:
forest(pc, var, ci95m, ci95p, slab = authoryear2, psize=1,
subset=(pub==1, SIMiv=("share", "loan", "duration"))
2. I have few doubts regarding the multilevel modeling;
rma.mv(pc, var, random = ~ 1 | author, data=codebook)
if I'm correct this should be a multilevel model nested at "author"
level; what I cannot understand If it is a varying intercept
(Y=A+BjX), a varying slope (Y=Aj+BX) or a varying intercept&slope
model (Y=Aj+BjX). Are there the formulas for it somewhere? So far I
only found the formulas for the estimators included in the metafor
package.
3. metareg1 <- rma.mv(pc, var, random = ~ 1 | author, mods = ~ pub +
SIMiv, data=codebook)
Again, if I'm correct this should be a multilevel meta regression
(correct me if I'm wrong); I have the same doubts as before.
Thank you again
Marco
On 25 August 2015 at 19:24, Michael Dewey wrote:
> Dear Marco
>
> When you change xlim it increases the width of the forest plot in the sense
> you describe. It does not push your text out of the way to make space for it
> but instead overprints it. You may like to use alim to truncate your
> confidence interval whiskers to fit within the space you see or make your
> labels shorter.
>
>
> On 25/08/2015 17:25, Marco Colagrossi wrote:
>>
>> I think I've not explained myself well. When I say "the width of the
>> forest plot" I mean the region above the observed outcome, the
>> "actual" forest plot, not the plot as a whole. Even if I change values
>> for Xlim, cex or ilab.xpos the width of that particular region within
>> the plot doesn't change.
>>
>> Best,
>>
>> Marco
>>
>> On 25 August 2015 at 18:11, Viechtbauer Wolfgang (STAT)
>> wrote:
>>>
>>> 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.colagro...@gmail.com]
>>>> Sent: Tuesday, August 25, 2015 17:59
>>>> To: Viechtbauer Wolfgang (STAT)
>>>> Cc: r-help@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
>
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html
__
R-help@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.
Re: [R] Metafor and forest(); not showing 'ilab' and text
The solution that you proposed works perfectly, thank you very much.
I'll wait for Wolfgang answer as I'm having few doubts about the models.
Thanks
On 31 August 2015 at 18:34, Michael Dewey wrote:
> Comments in line
>
> On 31/08/2015 16:08, Marco Colagrossi wrote:
>>
>> Thanks for your help,
>>
>> I got the mistake I was making and I managed to find a solution
>> regarding those graphs; I don't want to abuse of your patience but I
>> have three further questions:
>>
>> 1. Always regarding the forest plots, it is possible to make a
>> cross-subset? I try to explain my self better; I have one dummy
>> variable called pub and another variable called SIMiv that can take
>> the values of "share", "loan", "number" and "duration". How can I
>> subset my sample so that the forest shows only (for example) studies
>> when the dummy takes the value of 1 and the SIMiv variable takes the
>> values of "share" and "loan"?
>> Something like this:
>> forest(pc, var, ci95m, ci95p, slab = authoryear2, psize=1,
>> subset=(pub==1, SIMiv=("share", "loan", "duration"))
>>
>
> Do you not want something like
> (pub == 1) & (SIMIv %in% c("share", "loan", "duration"))
>
>
>> 2. I have few doubts regarding the multilevel modeling;
>> rma.mv(pc, var, random = ~ 1 | author, data=codebook)
>> if I'm correct this should be a multilevel model nested at "author"
>> level; what I cannot understand If it is a varying intercept
>> (Y=A+BjX), a varying slope (Y=Aj+BX) or a varying intercept&slope
>> model (Y=Aj+BjX). Are there the formulas for it somewhere? So far I
>> only found the formulas for the estimators included in the metafor
>> package.
>>
>
> I think it a random intercept but Wolfgang may correct me there.
>
>
>> 3. metareg1 <- rma.mv(pc, var, random = ~ 1 | author, mods = ~ pub +
>> SIMiv, data=codebook)
>> Again, if I'm correct this should be a multilevel meta regression
>> (correct me if I'm wrong); I have the same doubts as before.
>>
>> Thank you again
>>
>> Marco
>>
>> On 25 August 2015 at 19:24, Michael Dewey wrote:
>>>
>>> Dear Marco
>>>
>>> When you change xlim it increases the width of the forest plot in the
>>> sense
>>> you describe. It does not push your text out of the way to make space for
>>> it
>>> but instead overprints it. You may like to use alim to truncate your
>>> confidence interval whiskers to fit within the space you see or make your
>>> labels shorter.
>>>
>>>
>>> On 25/08/2015 17:25, Marco Colagrossi wrote:
>>>>
>>>>
>>>> I think I've not explained myself well. When I say "the width of the
>>>> forest plot" I mean the region above the observed outcome, the
>>>> "actual" forest plot, not the plot as a whole. Even if I change values
>>>> for Xlim, cex or ilab.xpos the width of that particular region within
>>>> the plot doesn't change.
>>>>
>>>> Best,
>>>>
>>>> Marco
>>>>
>>>> On 25 August 2015 at 18:11, Viechtbauer Wolfgang (STAT)
>>>> wrote:
>>>>>
>>>>>
>>>>> 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
>>
Re: [R] Metafor and forest(); not showing 'ilab' and text
I did read the help(rma.mv) and I also had look at the analysis by Konstantopoulos (2011) in the past few days. You have to apologize me but is the first meta analysis I'm trying to carry on, it is the first I'm working on R and moreover the terminology here is somehow different (and confusing) with respect to the terminology I was used in panel data analysis. It looks to me - correct me if I'm wrong - that a model such: rma.mv(pc, var, random = ~ 1 | author, data=codebook) or rma.mv(pc, var, random = ~ 1 | author, mods = ~ pub + SIMiv, data=codebook) it is a varying intercept model (using Gelman-Hill Yi = Aji+BXi+Ei). Why do you say that "Using "random = ~ 1 | author" is likely to be insufficient. You also need to add random effects at the observation level"? Could you please walk me through what you mean by that? I'll (try to) explain to you what I'm doing here so you might be able to help me out. I'm carrying on a meta-analysis (and ultimately, few meta-regressions) of the relationship between firm performances and bank-firm relationship. Since I have different proxies for the latter, I computed as effect size a raw partial correlation, a continuous Fisher’s z-score and the one-tail p-value as a continuous interpretation of the direction and the significance of an effect size. The number of studies in my meta-analysis is 29, but most of them have multiple cases so, ultimately, I have 98 different cases. All of the 29 studies have repeated yearly observation in the same country for different time span; let's say one from 1985 to 1991 in Spain, one from 1987 to 1999 in China, one from 1981 to 2002 in the US and so on. Even in case in which two different study investigates the same country and some of the years in the time span overlaps I'm sure that their population is drawn from different samples. My idea was too confront what in econometrics is called a study-fixed effect (or author fixed effect since authors have no more than one study in my analysis), that is: rma(pc, var, mods = ~ I(study), data=codebook) With a multilevel model, in order to account for the fact that observation from the same study are not independent. May I have your opinion on what I'm trying to do here guys? Do you think I should take into account also a autoregressive structure over time and correct that with struct="HAR" ? Sorry for the long mail, I wanted to explain as better as possible, and thank you again for your help, It is incredibly appreciated. Marco On 31 August 2015 at 19:28, Viechtbauer Wolfgang (STAT) wrote: > Have you read help(rma.mv)? It describes in detail what "random = ~ 1 | > author" does. Also, I think you may find some of these useful: > > http://www.metafor-project.org/doku.php/analyses#multivariate_multilevel_meta-analysis_models > > Especially: > http://www.metafor-project.org/doku.php/analyses:konstantopoulos2011 > > Using "random = ~ 1 | author" is likely to be insufficient. You also need to > add random effects at the observation level. > > 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: Marco Colagrossi [mailto:marco.colagro...@gmail.com] >> Sent: Monday, August 31, 2015 18:37 >> To: Michael Dewey >> Cc: Viechtbauer Wolfgang (STAT); r-help@r-project.org >> Subject: Re: [R] Metafor and forest(); not showing 'ilab' and text >> >> The solution that you proposed works perfectly, thank you very much. >> >> I'll wait for Wolfgang answer as I'm having few doubts about the models. >> >> Thanks >> >> On 31 August 2015 at 18:34, Michael Dewey >> wrote: >> > Comments in line >> > >> > On 31/08/2015 16:08, Marco Colagrossi wrote: >> >> >> >> Thanks for your help, >> >> >> >> I got the mistake I was making and I managed to find a solution >> >> regarding those graphs; I don't want to abuse of your patience but I >> >> have three further questions: >> >> >> >> 1. Always regarding the forest plots, it is possible to make a >> >> cross-subset? I try to explain my self better; I have one dummy >> >> variable called pub and another variable called SIMiv that can take >> >> the values of "share", "loan", "number" and "duration". How can I >> >> subset my sample so that the forest shows only (for example) studies >> >> when the dummy takes the value of 1 and t
