Marco Colagrossi
2015-Aug-31 16:36 UTC
[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 <lists at dewey.myzen.co.uk> 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 <lists at dewey.myzen.co.uk> 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) >>>> <wolfgang.viechtbauer at maastrichtuniversity.nl> 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.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 >>> >>> >>> >>> -- >>> Michael >>> http://www.dewey.myzen.co.uk/home.html >> >> > > -- > Michael > http://www.dewey.myzen.co.uk/home.html
Viechtbauer Wolfgang (STAT)
2015-Aug-31 17:28 UTC
[R] Metafor and forest(); not showing 'ilab' and text
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.colagrossi at gmail.com] > Sent: Monday, August 31, 2015 18:37 > To: Michael Dewey > Cc: Viechtbauer Wolfgang (STAT); r-help at 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 <lists at dewey.myzen.co.uk> > 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 <lists at dewey.myzen.co.uk> > 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) > >>>> <wolfgang.viechtbauer at maastrichtuniversity.nl> 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.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
Dear Wolfgang, Kindly please i have an issue with R code could you please help me. Best Regards On Mon, Aug 31, 2015 at 6:24 PM, Viechtbauer Wolfgang (STAT)-2 [via R] < ml-node+s789695n4711682h19 at n4.nabble.com> 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:[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=0>] > > Sent: Monday, August 31, 2015 18:37 > > To: Michael Dewey > > Cc: Viechtbauer Wolfgang (STAT); [hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=1> > > 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 <[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=2>> > > 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 <[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=3>> > > 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) > > >>>> <[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=4>> 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:[hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=5>] > > >>>>>> Sent: Tuesday, August 25, 2015 17:59 > > >>>>>> To: Viechtbauer Wolfgang (STAT) > > >>>>>> Cc: [hidden email] > <http:///user/SendEmail.jtp?type=node&node=4711682&i=6>; 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 > ______________________________________________ > [hidden email] <http:///user/SendEmail.jtp?type=node&node=4711682&i=7> > 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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Metafor-and-forest-not-showing-ilab-and-text-tp4711432p4711682.html > To start a new topic under R help, email > ml-node+s789695n789696h53 at n4.nabble.com > To unsubscribe from R, click here > <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=789695&code=bmF2aW5nMnVrQGdtYWlsLmNvbXw3ODk2OTV8LTczNzQxMTY0Ng==> > . > NAML > <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> >-- View this message in context: http://r.789695.n4.nabble.com/Metafor-and-forest-not-showing-ilab-and-text-tp4711432p4711683.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]]
Marco Colagrossi
2015-Sep-01 14:49 UTC
[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)
<wolfgang.viechtbauer at maastrichtuniversity.nl>
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.colagrossi at gmail.com]
>> Sent: Monday, August 31, 2015 18:37
>> To: Michael Dewey
>> Cc: Viechtbauer Wolfgang (STAT); r-help at 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 <lists at
dewey.myzen.co.uk>
>> 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 <lists at
dewey.myzen.co.uk>
>> 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)
>> >>>> <wolfgang.viechtbauer at
maastrichtuniversity.nl> 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.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