[R] Metafor and forest(); not showing 'ilab' and text
Navien
naving2uk at gmail.com
Mon Aug 31 19:29:05 CEST 2015
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>
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