[R-meta] Funnel Plots for Multilevel Meta

[Valeria Ivaniushina]

Dear Gerta,

Thank you so much for the references!

Best,
Valeria

On Sat, Dec 12, 2020 at 5:41 PM Dr. Gerta Rücker <
ruecker using imbi.uni-freiburg.de> wrote:

> Dear Valeria,
>
> You find discussion of these issues in the literature, for example:
>
> https://www.bmj.com/content/343/bmj.d4002 (Sterne et al. 2011,
> Recommendations for examining and interpreting funnel plot asymmetry in
> meta-analyses) - One rule of thumb is that looking at a funnel plot
> doesn't make much sense with less than 10 effects.
>
> https://onlinelibrary.wiley.com/doi/full/10.1002/jrsm.1452 (Marks-Anglin
> & Chen 2020, A historical review of publication bias)
>
> https://onlinelibrary.wiley.com/doi/10.1002/jrsm.1468 (Page et al. 2020,
> Investigating and dealing with publication bias and other reporting
> biases in meta‐analyses of health research: A review)
>
> Best,
>
> Gerta
>
> Am 12.12.2020 um 14:43 schrieb Valeria Ivaniushina:
> > Dear Michael and Wolfgang.
> >
> > at the end of Egger's regression / funnel plot thread, Wolfgang said: "To
> > what extent such a plot is indicative of publication bias / small study
> > effects is a different issue"
> >
> > Could you please say more on this topic?
> > Particularly I am interested in this: is a plot with 8 effects
> informative?
> > Or a plot with less than 20 effects?
> >
> > Best,
> > Valeria
> >
> > On Fri, Dec 11, 2020 at 11:28 PM Viechtbauer, Wolfgang (SP) <
> > wolfgang.viechtbauer using maastrichtuniversity.nl> wrote:
> >
> >> A funnel plot is simply a plot of the estimates against their standard
> >> errors (or some other measure of precision). So one can draw such a plot
> >> whether there are multiple estimates from the same study or not. Hence,
> >> funnel() in metafor will happily do so:
> >>
> >> library(metafor)
> >>
> >> dat <- dat.konstantopoulos2011
> >> res <- rma.mv(yi, vi, random = ~ 1 | district/school, data=dat)
> >> res
> >> funnel(res)
> >>
> >> One could indicate (with different colors or plotting symbols) which
> >> estimates belong to the same study.
> >>
> >> cols <- palette.colors(length(unique(dat$district)), palette="Alphabet")
> >> cols <- cols[as.numeric(factor(dat$district))]
> >> funnel(res, col=cols)
> >>
> >> Then one can see how points from the same study (or in this case,
> >> 'district') cluster together.
> >>
> >> To what extent such a plot is indicative of publication bias / small
> study
> >> effects is a different issue (but the same applies even to simpler
> >> meta-analyses with a single estimate per study).
> >>
> >> Best,
> >> Wolfgang
> >>
> >>> -----Original Message-----
> >>> From: R-sig-meta-analysis [mailto:
> >> r-sig-meta-analysis-bounces using r-project.org]
> >>> On Behalf Of Dylan Johnson
> >>> Sent: Friday, 11 December, 2020 20:03
> >>> To: Michael Dewey; r-sig-meta-analysis using r-project.org
> >>> Subject: Re: [R-meta] Funnel Plots for Multilevel Meta
> >>>
> >>> Hi Michael,
> >>>
> >>> Would it not be nonsensical to have multiple effects from the same
> article
> >>> in the funnel plot though?
> >>>
> >>> With the Egger's regression I was able to accommodate the fact that
> their
> >> is
> >>> nonindependence of the effects, but am unsure how to proceed with a
> funnel
> >>> plot.
> >>>
> >>> Dylan
> >>>
> >>> Dylan Johnson, MSc
> >>>
> >>> MA Student, School and Clinical Child Psychology
> >>> Department of Applied Psychology and Human Development
> >>>
> >>> University of Toronto
> >>> 252 Bloor Street West
> >>>
> >>> Toronto, ON M5S 1V6
> >>>
> >>> From: Michael Dewey<mailto:lists using dewey.myzen.co.uk>
> >>> Sent: December 11, 2020 6:12 AM
> >>> To: Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca>; r-sig-meta-
> >>> analysis using r-project.org<mailto:r-sig-meta-analysis using r-project.org>
> >>> Subject: Re: [R-meta] Funnel Plots for Multilevel Meta
> >>>
> >>> Dear Dylan
> >>>
> >>> Perhaps I misunderstand you but if you have the data for a regression
> >>> type test like Egger's do you not just plot that? The funnel() function
> >>> in metafor does that and I am sure equivalent solutions can be found in
> >>> meta and many other packages.
> >>>
> >>> Michael
> >>>
> >>> On 11/12/2020 01:14, Dylan Johnson wrote:
> >>>> Hello,
> >>>>
> >>>> Thanks everyone for helping me sort out the Egger's test with
> >> multi-level
> >>> meta modelling!
> >>>> Is there any option in R for producing Funnel plots that are
> appropriate
> >>> for the nonindependence? I imagine that the standard funnel plot would
> be
> >>> deceiving if it came from a multi-level design.
> >>>> Many thanks!
> >>>>
> >>>> Best,
> >>>> Dylan
> >>>>
> >>>> Dylan Johnson, MSc
> >>>>
> >>>> MA Student, School and Clinical Child Psychology
> >>>> Department of Applied Psychology and Human Development
> >>>>
> >>>> University of Toronto
> >>>> 252 Bloor Street West
> >>>>
> >>>> Toronto, ON M5S 1V6
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> >>
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> >
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