[R-meta] Funnel Plots for Multilevel Meta

[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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