[R-meta] Funnel Plots for Multilevel Meta

[Dylan Johnson]

Thank for the advice, I will try integrating the different colour into the clusters.



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



From: Viechtbauer, Wolfgang (SP)<mailto:wolfgang.viechtbauer using maastrichtuniversity.nl>
Sent: December 11, 2020 3:28 PM
To: Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca>; Michael Dewey<mailto:lists using dewey.myzen.co.uk>; 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



EXTERNAL EMAIL:

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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