[R-meta] Funnel Plots for Multilevel Meta

Fri, Dec 11, 2020 12:26 PM

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 at r-project.org]
On Behalf Of Dylan Johnson
Sent: Friday, 11 December, 2020 20:03
To: Michael Dewey; r-sig-meta-analysis at 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 at dewey.myzen.co.uk>
Sent: December 11, 2020 6:12 AM
To: Dylan Johnson<mailto:dylanr.johnson at mail.utoronto.ca>; r-sig-meta-
analysis at r-project.org<mailto:r-sig-meta-analysis at 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

[R-meta] Funnel Plots for Multilevel Meta

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