[R-meta] Funnel Plots for Multilevel Meta

[Michael Dewey]

Dear Valeria

Whatever choice you make, and Gerta has given you some valuable 
references, make sure you actually look at the plot with an open mind 
and interpret everything in it. It is just another way of looking at the 
data and may show other features than small study effects.

Michael

On 12/12/2020 13:43, Valeria Ivaniushina wrote:
> 
> 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 
> <mailto: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 <http://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
>     <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
>     <mailto: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
>     <mailto:lists using dewey.myzen.co.uk>>
>      >Sent: December 11, 2020 6:12 AM
>      >To: Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca
>     <mailto:dylanr.johnson using mail.utoronto.ca>>; r-sig-meta-
>      >analysis using r-project.org
>     <mailto:analysis using r-project.org><mailto: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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-- 
Michael
http://www.dewey.myzen.co.uk/home.html