[R-meta] Putting pooled effects from different multilevel meta analyses into the same forest plot
Dylan Johnson
dy|@nr@john@on @end|ng |rom m@||@utoronto@c@
Wed Dec 23 18:36:20 CET 2020
[cid:image002.png using 01D6D928.3583FD10]
I would like the Hedge’s g scale that runs along the x-axis to stretch further to the left and fill in some of that blank space
Thanks!
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 23, 2020 7:04 AM
To: Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca>; Viechtbauer, Wolfgang (SP)<mailto:wolfgang.viechtbauer using maastrichtuniversity.nl>
Cc: r-sig-meta-analysis using r-project.org<mailto:r-sig-meta-analysis using r-project.org>
Subject: Re: [R-meta] Putting pooled effects from different multilevel meta analyses into the same forest plot
EXTERNAL EMAIL:
Dear Dylan
Looking at the documentation for forest.default I see no parameter
plotwidth so it is being passed to any functions called within that use
the ... argument. What exactly are you trying to achieve here?
Michael
On 23/12/2020 00:54, Dylan Johnson wrote:
> Hello,
>
>
>
> Is there any reason that the plotwidth function isn�t working with the following forest plot:
>
>
>
> dev.new(width=10, height=1)
>
> forest(c(coef(m.overall), coef(m.overall2), coef(m.overall3)),
>
> c(vcov(m.overall), vcov(m.overall2), round(vcov(m.overall3), digits = 3)),
>
> slab=c("Threat (k=39)", "Deprivation (k=45)", "Composite (k=125)"),
>
> header=c("Inhibitory Control", "Hedge's g [95% CI]"), xlab="Hedge's g",
>
> top=2, refline=NA, xlim=c(-3.2,1), at=(c(0,-0.25,-0.50,-0.75)), psize=1, efac=0, plotwidth=unit(6, "cm") )
>
> addpoly(c(coef(m.overall), coef(m.overall2), coef(m.overall3)),
>
> c(vcov(m.overall), vcov(m.overall2), vcov(m.overall3)),
>
> rows=3:1, efac=2, annotate=FALSE, col = 2, border = 2)
>
>
>
> It doesn�t seem to change the width of the forest plot no matter what values I type in.
>
>
>
> Thank you
>
>
>
> 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 21, 2020 10:55 AM
> To: Michael Dewey<mailto:lists using dewey.myzen.co.uk>; Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca>
> Cc: r-sig-meta-analysis using r-project.org<mailto:r-sig-meta-analysis using r-project.org>
> Subject: RE: [R-meta] Putting pooled effects from different multilevel meta analyses into the same forest plot
>
>
>
> EXTERNAL EMAIL:
>
> As Michael suggested. Or, if you install the 'devel' version of metafor, then 'col' will also take a vector of colors in addpoly().
>
> Best,
> Wolfgang
>
>> -----Original Message-----
>> From: Michael Dewey [mailto:lists using dewey.myzen.co.uk]
>> Sent: Monday, 21 December, 2020 10:54
>> To: Dylan Johnson; Viechtbauer, Wolfgang (SP)
>> Cc: r-sig-meta-analysis using r-project.org
>> Subject: Re: [R-meta] Putting pooled effects from different multilevel meta
>> analyses into the same forest plot
>>
>> Dear Dylan
>>
>> Perhaps plot them one at a time?
>>
>> Michael
>>
>> On 20/12/2020 22:46, Dylan Johnson wrote:
>>> Apologies for not CC-ing the mailing list.
>>>
>>> As a last question, is there a way for me to make each of these polygons a
>> different colour as opposed to all the same:
>>>
>>> forest(c(coef(m.overall), coef(m.overall2), coef(m.overall3)),
>>> c(vcov(m.overall), vcov(m.overall2), round(vcov(m.overall3),
>> digits = 3)),
>>> slab=c("Threat (k=23)", "Deprivation (k=14)", "Composite (k=77)"),
>>> header=c("Cognitive Flexibility", "Hedge's g [95% CI]"),
>> xlab="Hedge's g",
>>> top=2, refline=NA, xlim=c(-3,1), at=log(c(.2, .5, 1)), psize=1,
>> efac=0)
>>>
>>> addpoly(c(coef(m.overall), coef(m.overall2), coef(m.overall3)),
>>> c(vcov(m.overall), vcov(m.overall2), vcov(m.overall3)),
>>> rows=3:1, efac=2, annotate=FALSE, col = 2)
>>>
>>> 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 20, 2020 3:26 PM
>>> To: Dylan Johnson<mailto:dylanr.johnson using mail.utoronto.ca>
>>> Cc: R meta<mailto:r-sig-meta-analysis using r-project.org>
>>> Subject: RE: Putting pooled effects from different multilevel meta
>> analyses into the same forest plot
>>>
>>> Please always cc the mailing list when replying.
>>>
>>> You could use addpoly() to draw the polygons on top. Continuing with the
>> example:
>>>
>>> addpoly(c(coef(res.r), coef(res.n), coef(res)),
>>> c(vcov(res.r), vcov(res.n), vcov(res)),
>>> rows=3:1, efac=2, annotate=FALSE)
>>>
>>> Best,
>>> Wolfgang
>>>
>>>> -----Original Message-----
>>>> From: Dylan Johnson [mailto:dylanr.johnson using mail.utoronto.ca]
>>>> Sent: Sunday, 20 December, 2020 20:38
>>>> To: Viechtbauer, Wolfgang (SP)
>>>> Subject: RE: Putting pooled effects from different multilevel meta
>> analyses
>>>> into the same forest plot
>>>>
>>>> Thanks for the script, I managed to get it working!
>>>>
>>>> Do you know if there is any way to get them to show up with the diamond
>>>> shape plotted instead of the squares? They are technically pooled effects
>> so
>>>> I think it would hammer that home better.
>>>>
>>>> Thanks!
>>>>
>>>> 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)
>>>> Sent: December 20, 2020 6:59 AM
>>>> To: Dylan Johnson; r-sig-meta-analysis using r-project.org
>>>> Subject: RE: Putting pooled effects from different multilevel meta
>> analyses
>>>> into the same forest plot
>>>>
>>>> Hi Dylan,
>>>>
>>>> Here is an example using rma(), but the same principle applies to models
>>>> fitted with rma.mv().
>>>>
>>>> dat <- dat.bcg
>>>> dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat)
>>>> res <- rma(yi, vi, data=dat)
>>>> res.r <- rma(yi, vi, data=dat, subset=alloc=="random")
>>>> res.n <- rma(yi, vi, data=dat, subset=alloc!="random")
>>>>
>>>> dev.new(width=10, height=6)
>>>> forest(c(coef(res.r), coef(res.n), coef(res)),
>>>> c(vcov(res.r), vcov(res.n), vcov(res)),
>>>> slab=c("With Random Assignment", "Without Random Assignment", "All
>>>> Studies"),
>>>> header=c("Subset", "Risk Ratio [95% CI]"), xlab="Risk Ratio (log
>>>> scale)",
>>>> top=2, refline=NA, xlim=c(-3,1), atransf=exp, at=log(c(.2, .5,
>> 1)),
>>>> psize=1, efac=0)
>>>>
>>>> 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: Sunday, 20 December, 2020 2:01
>>>>> To: r-sig-meta-analysis using r-project.org
>>>>> Subject: [R-meta] Putting pooled effects from different multilevel meta
>>>>> analyses into the same forest plot
>>>>>
>>>>> Hello,
>>>>>
>>>>> I am currently using the rma.mv function to carry out my metas and would
>>>>> like to display two pooled subgroups from one of them and an additional
>>>>> pooled estimate from another.
>>>>>
>>>>> Is there anyways to go about doing this?
>>>>>
>>>>> Many thanks!
>>>>>
>>>>> 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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--
Michael
http://www.dewey.myzen.co.uk/home.html
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