[R-meta] Putting pooled effects from different multilevel meta analyses into the same forest plot

Michael Dewey ||@t@ @end|ng |rom dewey@myzen@co@uk
Thu Dec 24 12:38:10 CET 2020 

You probably need to play with xlim or alim, I forget which. The 
function returns some of the settings so you know where to start from.

Michael

On 23/12/2020 17:36, Dylan Johnson wrote:
> 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 <mailto:lists using dewey.myzen.co.uk>>; Dylan 
> Johnson<mailto:dylanr.johnson using mail.utoronto.ca 
> <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 <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 
> <mailto:dylanr.johnson using mail.utoronto.ca>>
>>>> Cc: R meta<mailto:r-sig-meta-analysis using r-project.org 
> <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 
> <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
>>
>>       [[alternative HTML version deleted]]
>>
>>
>>
>>
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>>
> 
> --
> Michael
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Michael
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