[R-meta] Putting pooled effects from different multilevel meta analyses into the same forest plot
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 at dewey.myzen.co.uk> *Sent: *December 23, 2020 7:04 AM *To: *Dylan Johnson <mailto:dylanr.johnson at mail.utoronto.ca>; Viechtbauer, Wolfgang (SP) <mailto:wolfgang.viechtbauer at maastrichtuniversity.nl> *Cc: *r-sig-meta-analysis at r-project.org <mailto:r-sig-meta-analysis at 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 at maastrichtuniversity.nl>
Sent: December 21, 2020 10:55 AM
To: Michael Dewey<mailto:lists at dewey.myzen.co.uk <mailto:lists at dewey.myzen.co.uk>>; Dylan
Johnson<mailto:dylanr.johnson at mail.utoronto.ca <mailto:dylanr.johnson at mail.utoronto.ca>>
Cc: r-sig-meta-analysis at r-project.org<mailto:r-sig-meta-analysis at 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 at dewey.myzen.co.uk <mailto:lists at dewey.myzen.co.uk>] Sent: Monday, 21 December, 2020 10:54 To: Dylan Johnson; Viechtbauer, Wolfgang (SP) Cc: r-sig-meta-analysis at 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 at maastrichtuniversity.nl>
Sent: December 20, 2020 3:26 PM To: Dylan Johnson<mailto:dylanr.johnson at mail.utoronto.ca
<mailto:dylanr.johnson at mail.utoronto.ca>>
Cc: R meta<mailto:r-sig-meta-analysis at r-project.org
<mailto:r-sig-meta-analysis at 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 at mail.utoronto.ca
<mailto:dylanr.johnson at 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 at 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 at r-
project.org]
On Behalf Of Dylan Johnson Sent: Sunday, 20 December, 2020 2:01 To: r-sig-meta-analysis at 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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