[R-meta] Question on Forest Plot by subgroups
Gabriel Cotlier
g@b|k|m01 @end|ng |rom gm@||@com
Wed Jun 21 06:24:53 CEST 2023
Hello Wolfgang,
Thanks a lot!
I am happy to participate on the mailing list and share coding experience
in meta-analysis with metafor.
Kind regards,
Gabriel
On Tue, Jun 20, 2023 at 3:07 PM Viechtbauer, Wolfgang (NP) <
wolfgang.viechtbauer using maastrichtuniversity.nl> wrote:
> Dear Gabriel,
>
> Glad to hear you figured things out and nice to report this back to the
> list.
>
> Best,
> Wolfgang
>
> >-----Original Message-----
> >From: R-sig-meta-analysis [mailto:
> r-sig-meta-analysis-bounces using r-project.org] On
> >Behalf Of Gabriel Cotlier via R-sig-meta-analysis
> >Sent: Tuesday, 20 June, 2023 9:04
> >To: R Special Interest Group for Meta-Analysis
> >Cc: Gabriel Cotlier
> >Subject: Re: [R-meta] Question on Forest Plot by subgroups
> >
> >Hello all,
> >
> >Yesterday I posted a solution for the plotting forest plot by subgroups
> for
> >my particular case and I was actually making the mistake when choosing the
> >variable for the argument "order" which I corrected in the previously
> >posted code (found my own mistake in the argument "order").
> >
> >But I also posted that was redundant information in my case to use
> >subset=(alloc
> >== 1) for the subgroups models: res.s, res.r and res.a and indeed it is if
> >I use "alloc" as follows:
> >
> >res.s <- rma(yi, subset=(alloc == 1), vi, data=dat)
> >res.r <- rma(yi, subset=(alloc == 1), vi, data=dat)
> >res.a <- rma(yi, vi, subset=(alloc == 1), data=dat)
> >
> >However, I found out that this gives the same overall result for each
> >sub-group as for the total data.
> >Therefore I correct it herein as follows: to get at the end of each
> >subgroup its particular overall results the use subset= c() is needed.
> >It worked for me as follows:
> >
> >### fit random-effects model in the three subgroups
> >res.s <- rma(yi, vi, subset= c(Type == "Rainfed"), data=dat)
> >res.r <- rma(yi, vi, subset = c(Type == "Experimental"), data=dat)
> >res.a <- rma(yi, vi, subset = c(Type == "Computational simulation"),
> >data=dat)
> >
> >In this way it will give the overall model results for each subgroup
> >correctly together with the overall result for the complete dataset at the
> >end.
> >
> >Sorry for the confusion.
> >Kind regards,
> >Gabriel
> >
> >On Mon, Jun 19, 2023 at 5:49 PM Gabriel Cotlier <gabiklm01 using gmail.com>
> wrote:
> >
> >> Hello all,
> >>
> >> I found the solution to the problem to the code I plotted previously.
> The
> >> problem was that I was ordering by "alloc" which is a column of sing()
> of
> >> correlations and not by the column that divide the groups (3 groups
> >> expressed in a column named "Type" : Computational
> >> simulation","Experimental","Natural Rainfed") which in my case is named
> >> "Type",after correcting this I also remove unnecessary redundant
> >> information subset=(alloc == 1) in each of the models res.s, res.r and
> >> res.a. Please find the corrected working code below with highlighted
> >> locations where modifications were made :
> >>
> >> ############################## CODE
> >> ###########################################
> >>
> >> pdf(file="ForestPlotCompleteDataSetRahul_Test.pdf", width = 12, height =
> >> 35)
> >>
> >> mlabfun <- function(text, res) {
> >> list(bquote(paste(.(text),
> >> " (Q = ", .(formatC(res$QE, digits=2, format="f")),
> >> ", df = ", .(res$k - res$p),
> >> ", p ", .(metafor:::.pval(res$QEp, digits=2,
> >> showeq=TRUE, sep=" ")), "; ",
> >> I^2, " = ", .(formatC(res$I2, digits=1,
> format="f")),
> >> "%, ",
> >> tau^2, " = ", .(formatC(res$tau2, digits=2,
> >> format="f")), ")")))}
> >>
> >> forest(res,
> >> top = 2,
> >> #xlim=c(-8, 6),
> >> #alim = c(-3.36077, 5.181815),
> >> alim = c(-3.8, 6),
> >> #at=log(c(0.05, 0.25, 1, 4)),
> >> #atransf=exp,
> >> #width = 4,
> >> showweights = TRUE,
> >> ilab=cbind(ni), # content of extra columns of information
> >> ilab.xpos=c(-4.6), # position of extra columns of information
> >> cex=0.75,
> >> ylim=c(-1, 161), # rows in the y-axis from min-row to max-row
> with
> >> text.
> >> slab = paste(dat$Authors, dat$Year, sep = ", "),
> >> order=Type,
> >> rows=c(2:15,19:85,89:156), # this divide by groups the studies (3
> >> groups)
> >> mlab=mlabfun("RE Model for All Studies", res),
> >> #psize= 1 ,
> >> efac = 0.2, # size of the polygon (the diamond)
> >> # header="Author(s) and Year")
> >> )
> >> # abline(h=res$k+8, lwd=2, col="white")
> >>
> >> op <- par(cex=0.75, font=2)
> >>
> >> ### add additional column headings to the plot
> >> text(c(-15), res$k+10, c("Author(s) and Year"), cex = 1.2, font = 2)
> >> text(c(-4.6), res$k+10, c("Samples size"), cex = 1.2, font = 2)
> >> text(c(9.7), res$k+10, c("Weight"),cex = 1.2, font=2)
> >> text(c(9.7), res$k+9.3, c("%"),cex = 1.2, font=2)
> >> text(c(12.6), res$k+10, c("Fisher's zr [95% CI]"),cex = 1.2, font=2)
> >> text(c(res$k+13), c("Complete Dataset"), cex = 2, font = 2)
> >>
> >> par(font=4)
> >>
> >> ### add text for the subgroups
> >> text(-17.2, c(16,86,157), pos=4, c("Computational simulation",
> >> "Experimental",
> >> "Natural Rainfed"), cex = 1.3)
> >>
> >> par(op)
> >>
> >> ### fit random-effects model in the three subgroups
> >> res.s <- rma(yi, vi, data=dat)
> >> res.r <- rma(yi, vi, data=dat)
> >> res.a <- rma(yi, vi, data=dat)
> >>
> >> ### add summary polygons for the three subgroups
> >> addpoly(res.s, row= 88, mlab=mlabfun("RE Model for Subgroup",
> res.s),efac
> >> = 0.2, col='red')
> >> addpoly(res.r, row= 18, mlab=mlabfun("RE Model for Subgroup",
> res.r),efac
> >> = 0.2, col='green')
> >> addpoly(res.a, row= 1, mlab=mlabfun("RE Model for Subgroup",
> res.a),efac =
> >> 0.2, col='blue')
> >>
> >>
> >> dev.off()
> >>
> >>
> >>
> >>
> >>
> >> On Mon, Jun 19, 2023 at 3:46 PM Gabriel Cotlier <gabiklm01 using gmail.com>
> >> wrote:
> >>
> >>> Hello all,
> >>>
> >>> I have taken an example from here
> >>> <
> https://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups>
> >and
> >>> modified it to my case study of Fisher's z correlations meta-analysis
> with
> >>> the code below.
> >>> I would like to plot a forest plot in which each of the subgroups ( 3
> >>> groups expressed in a column named "Type" : Computational
> >>> simulation","Experimental","Natural Rainfed") each showing the studies
> >>> (rows) with positive correlations and those with negative correlations
> >>> divided in agreement to the line of no effect located at zero. I have
> used
> >>> a column named "alloc" which has a 1 for those correlations (rows) with
> >>> positive value and -1 for those with negative value, however for some
> >>> reason it does not work as expected. It mixes the lines from
> >>> different groups, ploting them where they do not correspond and also
> does
> >>> not plot the model summary for the second and third group.
> >>> I tried to change several arguments to solve it, however
> unsuccessfully.
> >>>
> >>> What could be the error?
> >>> Thanks a lot for your help.
> >>>
> >>> ############################## CODE
> >>> ###########################################
> >>>
> >>> pdf(file="ForestPlotCompleteDataSetbyGroups.pdf", width = 12, height =
> 35)
> >>>
> >>> mlabfun <- function(text, res) {
> >>> list(bquote(paste(.(text),
> >>> " (Q = ", .(formatC(res$QE, digits=2, format="f")),
> >>> ", df = ", .(res$k - res$p),
> >>> ", p ", .(metafor:::.pval(res$QEp, digits=2,
> >>> showeq=TRUE, sep=" ")), "; ",
> >>> I^2, " = ", .(formatC(res$I2, digits=1,
> format="f")),
> >>> "%, ",
> >>> tau^2, " = ", .(formatC(res$tau2, digits=2,
> >>> format="f")), ")")))}
> >>> forest(res,
> >>> top = 2,
> >>> # xlim=c(-8, 6),
> >>> # alim = c(-3.36077, 5.181815),
> >>> alim = c(-3.8, 6),
> >>> # at=log(c(0.05, 0.25, 1, 4)),
> >>> # atransf=exp,
> >>> # width = 4,
> >>> showweights = TRUE,
> >>> ilab=cbind(ni), # content of extra columns of information
> >>> ilab.xpos=c(-4.6), # position of extra columns of information
> >>> cex=0.75,
> >>> ylim=c(-1, 161), # rows in the y-axis from min-row to max-row
> with
> >>> text.
> >>> slab = paste(dat$Authors, dat$Year, sep = ", "),
> >>> order=alloc,
> >>> rows=c(2:15,19:85,89:156), # this divide by groups the studies
> (3
> >>> groups) from column named "Type"
> >>> mlab=mlabfun("RE Model for All Studies", res),
> >>> #psize= 1 ,
> >>> efac = 0.2, # size of the polygon (the diamond)
> >>> # header="Author(s) and Year")
> >>> )
> >>>
> >>> op <- par(cex=0.75, font=2)
> >>>
> >>> text(c(-15), res$k+10, c("Author(s) and Year"), cex = 1.2, font = 2)
> >>> text(c(-4.6), res$k+10, c("Samples size"), cex = 1.2, font = 2)
> >>> text(c(9.7), res$k+10, c("Weight"),cex = 1.2, font=2)
> >>> text(c(9.7), res$k+9.3, c("%"),cex = 1.2, font=2)
> >>> text(c(12.6), res$k+10, c("Fisher's zr [95% CI]"),cex = 1.2, font=2)
> >>> text(c(res$k+13), c("Complete Dataset"), cex = 2, font = 2)
> >>>
> >>> par(font=4)
> >>>
> >>> text(-17.2, c(16,86,157), pos=4, c("Computational simulation",
> >>> "Experimental",
> >>> "Natural Rainfed"), cex = 1.3)
> >>> par(op)
> >>>
> >>> ### fit random-effects model in the three subgroups
> >>> res.s <- rma(yi, vi, subset=(alloc == 1), data=dat)
> >>> res.r <- rma(yi, vi, subset=(alloc == 2), data=dat)
> >>> res.a <- rma(yi, vi, subset=(alloc == 3), data=dat)
> >>>
> >>> ### add summary polygons for the three subgroups
> >>> addpoly(res.s, row= 88, mlab=mlabfun("RE Model for Subgroup",
> res.s),efac
> >>> = 0.2, col='red')
> >>> addpoly(res.r, row= 18, mlab=mlabfun("RE Model for Subgroup",
> res.r),efac
> >>> = 0.2, col='green')
> >>> addpoly(res.a, row= 1, mlab=mlabfun("RE Model for Subgroup",
> res.a),efac
> >>> = 0.2, col='blue')
> >>>
> >>> dev.off()
>
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