[R-meta] question on scatter plot of estimates (Fisher's Z) against the standard error

[Viechtbauer, Wolfgang (NP)]

Dear Gabriel,

The funnel() function accepts vectors for 'col' and 'pch'. So you could do:

ri <- c(0.5, 0.6, 0.7, 0.8, 0.9)
ni <- c(100,110,150,200,250)
dat <-escalc(measure = "ZCOR", ri = ri, ni = ni)
funnel_all <- rma.mv(yi,  vi,  data=dat)

grp <- c(1,2,1,1,2)
cols <- c("red","blue")
pchs <- c(19,15)
funnel(funnel_all, back=NA, level=0, refline=1, yaxis="seinv", col=cols[grp], pch=pchs[grp])
grid()
abline(v=1, col="blue", lwd=2)

Best,
Wolfgang

> -----Original Message-----
> From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> On Behalf
> Of Gabriel Cotlier via R-sig-meta-analysis
> Sent: Tuesday, November 7, 2023 08:50
> To: Dr. Gerta Rücker <gerta.ruecker using uniklinik-freiburg.de>
> Cc: Gabriel Cotlier <gabiklm01 using gmail.com>; R Special Interest Group for Meta-
> Analysis <r-sig-meta-analysis using r-project.org>
> Subject: Re: [R-meta] question on scatter plot of estimates (Fisher's Z) against
> the standard error
>
> Hello all,
> According to:
> https://www.metafor-project.org/doku.php/plots:funnel_plot_variations I
> think it could be the argument:
>
>    - yaxis="seinv" for the inverse of the standard errors
>
> Is what gives the 1/SE for each element in the vector of effect sizes in
> the x-axis.
>
> How can I "stand alone"—that would be outside the metafore package or not
> using the funnel function—to plot the same scatterplot of effect sizes
> (x-axis) against 1/SE (y-axis) in communion and a simple R scatter
> plot—without the funnel background—and afterwards use it to further cluster
> by coloring or using shapes ("pch") the effect sizes according to different
> categorical variables in the data frame?
>
> Thanks a lot for your help.
> Kind regards,
> Gabriel
>
> On Tue, Nov 7, 2023 at 9:13 AM Gabriel Cotlier <gabiklm01 using gmail.com> wrote:
>
> > Dear Greta and colleges,
> >
> > As can be seen below, Greta has provided a nice solution to a problem I
> > could not solve before, which is to have as an output of metafor's package
> > function funnel() for plotting the funnel plot without the background of
> > the funnel itself, which I very slightly modified as follows:
> >
> > ###################
> > ##
> > ##.  CODE FUNNEL
> > ##
> > ###################
> >
> > ## data
> > ri <- c(0.5, 0.6, 0.7, 0.8, 0.9)
> > ni <- c(100,110,150,200,250)
> > dat <-escalc(measure = "ZCOR",  ri = ri, ni = ni)
> >
> > ## model
> > funnel_all <- rma.mv(yi,  vi,  data=dat)
> >
> > ## get max and min values for plot
> > #funnel_all$yi
> > #min(funnel_all$yi)
> > #max(funnel_all$yi)
> >
> > ## funnel plot
> > f1 <- funnel(funnel_all,
> >              back = "white",
> >              # shade = "white",
> >              yaxis = "seinv",
> >              level = 0,
> >              # ylim = c(1, 5),
> >              refline=0,
> >              main="my plot",
> >              ylab = "Presicion (1/SE)",
> >              xlim = c(0.53,1.5))
> > # shade = c("white", "gray55", "gray75"),
> > # refline = 0)
> > # bg = "grey")
> > # legend = TRUE)
> > #grid(NULL, NULL,lwd = 1.6)
> > abline(h=c(9.849, 11.316, 12.783, 14.249, 15.716 ), col="grey", lwd=1,
> > lty=3)
> > abline(v=1, col="blue", lwd=2)
> > abline(v=c( 0.6, 0.8, 1, 1.2, 1.4), col="grey", lwd=1, lty=3)
> >
> > This has been a very efficient solution for my problem of getting exactly
> > the same funnel plot as the result of the metafore package
> > function funnel() without the funnel as a background. However, now I am
> > facing the challenge of having plotted the same funnel plot as the
> > output from the metafor's funnel() function without the background but
> > without the option of clustering by coloring or giving different point
> > shapes to the effect szes (points in the funnel plot) according to a
> > categorical in my data frame. I assume—probably wrongly—that for this task
> > I would have to reproduce the same funnel plot as is output from the funnel
> > plot function in the metafore package without the funnel background, as in
> > the code above, and use my data frame with the categorical variables to
> > color the points or give them different shapes and sizes using the
> > categorical variables in my data frame. Now the funnel plot function plots
> > in the x-axis the effect sizes, something I can easily get from my data
> > frame, but in the y-axis it uses 1/standad error (or 1 / SD). The
> > problem is that, as far as I understand, the standard error (SE)
> > corresponds to the standard deviation, or the R function sd() which gives
> > one value per input vector. Therefore, for some reason, plotting the effect
> > sizes (a vector class numeric) in the x-axis and 1/sd(effect_sizes) will
> > give me a number, not a vector of the same length as the effect sizes.
> >
> > *Therefore, how could one reproduce the same funnel plot as in the
> > metafore function (without the funnel background, just a scatterplot)
> > with an x-axis composed of the vector of effect sizes and a y-axis with
> > another vector corresponding to 1/stands error (1/SE) of each element in
> > the x-axis--If 1/SE is is equal to 1/sd(efect_sizes) which is a scaler and
> > not a vector ?*
> >
> > I think maybe this could be achieved somehow by giving, in the y-axis, a
> > kind of *"element-wise 1/SE"* to each element in the x-axis; that would
> > be an value corresponding to 1/SE to each of the elements in the vector of
> > effect sizes in the x-axis. Could this be the idea behind the funnel plot
> > function with 1/SE on the y-axis?
> >
> > If so, can this be somehow achieved following the example provided by
> > Greta below?
> >
> > ri <- c(0.5, 0.6, 0.7, 0.8, 0.9)
> > ni <- c(100,110,150,200,250)
> > dat <-escalc(measure = "ZCOR",  ri = ri, ni = ni)
> >
> > Thanks a lot for your help and guidance.
> > Kind regards,
> > Gabriel