[R-meta] Using rcalc() in metafor

[Yuhang Hu]

Dear  Lukasz,

Thanks.
Regarding question 1, could you please elaborate, in what ways a non-positive
definite V matrix can invalidate the results of my rma.mv() model?

Regarding question 2, I think your answer doesn't produce the
desired output. Maybe, we can, instead, do:

transf.ztor(coef(summary(res))[c("estimate","ci.lb","ci.ub")])

However, as asked in question 2, how can I convert 'vcov(res)' from "rtoz"
scale back to "ztor" scale?

Thanks,
Yuhang

On Fri, Aug 4, 2023 at 7:23 PM Lukasz Stasielowicz <
lukasz.stasielowicz using uni-osnabrueck.de> wrote:

> Dear Yuhang,
>
>
> 1. Playing around with the imputation settings for the V matrix is one
> option, e.g.,
> impute_covariance_matrix from the clubSandwich package
> or
> vcalc from the metafor package.
>
> There is certainly a trade-off. The risk of getting non-positive
> definite matrices can be reduced by simplifying the covariance
> structure, but it will probably lead to less realistic assumptions.
> However, one could conduct sensitivity analyses by using different
> imputation settings for the V matrix and checking whether the main
> findings change substantially.
>
>
> 2. The mean effect size and its confidence interval can be transformed
> using predict:
> predict(res, transf=transf.ztor)
>
>
>
> Best,
>
> Lukasz
> --
> Lukasz Stasielowicz
> Osnabrück University
> Institute for Psychology
> Research methods, psychological assessment, and evaluation
> Lise-Meitner-Straße 3
> 49076 Osnabrück (Germany)
> Twitter: https://twitter.com/l_stasielowicz
>
> On 04.08.2023 12:00, r-sig-meta-analysis-request using r-project.org wrote:
> > Send R-sig-meta-analysis mailing list submissions to
> >       r-sig-meta-analysis using r-project.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis
> > or, via email, send a message with subject or body 'help' to
> >       r-sig-meta-analysis-request using r-project.org
> >
> > You can reach the person managing the list at
> >       r-sig-meta-analysis-owner using r-project.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of R-sig-meta-analysis digest..."
> >
> >
> > Today's Topics:
> >
> >     1. Using rcalc() in metafor (Yuhang Hu)
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 4 Aug 2023 11:12:01 +0800
> > From: Yuhang Hu <yh342 using nau.edu>
> > To: R meta <r-sig-meta-analysis using r-project.org>
> > Subject: [R-meta] Using rcalc() in metafor
> > Message-ID:
> >       <
> CA+dzWjp1xS_+zU2gYv2YeR04zM4qdK3U9KXy9dBJmFRShyaO6g using mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello All (re-posting this in case, it slipped through the cracks),
> >
> > In my data below, I have numerous NAs for the correlations reported for a
> > set of 8 variables of interest across my studies. Two questions:
> >
> > 1- rma.mv() says that my V is non-positive definite. To what extent can
> I
> > ignore this and if not ignorable, what other options do I have?
> >
> > 2- How can I convert back the 'coef(res)' and 'vcov(res)' from the "rtoz"
> > scale to the original "r" scale ?
> >
> > Thanks,
> > Yuhang
> >
> > # Data and code: #
> >
> > dat <- read.csv("https://raw.githubusercontent.com/ilzl/i/master/j.csv")
> >
> > tmp <- rcalc(ri ~ var1 + var2 | Study, ni=N, data=dat, rtoz = TRUE)
> > V <- tmp$V
> > dat <- tmp$dat
> >
> > res <- rma.mv(yi~ var1.var2 - 1, V,
> >                 random = ~var1.var2 | Study,
> >                 data=dat, control = list(nearpd=TRUE), sparse = TRUE) |>
> >    robust(cluster = Study, clubSandwich = TRUE)
> >
> >       [[alternative HTML version deleted]]
> >
> >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > R-sig-meta-analysis mailing list @ R-sig-meta-analysis using r-project.org
> > To manage your subscription to this mailing list, go to:
> > https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis
> >
> >
> > ------------------------------
> >
> > End of R-sig-meta-analysis Digest, Vol 75, Issue 1
> > **************************************************
>
>

	[[alternative HTML version deleted]]