[R-sig-ME] metafor: estimate correlation between response variables (meta-analysis)
Viechtbauer Wolfgang (SP)
wolfgang.viechtbauer at maastrichtuniversity.nl
Wed Dec 14 11:14:00 CET 2016
So there really is a 4x4 var-cov matrix for each study then. So, like this:
trt1-var1 trt1-var2 trt2-var1 trt2-var2
trt1-var1 v_11 cov_11,12 cov_11,21 cov_11,22
trt1-var2 v_12 cov_12,21 cov_12,22
trt2-var1 v_21 cov_21,22
trt2-var2 v_22
(leaving out subscript i -- but there is such a 4x4 block for each study).
And the covariance for different treatments (for the same variable?) is known. So that would be cov_11,21 and cov_12,22. That leaves 4 unknown covariances. So yes, one could impute those (by making some reasonable assumptions about the correlations and then back-computing the covariances using appropriate equations) followed by a sensitivity analysis.
I agree that implementing something like this can be a bit tricky, but can be done.
Best,
Wolfgang
> -----Original Message-----
> From: Gustaf Granath [mailto:gustaf.granath at gmail.com]
> Sent: Tuesday, December 13, 2016 15:55
> To: r-sig-mixed-models at r-project.org
> Cc: Viechtbauer Wolfgang (SP)
> Subject: Re: metafor: estimate correlation between response variables
> (meta-analysis)
>
> Hi,
>
> Im sorry if my toy example wasnt clear. You almost got it right though.
> But yi is not independent for different treatments within a study. I
> have the estimated covariance though, so no problem to account for this.
> In my example I did include this covariance when I constructed V (I used
> the outcome covariance in the berkey1998 data to illustrate this). If I
> understand you correctly, the best way check the influence of
> within-study correlation between responses, is to manually add
> covariances (try a range of reasonable values) between responses in V. I
> will try that - although, Im not sure that it is easy to implement.
>
> Thanks,
>
> Gustaf
>
> On 2016-12-13 13:41, Viechtbauer Wolfgang (SP) wrote:
> > I have a hard time making sense of that toy example.
> >
> > But if I understand you correctly, you have data like this:
> >
> > study trt respvar yi vi
> > -----------------------
> > 1 1 1 . .
> > 1 1 2 . .
> > 1 2 1 . .
> > 1 2 2 . .
> > 2 1 1 . .
> > 2 1 2 . .
> > 2 2 1 . .
> > 2 2 2 . .
> > ...
> >
> > where 'yi' and 'vi' are the observed outcomes and corresponding
> variances.
> >
> > Within studies, can we assume that 'yi' is independent for different
> treatments? Then V (the var-cov matrix of the 'yi' vector) will be block-
> diagonal, each block being a 2x2 matrix (since you only need to consider
> the covariance between 'yi' for respvar 1 and 'yi' for respvar 2). And
> the problem is that the covariances are unknown. Correct so far?
> >
> > If so, the 'R' argument has nothing to do with this. If you want to
> approach this by means of a sensitivity analysis, then just impute the
> unknown covariances directly into 'V' and analyze by means of an
> appropriate multilevel/multivariate model. Something like this:
> >
> > dat$study.trt <- interaction(dat$study, dat$trt)
> > rma.mv(yi, V, mods = ~ factor(trt) - 1, random = list(~ 1 | study, ~
> respvar | study.trt), struct="UN", data=dat)
> >
> > To impute the covariances, you may be able to use cor*sqrt(v1*v2),
> where 'cor' is some kind of assumed correlation (maybe constant across
> studies, maybe not). However, whether this is appropriate depends on your
> outcome measure. For example, this would be fine for means or mean
> differences, but the covariance between standardized mean differences
> cannot be computed that way (see Gleser & Olkin, 2009, for the correct
> equation).
> >
> > Gleser, L. J., & Olkin, I. (2009). Stochastically dependent effect
> sizes. In H. Cooper, L. V. Hedges, & J. C. Valentine (Eds.), The handbook
> of research synthesis and meta-analysis (2nd ed., pp. 357-376). New York:
> Russell Sage Foundation.
> >
> > Best,
> > Wolfgang
> >
> >> -----Original Message-----
> >> From: R-sig-mixed-models [mailto:r-sig-mixed-models-bounces at r-
> >> project.org] On Behalf Of Gustaf Granath
> >> Sent: Tuesday, December 13, 2016 11:42
> >> To: r-sig-mixed-models at r-project.org
> >> Subject: [R-sig-ME] metafor: estimate correlation between response
> >> variables (meta-analysis)
> >>
> >> Hi,
> >> Im trying the estimate the correlation between two response variable
> in
> >> a meta-analysis. Basically, are effects on y1 associated with effects
> on
> >> y2 across studies. Unfortunately, I dont have information on y1-y2
> >> correlations within each study. In addition, each study contain
> multiple
> >> treatments, adding within-study dependence for each response variable.
> >>
> >> Because I dont have the y1-y2 covariance in each study, my idea is to
> >> run analyses with different covariance/correlation values to explore
> how
> >> this covariance affect the result. Reading the rma.mv() documentation,
> >> this seems possible through the R= argument, but I cant figure out
> how.
> >> Alternatively, I can add covariances in the matrix describing the
> known
> >> var-covariance matrix of the within-study dependence, but it seemed
> like
> >> the R argument is a easier solution (I may be wrong though). Below
> >> follow code illustrating my problem using the dat.berkey1998 example.
> >>
> >> Cheers
> >>
> >> Gustaf
> >>
> >> # Estimate correlation between two response variables
> >> # with within-study dependence
> >> library(metafor)
> >>
> >> # Make up an example based on the berkey1998 data.
> >> # Multiple outcomes (multiple treatments)
> >> # within each study, for each response variable, are created.
> >> # Covariances between response variables (within studies) are unknown.
> >> dat <- get(data(dat.berkey1998))
> >> st.vcov <- dat[, c("v1i", "v2i")] # save vcov matrices to add later
> >> dat <- rbind(dat, dat)
> >> dat <- dat[order(dat$trial, dat$outcome),] # fix order
> >> dat[,c("v1i", "v2i")] <- rbind(st.vcov,st.vcov) # put back matrices
> >> dat$trial.treat <-paste(rep(1:2, nrow(dat)/2), dat$trial, sep="_") #
> id
> >> for treatments within trials
> >>
> >> # Covariances within studies, for each response variable, is known.
> >> Hence, a
> >> # varcov-matrix for each study and response, can be made and added as
> >> blocks
> >> # in a large varcov-matrix for the data set.
> >> # First a within-study dependence dummy must be added
> >> dat$stud.unit <- interaction(dat$trial, dat$outcome) # within-trial
> >> dependence dummy
> >> # Put together known varcov matrix
> >> V <- bldiag(lapply(split(dat[,c("v1i", "v2i")], dat$stud.unit),
> >> as.matrix))
> >>
> >> # plot relationship between response variables
> >> dat.wide <- reshape(dat, direction="wide", v.names = "yi", timevar =
> >> "outcome", idvar = "trial.treat")
> >> plot(yi.AL ~yi.PD, dat.wide)
> >> cor(dat.wide$yi.AL, dat.wide$yi.PD)
> >> # r = 0.39, if using the study outcomes ignoring all
> >> dependence/uncertainty.
> >>
> >> # Run analysis
> >> res <- rma.mv(yi, V, mods = ~ outcome - 1,
> >> random = ~ outcome | trial,
> >> struct="UN", data=dat, method="REML")
> >> print(res, digits=3)
> >> # correlation = 0.51, when accounting for dependence etc. But, y1 and
> y2
> >> are assumed to be independent
> >> # within each study. How to perform sensitivity analyses by adding
> >> different values
> >> # on this within-study correlation between the two response variables?
> >>
> >> --
> >> Gustaf Granath (PhD)
> >> Post doc
> >> Swedish University of Agricultural Sciences
> >> Department of Ecology
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