[R-meta] Calculating variances and z transformation for tetrachoric, biserial correlations?
Viechtbauer Wolfgang (SP)
wolfgang.viechtbauer at maastrichtuniversity.nl
Mon Jul 3 00:27:24 CEST 2017
As James mentioned, just use:
Var(z) = Var(r) / (1 - r^2)^2
to compute the sampling variance of a Fisher's r-to-z transformed coefficient. So, for example:
dat1 <- escalc(measure="COR", ri=0.42, ni=23, add.measure=TRUE)
dat2 <- escalc(measure="RBIS", m1i=2.5, m2i=2.0, sd1i=1.1, sd2i=0.9, n1i=20, n2i=20, add.measure=TRUE)
dat3 <- escalc(measure="RTET", ai=10, bi=4, ci=6, di=12, add.measure=TRUE)
dat <- rbind(dat1, dat2, dat3)
dat
dat$vi <- dat$vi / (1 - dat$yi^2)^2
dat$yi <- transf.rtoz(dat$yi)
dat
You can also do this with the polyserial coefficient.
Note that for standard correlations, this results in using to 1/(n-1) for the variance (e.g., 1/22 in this example). To use the slightly more accurate 1/(n-3):
dat$vi[1] <- 1/(23-3)
dat
To compare:
escalc(measure="ZCOR", ri=0.42, ni=23, add.measure=TRUE)
Best,
Wolfgang
>-----Original Message-----
>From: Mark White [mailto:markhwhiteii at gmail.com]
>Sent: Monday, July 03, 2017 00:02
>To: Viechtbauer Wolfgang (SP)
>Cc: r-sig-meta-analysis at r-project.org
>Subject: Re: [R-meta] Calculating variances and z transformation for
>tetrachoric, biserial correlations?
>
>Thanks for your prompt and detailed responses!
>
>All of the effect sizes I culled that were from 2x2 tables, Ms and SDs, or
>t- and F-statistics were artificially dichotomized (either both or one
>variable, respectively). So they are, in fact, coming from a truly
>continuous distribution, so I believe that they can all be compared to one
>another.
>
>So it seems like:
>
>1. The 217 "regular" correlations can be converted from r to z, and then I
>can use the 1/(N-3) variance for that.
>
>2. The 10 effect sizes where only one variable was dichotomized can be
>converted to d (via Ms and SDs, or ts and Fs), which can then be converted
>to r_{eg} to z, via James's 2014 paper. I can also use his calculations
>for the variance of z from r_{eg}.
>
>(I would be doing this instead of `metafor::escalc`, because even though I
>could directly convert r_{bis} to z using the normal Fisher's r to z
>transformation, there is no way to go from var(RBIS) to var(Z), and using
>1/(N-3) is not appropriate).
>
>3. The issue is the 12 effect sizes from 2x2 contingency tables since even
>though I could convert directly from r_{tet} to z using Fisher's
>transformation, there is no way to go from var(RTET) to var(Z), and using
>1/(N-3) is not appropriate. I suppose I could go from an odds ratio to d
>to r_{eg} to z, using James's 2014 paper?
>
>4. The other issue is, even though I could get the r_{poly} to z, I could
>not get the var(r_{poly}) to var(z), and again using 1/(N-3) is not
>appropriate.
>
>How much would it harm the meta-analysis if 217 of my 240 effect sizes had
>the correct estimation of 1/(N-3), but the other 23 effects—transformed
>from r_{bis}, r_{poly}, r_{tet}—to z and then their variances estimated
>incorrectly using 1/(N-3)? It seems like, although I can get comparable
>effect sizes now, I cannot transform their variances appropriately.
>
>Thanks,
>Mark
>
>On Sun, Jul 2, 2017 at 4:30 PM, Viechtbauer Wolfgang (SP)
><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
>Let me address the computations first (that's the easy part).
>
>Tetrachoric correlation: For tetrachoric correlations, escalc() computes
>the MLE (requires an iterative routine -- optim() is used for that). The
>sampling variance is estimated based on the inverse of the Hessian
>evaluated at the MLE. There is no closed form solution for that.
>
>Biserial correlation (from *t*- or *F*-statistic): You can use a trick
>here if you still want to use escalc(). If you know t (or t = sqrt(F)),
>then just use escalc(measure="RBIS", m1i=t*sqrt(2)/sqrt(n), m2i=0, sd1i=1,
>sd2i=1, n1i=n, n2i=n), where n is the size of the groups (not the total
>sample size). For example, using the example from Jacobs & Viechtbauer
>(2017):
>
>escalc(measure="RBIS", m1i=1.68*sqrt(2)/sqrt(10), m2i=0, sd1i=1, sd2i=1,
>n1i=10, n2i=10)
>
>yields yi = 0.4614 and vi = 0.0570, exactly as in the example. You used
>equation (13) to compute the sampling variances, which is the approximate
>equation. escalc() uses the 'exact' one (equation 12). That way, you are
>also consistent with what you get for the case of "Biserial correlation
>(from *M *and *SD*)".
>
>Biserial correlation (from *M *and *SD*): As mentioned above, escalc()
>uses equation (12) from Jacobs & Viechtbauer (2017) to compute/estimate
>the sampling variance.
>
>Square-root of eta-squared: You cannot use the large-sample variance of a
>regular correlation coefficient for this. The right thing to do is to
>compute a polyserial correlation coefficient here (the extension of the
>biserial to more than two groups). You can do this using the polycor
>package. Technically, the polyserial() function from that package requires
>you to input the raw data, which you don't have. If you have the means and
>SDs, you can just simulate raw data with exactly those means and SDs and
>use that as input to polyserial(). The means and SDs are sufficient
>statistics here, so you should always get the same result regardless of
>what specific values are simulated. Here is an example:
>
>x1 <- scale(rnorm(10)) * 2.4 + 10.4
>x2 <- scale(rnorm(10)) * 2.8 + 11.2
>x3 <- scale(rnorm(10)) * 2.1 + 11.5
>
>x <- c(x1, x2, x3)
>y <- rep(1:3,each=10)
>
>polyserial(x, y, ML=TRUE, std.err=T, control=list(reltol=1e12))
>
>If you run this over and over, you will (should) always get the same
>polyserial correlation coefficient of 0.2127. The standard error is
>~0.195, but it changes very slightly from run to run due to minor
>numerical differences in the optimization routine. Note that I increased
>the convergence tolerance a bit to avoid that those numerical issues also
>affect the estimate itself. But these minor differences are essentially
>inconsequential anyway.
>
>If you do not have the means and SDs, then well, don't know what to do off
>the top of my head. But again, don't treat the converted value as if it
>was a correlation coefficient. It is not.
>
>Now for your question what/how to combine:
>
>The various coefficients (Pearson product-moment correlation coefficients,
>biserial correlations, polyserial correlations, tetrachoric correlations)
>are directly comparable, at least in principle (assuming that the
>underlying assumptions hold -- e.g., bivariate normality for the
>observed/latent variables). I just saw that James also posted an answer
>and he raises an important issue about the theoretical comparability of
>the various coefficients, esp. when they arise from different sampling
>designs. I very much agree that this needs to be considered. You could
>take a pragmatic / empirical approach though by coding the type of
>coefficient / design from which the coefficient arose and examine
>empirically whether there are any systematic differences (i.e., via a
>meta-regression analysis) between the types.
>
>As James also points out, you can use Fisher's r-to-z transformation on
>all of these coefficients, but to be absolutely clear: Only for Pearson
>product-moment correlation coefficients is the variance then approximately
>1/(n-3). I have seen many cases where people converted all kinds of
>statistics to 'correlations', then applied Fisher's r-to-z transformation,
>and then used 1/(n-3) as the variance, which is just flat out wrong in
>most cases. Various books on meta-analysis even make such faulty
>suggestions.
>
>Also, Fisher's r-to-z transformation will *only* be a variance stabilizing
>transformation for Pearson product-moment correlation coefficients (e.g.,
>the actual variance stabilizing transformation for biserial correlation
>coefficients is given by equation 17 in Jacobs & Viechtbauer, 2017 -- and
>even that is just an approximation, since it is based on Soper's
>approximate formula). If you apply Fisher's r-to-z transformation to other
>types of coefficients, you have to use the right sampling variance (see
>James' mail). Also note: You cannot mix different transformations (i.e.,
>use Fisher's r-to-z transformation for all).
>
>Whether applying Fisher's r-to-z transformation to other coefficients
>(other than 'regular' correlation coefficients) is actually advantageous
>is debatable. Again, you do not get the nice variance stabilizing
>properties here (the transformation may still have some normalizing
>properties). If I remember correctly, James examined this in his 2014
>paper, at least for biserial correlations (James, please correct me if I
>misremember).
>
>Best,
>Wolfgang
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