[R-meta] Calculating variances and z transformation for tetrachoric, biserial correlations?
Mark White
markhwhiteii at gmail.com
Mon Jul 3 00:01:55 CEST 2017
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
>
> --
> Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and
> Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD
> Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com
>
> >-----Original Message-----
> >From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces at r-
> >project.org] On Behalf Of Mark White
> >Sent: Sunday, July 02, 2017 20:05
> >To: r-sig-meta-analysis at r-project.org
> >Subject: [R-meta] Calculating variances and z transformation for
> >tetrachoric, biserial correlations?
> >
> >Hello,
> >
> >I have converted a number of summary statistics (contingency tables, *t-*
> >and
> >*F*-statistics,* M*s and *SD*s) to tetrachoric and biserial correlations.
> >The other effect sizes that I directly observed were raw correlations. I
> >have my model all set up to run, but I am unsure as to what to do about
> >these effect sizes. I see two options:
> >
> >1. Submit raw, tetrachoric, and biserial correlations and their variances
> >to analyses directly (what I have now).
> >
> >2. Do Fisher's r-to-z transformation and *then *submit those to analyses.
> >The problem here is: How do I convert tetrachoric and biserial
> >correlations
> >to Fisher's z? And if I do that, can I just use N to calculate the
> >variance? Or, do I have to also convert the variances of tetrachoric and
> >biserial correlations?
> >
> >In either case, I am not sure how `metafor::escalc` calculates variances
> >for tetrachoric (`RTET`) and biserial (`RBIS`) correlations. I tried
> >looking through the code for `metafor::escalc` on GitHub, but could not
> >figure out the calculations.
> >
> >I have included a table describing my effect sizes and how I calculated
> >them/their variances below.
> >
> >What do you all think would be the best way to handle these data?
> >
> >*Effect size*
> >
> >*k*
> >
> >*Effect size calculation*
> >
> >*Variance calculation*
> >
> >Raw correlation
> >
> >217
> >
> >Directly observed
> >
> >Typical large-samples estimation (see Hedges, 1989, Equation 5), using
> >`metafor::escalc`
> >
> >Tetrachoric correlation
> >
> >12
> >
> >From 2 x 2 contingency tables, using `metafor::escalc`
> >
> >From 2 x 2 contingency tables, using `metafor::escalc`
> >
> >
> >*Unsure what the formula is*
> >
> >Biserial correlation (from *t*- or *F*-statistic)
> >
> >8
> >
> >From *t*- or *F*-statistic to point-biserial correlation (using
> >`compute.es::tes`
> >and `compute.es::fes`) to biserial correlation (self-written function
> >based
> >on Jacobs & Viechtbauer, 2016, assuming *n*s equal across conditions)
> >
> >From *n*, using self-written function based on Soper's method (Jacobs &
> >Viechtbauer, 2016, Equation 13, assuming *n*s equal across conditions)
> >
> >Biserial correlation (from *M *and *SD*)
> >
> >2
> >
> >From means and standard deviations directly, using `metafor::escalc`
> >
> >From means and standard deviations directly, using `metafor::escalc`
> >
> >
> >*Unsure what the formula is*
> >
> >Square-root of eta-squared
> >
> >1
> >
> >F-statistic to Cohen’s *f* (Cohen, 1988) to eta-squared to square-root of
> >eta-squared as an approximation of a raw correlation coefficient (Lakens,
> >2013), using self-written function
> >
> >*This was a one-way ANOVA with three means (low, medium, high prejudice).*
> >
> >Typical large-samples estimation (see Hedges, 1989, Equation 5), using
> >`metafor::escalc`
> >
> >Best,
> >Mark
>
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