[R] Metafor -can't calculate heterogeneity with non-positive sampling variances

[Michael Dewey]

At 16:38 27/08/2014, Owen, Branwen wrote:
>Thank you very much for your quick reply Wolfgang. The 0 does make 
>sense - I'm working on some behavioural data and in one study none 
>reported that particular behaviour. Up til now I have been 
>calculating I2 without that study, as it's on the small side I don't 
>think it makes much difference. I'm just beginning to wonder if 
>there is another way.

Branwen
I have not tried this but if your dataset contains proportions as 
your text implies then why not supply xi and ni to rma.uni and then 
get it to compute one of the range of options outlined in the 
documentation for escalc? The Freeman-Tukey one might be worth considering.

Of course I may have misunderstood your brief description.

>I'll think about it some more best wishes Branwen 
>________________________________________ From: Viechtbauer Wolfgang 
>(STAT) [wolfgang.viechtbauer at maastrichtuniversity.nl] Sent: 27 
>August 2014 17:30 To: Owen, Branwen; r-help at r-project.org Subject: 
>RE: [R] Metafor -can't calculate heterogeneity with non-positive 
>sampling variances The warning message pretty much says it: When one 
>of the variances is zero, then the I^2 statistic (and various other 
>things) cannot be computed, at least if one sticks to the usual 
>equations/methods. So, if you think the 0 sampling variances really 
>make sense and you really want to get something like I^2, you will 
>have to come up with a creative solution. On the metafor package 
>website, I explain how I^2 is computed (for the random-effects 
>model): 
>http://www.metafor-project.org/doku.php/faq#how_are_i_2_and_h_2_computed_i 
>The crux of the problem is how to compute the 'typical' within-study 
>variance (s^2). With any vi=0, you get division by zero in the 
>equation given. So, you will have to compute s^2 in a different way. 
>You could leave out the studies where vi=0, but this doesn't seem 
>quite right, because this will inflate s^2. You could just take the 
>simple average of the vi values and use that for s^2, but then it's 
>not really I^2 anymore (it's I^2-like). My question would be: How 
>come you have studies where the sampling variance is estimated to be 
>zero and does that really make sense? Maybe the solution is not to 
>fix the computation of I^2, but to consider if vi=0 is really 
>sensible. Best, Wolfgang > -----Original Message----- > From: 
>r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] > 
>On Behalf Of Owen, Branwen > Sent: Wednesday, August 27, 2014 
>13:48 > To: r-help at r-project.org > Subject: [R] Metafor -can't 
>calculate heterogeneity with non-positive > sampling variances > > 
>Hi, I'm doing a meta-analysis in metafor. All is fine except when 
>there > are 0s in the values that i'm pooling, then i get a pooled 
>estimate but > not the I2 that i am also interested in. > for 
>example: > > summary(rma.1<- > 
>rma(yi,vi,data=mix,method="ML",knha=F,weighted=F,intercept=T)) > 
>(where yi are the study outcomes, one of which is 0, and vi is the > 
>variance of the study outcomes) > > Random-Effects Model (k = 17; 
>tau^2 estimator: 
>ML) > >   logLik  deviance       AIC       BIC      AICc >  13.0539 
>      Inf  -22.1077  -20.4413  -21.2506 > > tau^2 (estimated amount 
>of total heterogeneity): 0.0119 (SE = 0.0043) > tau (square root of 
>estimated tau^2 value):      0.1089 > > Model Results: > > 
>estimate       se     zval     pval    ci.lb    ci.ub >   0.1837 
>0.0274   6.7154   <.0001   0.1301   0.2374      *** > > --- > 
>Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > > 
>Warning messages: > 1: In rma(yi, vi, data = mix, method = "ML", 
>knha = F, weighted = F,  : >   There are outcomes with non-positive 
>sampling variances. > 2: In rma(yi, vi, data = mix, method = "ML", 
>knha = F, weighted = F,  : >   Cannot compute Q-test, I^2, or H^2 
>with non-positive sampling > variances. > > Is there any way around 
>this? > thanks > Branwen > 
>________________________________________ > From: 
>r-help-bounces at r-project.org [r-help-bounces at r-project.org] on > 
>behalf of r-help-owner at r-project.org [r-help-owner at r-project.org] > 
>Sent: 27 August 2014 13:36 > To: Owen, Branwen > Subject: Metafor 
>-can't calculate heterogeneity with non-positive > sampling 
>variances > > Message rejected by filter rule match > > > 
>______________________________________________ > 
>R-help at r-project.org mailing list > 
>https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the 
>posting guide http://www.R-project.org/posting- > guide.html > and 
>provide commented, minimal, self-contained, reproducible code.

Michael Dewey
info at aghmed.fsnet.co.uk
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