[R-meta] Problems using rma.mh
Dear Gerta, Thanks -- it's good at least to know that it's not only me seeing the error :-) Regarding continuity correction: I agree; but given that a correction is sometimes applied even to Mantel-Haenszel pooling in extreme cases (such as when all studies have zero events in the same arm, as in my example), I wondered whether a similar argument could/should be applied to other associated statistics. I have copied Wolfgang into this email: Wolfgang, could you take a look at the issue with rma.mh, please? Many thanks, David. On Fri, Jun 12, 2020 at 10:54 AM Gerta Ruecker
<ruecker at imbi.uni-freiburg.de> wrote:
Dear David, With "I can't locate" I meant that I see the same error, but don't know why :-( With respect to the homogeneity statistics you asked for: I don't think they are implemented, this would be a question for Guido (who will be back at work on Monday). I don't find any hint to them when typing help(metabin). In principle, I think it preferable to avoid continuity corrections. Maybe Wolfgang can solve the problem with rma.mh and also answer the other question? Best, Gerta Am 12.06.2020 um 11:45 schrieb David Fisher:
Dear Gerta, Many thanks for your reply. Firstly: apologies, I was inconsistent in the naming of my dataset in my example code, as you spotted. But no, this doesn't solve my original problem :-) When you say "I cannot locate", do you mean you do not see the same error message? Thankyou for pointing me towards the alternative package "metabin". Can you tell me whether it can be used to calculate the Breslow-Day (and/or Tarone) statistics for homogeneity of odds ratios? Or, could you tell me whether you would expect these statistics to be calculated using raw counts, or using continuity-corrected counts? Thanks again, David. On Fri, Jun 12, 2020 at 10:24 AM Gerta Ruecker <ruecker at imbi.uni-freiburg.de> wrote:
Once more. Here is the code with OR and without continuity correction: library(metafor) dat2007 <- dat.nielweise2007 library(meta) m1 <- metabin(ai, n1i, ci, n2i, sm = "OR", incr = 0, data = dat2007) m2 <- metabin(ai, n1i, ci, n2i, sm = "OR", incr = 0, data=dat2007[dat2007$ai==0,]) m1 m2 For m2, with only zero events, you obtain OR = 0, but without estimates for the standard error and thus without confidence intervals. See forest(m2) Best, Gerta Am 12.06.2020 um 11:15 schrieb Gerta Ruecker:
Dear David, Your code defines a data set called dat, but not dat2007. But this doesn't seem to be the problem (I can't locate). Maybe the double zero is the problem? You could try the meta package: library(metafor) dat2007 <- dat.nielweise2007 library(meta) m1 <- metabin(ai, n1i, ci, n2i, data = dat2007) m2 <- metabin(ai, n1i, ci, n2i, data=dat2007[dat2007$ai==0,]) m1 m2 Best, Gerta Am 12.06.2020 um 11:01 schrieb David Fisher:
Dear metafor community, I am a Stata user with only limited knowledge of R. I am trying to validate some Stata code by comparing with output from metafor; in particular, sparse data/zero cells using Mantel-Haenszel methods. My reference is Wolfgang's page "http://www.metafor-project.org/doku.php/tips:comp_mh_different_software". If I type: library(metafor) dat <- dat.nielweise2007 rma.mh(measure="OR", ai=ai, n1i=n1i, ci=ci, n2i=n2i, data=dat) ...then I successfully obtain the output shown on the webpage. However, if I alter the command in (seemingly) any way, I get the following error: Error in sprintf(format, names(x)) : invalid format '%NA'; use format %s for character objects For instance, if I limit the dataset to studies with zero events in the treatment arm: rma.mh(measure="OR", ai=ai, n1i=n1i, ci=ci, n2i=n2i, data=dat2007[which(dat2007$ai==0),]) ...and similarly if I attempt to use another data frame, or import from Stata using "read.dta". Furthermore, I do not appear to have the same issue if I use another model. For instance, the following runs with no problem: rma(measure="OR", ai=ai, n1i=n1i, ci=ci, n2i=n2i, data=dat2007[which(dat2007$ai==0),]) I am using a fresh install of R 4.0.1 and of the metafor package. Could someone point me in the right direction? Many thanks, David.
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-- Dr. rer. nat. Gerta R?cker, Dipl.-Math. Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg Stefan-Meier-Str. 26, D-79104 Freiburg, Germany Phone: +49/761/203-6673 Fax: +49/761/203-6680 Mail: ruecker at imbi.uni-freiburg.de Homepage: https://www.uniklinik-freiburg.de/imbi.html
-- Dr. rer. nat. Gerta R?cker, Dipl.-Math. Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg Stefan-Meier-Str. 26, D-79104 Freiburg, Germany Phone: +49/761/203-6673 Fax: +49/761/203-6680 Mail: ruecker at imbi.uni-freiburg.de Homepage: https://www.uniklinik-freiburg.de/imbi.html