[R-meta] Problems using rma.mh

[David Fisher]

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 using 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 using 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.
> >>>>
> >>>> _______________________________________________
> >>>> R-sig-meta-analysis mailing list
> >>>> R-sig-meta-analysis using r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-meta-analysis
> >> --
> >>
> >> Dr. rer. nat. Gerta Rücker, 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 using imbi.uni-freiburg.de
> >> Homepage: https://www.uniklinik-freiburg.de/imbi.html
> >>
> --
>
> Dr. rer. nat. Gerta Rücker, 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 using imbi.uni-freiburg.de
> Homepage: https://www.uniklinik-freiburg.de/imbi.html
>