[R-meta] Problems using rma.mh

[Gerta Ruecker]

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