[R-meta] Problems using rma.mh

[Gerta Ruecker]

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 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