R help - Jul 2019 - Conditional Logistic Regression with Multilevel Data [using clogistic() in Epi and lmer() in lme4???]

Hi Marc and Wolfgang,


Thanks for your help. Is the following interpretation of your exchange correct?


I need to use the glmer() function in the lme4 package (first installing the
devel version of metaphor). I can specify both site and matched pairing as
random effects using (1 | site / id).


Is this understanding correct?


Thanks,


Heather


Heather Hensman Kettrey, PhD

Assistant Professor of Sociology

Clemson University

________________________________
From: Wolfgang Viechtbauer <wolfgang.viechtbauer at
maastrichtuniversity.nl>
Sent: Wednesday, July 3, 2019 9:15:50 AM
To: Marc Schwartz
Cc: Heather H Kettrey; R-help
Subject: Re: [R] Conditional Logistic Regression with Multilevel Data [using
clogistic() in Epi and lmer() in lme4???]

Ouch, that was a brain fart on my part!

But indeed, since we can fit a 'single-site model' using glmer() (as
shown), we should be able to just add 'site' as another random effect
with (1 | site / id).

Best,
Wolfgang

On July 3, 2019 1:26:54 PM GMT+02:00, Marc Schwartz <marc_schwartz at
me.com> wrote:
>Wolfgang,
>
>Perhaps I am missing something here, but with clogit(), or Heather's
>initial attempt at using clogistic(), as both have 'strata'
arguments,
>wouldn't the 'strata' argument need to be able to accept a
nested
>structure, along the lines of strata(id / site)?
>
>On the page that you link to below, I don't see an example of that type
>of nesting structure.
>
>The mixed effects models would generally support a nested random
>effects specification, if that makes sense here.
>
>Regards,
>
>Marc Schwartz
>
>
>> On Jul 3, 2019, at 4:41 AM, Viechtbauer, Wolfgang (SP)
><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
>>
>> Dear Heather,
>>
>> You can do this with clogit() from the 'survival' package,
using
>strata(). See:
>>
>>
>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metafor-2Dproject.org_doku.php_tips-3Aclogit-5Fpaired-5Fbinary-5Fdata&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=dvbBssAbENU3KBtLTcWb64QHTComM-RmP8my38CxhW0&e>>
>> You can also use lme4::glmer(), glmmML::glmmML(), or
>metafor::rma.glmm() for that. [1]
>>
>> [1] Rerunning this example, I noticed a slight issue with the
>structuring of the output from rma.glmm() -- if you want to run that
>example, install the 'devel' version of metafor as described here:
>>
>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__wviechtb.github.io_metafor_-23installation&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=POvfvp_zMlzeLnfGS2EavvZp1-P_0utedAIqz994QkI&e>>
>> Best,
>> Wolfgang
	[[alternative HTML version deleted]]

Hi Heather,

I would defer to the mixed models experts, but I think that the basic approach
using nested random effects seems to make sense.

I don?t know that there is a dependency of glmer()/lme4 on metafor for this
specific use case, but would defer to Wolfgang on that point.

Regards,

Marc

> On Jul 3, 2019, at 10:40 AM, Heather H Kettrey <hkettre at
clemson.edu> wrote:
> 
> Hi Marc and Wolfgang,
> 
> Thanks for your help. Is the following interpretation of your exchange
correct?
> 
> I need to use the glmer() function in the lme4 package (first installing
the devel version of metaphor). I can specify both site and matched pairing as
random effects using (1 | site / id).
> 
> Is this understanding correct?
> 
> Thanks,
> 
> Heather 
> 
> Heather Hensman Kettrey, PhD
> Assistant Professor of Sociology
> Clemson University
> From: Wolfgang Viechtbauer <wolfgang.viechtbauer at
maastrichtuniversity.nl>
> Sent: Wednesday, July 3, 2019 9:15:50 AM
> To: Marc Schwartz
> Cc: Heather H Kettrey; R-help
> Subject: Re: [R] Conditional Logistic Regression with Multilevel Data
[using clogistic() in Epi and lmer() in lme4???]
>  
> Ouch, that was a brain fart on my part!
> 
> But indeed, since we can fit a 'single-site model' using glmer()
(as shown), we should be able to just add 'site' as another random
effect with (1 | site / id).
> 
> Best,
> Wolfgang
> 
> On July 3, 2019 1:26:54 PM GMT+02:00, Marc Schwartz <marc_schwartz at
me.com> wrote:
> >Wolfgang,
> >
> >Perhaps I am missing something here, but with clogit(), or
Heather's
> >initial attempt at using clogistic(), as both have 'strata'
arguments,
> >wouldn't the 'strata' argument need to be able to accept a
nested
> >structure, along the lines of strata(id / site)?
> >
> >On the page that you link to below, I don't see an example of that
type
> >of nesting structure.
> >
> >The mixed effects models would generally support a nested random
> >effects specification, if that makes sense here.
> >
> >Regards,
> >
> >Marc Schwartz
> >
> >
> >> On Jul 3, 2019, at 4:41 AM, Viechtbauer, Wolfgang (SP)
> ><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
> >> 
> >> Dear Heather,
> >> 
> >> You can do this with clogit() from the 'survival' package,
using
> >strata(). See:
> >> 
> >>
>
>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metafor-2Dproject.org_doku.php_tips-3Aclogit-5Fpaired-5Fbinary-5Fdata&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=dvbBssAbENU3KBtLTcWb64QHTComM-RmP8my38CxhW0&e=
> >> 
> >> You can also use lme4::glmer(), glmmML::glmmML(), or
> >metafor::rma.glmm() for that. [1]
> >> 
> >> [1] Rerunning this example, I noticed a slight issue with the
> >structuring of the output from rma.glmm() -- if you want to run that
> >example, install the 'devel' version of metafor as described
here:
> >> 
> >>
https://urldefense.proofpoint.com/v2/url?u=https-3A__wviechtb.github.io_metafor_-23installation&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=POvfvp_zMlzeLnfGS2EavvZp1-P_0utedAIqz994QkI&e=
> >> 
> >> Best,
> >> Wolfgang
	[[alternative HTML version deleted]]

No need to install metafor for lme4.

Best,
Wolfgang



On July 3, 2019 5:19:13 PM GMT+02:00, Marc Schwartz <marc_schwartz at
me.com> wrote:
>Hi Heather,
>
>I would defer to the mixed models experts, but I think that the basic
>approach using nested random effects seems to make sense.
>
>I don?t know that there is a dependency of glmer()/lme4 on metafor for
>this specific use case, but would defer to Wolfgang on that point.
>
>Regards,
>
>Marc
>
>
>> On Jul 3, 2019, at 10:40 AM, Heather H Kettrey <hkettre at
clemson.edu>
>wrote:
>> 
>> Hi Marc and Wolfgang,
>> 
>> Thanks for your help. Is the following interpretation of your
>exchange correct?
>> 
>> I need to use the glmer() function in the lme4 package (first
>installing the devel version of metaphor). I can specify both site and
>matched pairing as random effects using (1 | site / id).
>> 
>> Is this understanding correct?
>> 
>> Thanks,
>> 
>> Heather 
>> 
>> Heather Hensman Kettrey, PhD
>> Assistant Professor of Sociology
>> Clemson University
>> From: Wolfgang Viechtbauer
><wolfgang.viechtbauer at maastrichtuniversity.nl>
>> Sent: Wednesday, July 3, 2019 9:15:50 AM
>> To: Marc Schwartz
>> Cc: Heather H Kettrey; R-help
>> Subject: Re: [R] Conditional Logistic Regression with Multilevel Data
>[using clogistic() in Epi and lmer() in lme4???]
>>  
>> Ouch, that was a brain fart on my part!
>> 
>> But indeed, since we can fit a 'single-site model' using
glmer() (as
>shown), we should be able to just add 'site' as another random
effect
>with (1 | site / id).
>> 
>> Best,
>> Wolfgang
>> 
>> On July 3, 2019 1:26:54 PM GMT+02:00, Marc Schwartz
><marc_schwartz at me.com> wrote:
>> >Wolfgang,
>> >
>> >Perhaps I am missing something here, but with clogit(), or
Heather's
>> >initial attempt at using clogistic(), as both have 'strata'
>arguments,
>> >wouldn't the 'strata' argument need to be able to
accept a nested
>> >structure, along the lines of strata(id / site)?
>> >
>> >On the page that you link to below, I don't see an example of
that
>type
>> >of nesting structure.
>> >
>> >The mixed effects models would generally support a nested random
>> >effects specification, if that makes sense here.
>> >
>> >Regards,
>> >
>> >Marc Schwartz
>> >
>> >
>> >> On Jul 3, 2019, at 4:41 AM, Viechtbauer, Wolfgang (SP)
>> ><wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
>> >> 
>> >> Dear Heather,
>> >> 
>> >> You can do this with clogit() from the 'survival'
package, using
>> >strata(). See:
>> >> 
>> >>
>>
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metafor-2Dproject.org_doku.php_tips-3Aclogit-5Fpaired-5Fbinary-5Fdata&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=dvbBssAbENU3KBtLTcWb64QHTComM-RmP8my38CxhW0&e>
>> >> 
>> >> You can also use lme4::glmer(), glmmML::glmmML(), or
>> >metafor::rma.glmm() for that. [1]
>> >> 
>> >> [1] Rerunning this example, I noticed a slight issue with the
>> >structuring of the output from rma.glmm() -- if you want to run
that
>> >example, install the 'devel' version of metafor as
described here:
>> >> 
>> >>
>https://urldefense.proofpoint.com/v2/url?u=https-3A__wviechtb.github.io_metafor_-23installation&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=BBiFu06xLWCETvNuhD6uw-_crP2zH6EmpC772CQach0&m=PP2LCJ_pE4EwJysp-nsvWt8oIJqJ0nhFvSMBuh7T-ww&s=POvfvp_zMlzeLnfGS2EavvZp1-P_0utedAIqz994QkI&e>
>> >> 
>> >> Best,
>> >> Wolfgang