[R-sig-ME] Zhang 2011 (re)analysis

[Ben Bolker]

On 11-10-31 05:22 AM, Reinhold Kliegl wrote:
> One problem appears to be that 111 id's are renumbered from 1 to 55
> (56) in the two groups.
> Unfortunately, it also appears that there is no unique mapping to
> treatment groups. So there are some subjects with 8 values assigned to
> one of the groups.

  Thanks.  It looks like IDs are nested within center (not within
treatment).  That doesn't seem to change the story very much (as far as
, though (Zhang et al don't report estimated random-effect variances ...)



>> library(geepack)
>> data(respiratory)
>> resp1 <- respiratory
>> resp1 <- transform(resp1,
> +                          center=factor(center),
> +                          id=factor(id))
>>
>> str(resp1)
> 'data.frame':	444 obs. of  8 variables:
>  $ center  : Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
>  $ id      : Factor w/ 56 levels "1","2","3","4",..: 1 1 1 1 2 2 2 2 3 3 ...
>  $ treat   : Factor w/ 2 levels "A","P": 2 2 2 2 2 2 2 2 1 1 ...
>  $ sex     : Factor w/ 2 levels "F","M": 2 2 2 2 2 2 2 2 2 2 ...
>  $ age     : int  46 46 46 46 28 28 28 28 23 23 ...
>  $ baseline: int  0 0 0 0 0 0 0 0 1 1 ...
>  $ visit   : int  1 2 3 4 1 2 3 4 1 2 ...
>  $ outcome : int  0 0 0 0 0 0 0 0 1 1 ...
>> detach("package:geepack") ## allow detaching of doBy
>> detach("package:doBy")    ## allow detaching of lme4
> 
> The data appear also in the HSAUR package, here the 111 subjects
> identified with 5 months (visits) each.  I suspect month 0 was used as
> baseline.
>> library(HSAUR)
>> data(respiratory)
>> resp2 <- respiratory
>>
>> str(resp2)
> 'data.frame':	555 obs. of  7 variables:
>  $ centre   : Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
>  $ treatment: Factor w/ 2 levels "placebo","treatment": 1 1 1 1 1 1 1 1 1 1 ...
>  $ sex      : Factor w/ 2 levels "female","male": 1 1 1 1 1 1 1 1 1 1 ...
>  $ age      : num  46 46 46 46 46 28 28 28 28 28 ...
>  $ status   : Factor w/ 2 levels "poor","good": 1 1 1 1 1 1 1 1 1 1 ...
>  $ month    : Ord.factor w/ 5 levels "0"<"1"<"2"<"3"<..: 1 2 3 4 5 1 2 3 4 5 ...
>  $ subject  : Factor w/ 111 levels "1","2","3","4",..: 1 1 1 1 1 2 2 2 2 2 ...
> 
> Reinhold
> 
> On Sun, Oct 30, 2011 at 10:00 PM, Ben Bolker <bbolker at gmail.com> wrote:
>>
>>  There's a fairly recent paper by Zhang et al (2011) of interest to
>> folks on this list
>>
>> DOI: 10.1002/sim.4265
>>
>>  In response to a post on the AD Model Builder users' list, I took a
>> quick shot at re-doing some of their results (they have extensive
>> simulation results, which I haven't tried to replicate yet, and an
>> analysis of binary data from Davis (1991) which is included (I *think*
>> it's the same data set -- the description and size of the data set match
>> exactly) in the geepack data set).
>>
>>  If anyone's interested, my results so far are posted at
>>
>> http://glmm.wikidot.com/local--files/examples/Zhang_reanalysis.Rnw
>> http://glmm.wikidot.com/local--files/examples/Zhang_reanalysis.pdf
>>
>>  So far the R approaches I've tried agree closely with each other and
>> with glmmADMB (except MASS::glmmPQL, which I expected to be different --
>> the rest all use either Laplace approx. or AGHQ).  They *don't* agree
>> with the results Zhang et al got, yet -- I'm sure there's something I'm
>> missing in the contrasts or otherwise ...
>>
>>  Suggestions or improvements are welcome.
>>
>>  cheers
>>    Ben Bolker
>>
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