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

[Reinhold Kliegl]

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.
> 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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