R help - Mar 2015 - lme random interactions

I have a method comparison problem, comparing Labs where a set of compounds are
assayed on 3 different dates for each lab. Both labs will be used to assess
compounds in the future, so the scientists will potentially contrast a compound
at assayed at Lab A with one assayed at Lab B, This implies I ought to regard
the Lab*Compound interaction as random. I also have the date within Lab as a
random term and the Compound*date as random (and as separate variances for each
Lab).

If I regard the Compound*Lab effect as fixed this code works

lme.out <- lme ( data=data, Resp ~ Lab + Compound + Compound:Lab,
   random = pdIdent(~Lab-1|Date)  ,
    weights = varIdent(form=~1|Lab)
)

The trouble is when I try to regard it as random, eg.

lme2.out <- lme ( data=data, Resp ~ Lab + Compound,
   random = list( ~Compound:Lab,  pdIdent(~Lab-1|Date)  ),
    weights = varIdent(form=~1|Lab)
  )

It appears as if the random interaction is not allowed ... Is this right ? Is
there a way to fit the interaction as random together with the other random
terms ?

I have tried lme4 but note that "lme4 does not currently implement
nlme's features for modeling heteroscedasticity" but "does
implement crossed random effects". No joy in my hands though. Nor with lmer
...

Any help gratefully received, thanks,

Brian (trying to convert from SAS !)



________________________________

AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:26}}

Dear Brian,

You want

data$CompLab <- interaction(data$Compound, data$Lab)
lme ( data=data, Resp ~ Lab * Compound,
   random = list(CombLab = ~ 1, Date = pdIdent(~0 + Lab)) ,
    weights = varIdent(form=~1|Lab)
)

Note that this is untested since you didn't provide a reproducible example.

However, you have only very few levels of Date. See "Should I treat factor
xxx as fixed or random?" on http://glmm.wikidot.com/faq
Furthermore, you are estimating a lot of parameters. Make you that you have
enough data.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-03-16 11:10 GMT+01:00 Middleton, Brian J <
Brian.Middleton at astrazeneca.com>:
> I have a method comparison problem, comparing Labs where a set of
> compounds are assayed on 3 different dates for each lab. Both labs will be
> used to assess compounds in the future, so the scientists will potentially
> contrast a compound at assayed at Lab A with one assayed at Lab B, This
> implies I ought to regard the Lab*Compound interaction as random. I also
> have the date within Lab as a random term and the Compound*date as random
> (and as separate variances for each Lab).
>
> If I regard the Compound*Lab effect as fixed this code works
>
> lme.out <- lme ( data=data, Resp ~ Lab + Compound + Compound:Lab,
>    random = pdIdent(~Lab-1|Date)  ,
>     weights = varIdent(form=~1|Lab)
> )
>
> The trouble is when I try to regard it as random, eg.
>
> lme2.out <- lme ( data=data, Resp ~ Lab + Compound,
>    random = list( ~Compound:Lab,  pdIdent(~Lab-1|Date)  ),
>     weights = varIdent(form=~1|Lab)
>   )
>
> It appears as if the random interaction is not allowed ... Is this right ?
> Is there a way to fit the interaction as random together with the other
> random terms ?
>
> I have tried lme4 but note that "lme4 does not currently implement
nlme's
> features for modeling heteroscedasticity" but "does implement
crossed
> random effects". No joy in my hands though. Nor with lmer ...
>
> Any help gratefully received, thanks,
>
> Brian (trying to convert from SAS !)
>
>
>
> ________________________________
>
> AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:26}}
>
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>
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