# [R] crossed random effects

Spencer Graves spencer.graves at pdf.com
Wed Jul 2 02:07:26 CEST 2003

```	  How many mum's and pop's do you have, and how many observations do
you have of each mum-pop combination?  If you want mum nested within
pop, do I infer correctly that each mum has mated with only one pop, but
that each pop may have offspring by multiple mums?  The table of mum-pop
combinations might help explain why you got, "Error in chol((value +
t(value))/2) : non-positive definite matrix in chol".

If you can get an answer ignoring pop, then you might be able to get
an answer with pop as a separate random term without specifying mum
nested within pop.  Also, I'd check very carefully the specification of
nesting:  I've messed that up more than once, and I'm bald now, because
I tore all my hair out before I figured out what I was doing wrong.
(Well, there is a slight exageration there.)  Have you tried a very
simple toy problem (or a published example) with nesting to make sure
you can get the correct answer?

hope this helps.
spencer graves

Sarah Mclean wrote:
> Hi,
>
> thanks for the advice. I have looked at the Pinheiro
> and Bates book and I've tried simplifying my model.
>
> I've narrowed the problem down to having mum nested
> within pop. If I run the analysis on each population
> separately, the interaction between mo and su with mum
> works fine.
>
> If I could analyse all of the pops at once this would
> be preferable because I have multiple responses and
> pops to test so it would take a bit of time. I'm
> hoping there is any easier way.
>
> Thanks
> Sarah
>
>  --- Spencer Graves <spencer.graves at PDF.COM> wrote: >
>   Have you studied Pinhiero and Bates (2000) Mixed
>
>>Effects Models in S
>>and S-Plus (Springer)?
>>
>>	  Also, have you tried simplifying your "lme" call
>>until you get
>>something that works, then start adding back terms
>>in various
>>configurations until it breaks?
>>
>>	  Have you tried to compute how many coefficients
>>are estimated in both
>>fixed and random terms and evaluate whether all are
>>estimable?  For
>>example, with 2 factors at 2 levels each, if you
>>don't have all 4
>>possible combinations, you can't estimate the
>>interaction -- even if you
>>have thousands of replications of each.
>>
>>	  Finally, you can always try to read the code.
>>I've learned a lot
>>about S-Plus / R by doing that -- and solved a lot
>>of my own problems
>>that way.
>>
>>hope this helps.  spencer graves
>>
>>Sarah Mclean wrote:
>>
>>>Hi,
>>>
>>>if I have posted this twice, please ignore this.
>>
>>I'm
>>
>>>not sure if I sent it to the correct e-mail
>>
>>
>>>the first time.
>>>
>>>I have a data set on germination and plant growth
>>
>>with
>>
>>>the following variables:
>>>
>>>dataset=fm
>>>mass (response)
>>>sub (fixed effect)
>>>moist (fixed effect)
>>>pop (fixed effect)
>>>mum (random effect nested within population)
>>>iheight (covariate)
>>>plot (random effect- whole plot factor for
>>
>>split-plot
>>
>>>design).
>>>
>>>I want to see if moist or sub interacts with mum
>>
>>for
>>
>>>any of the pops, but I am getting an error
>>
>>message.
>>
>>>This is the formula I used:
>>>fm\$pmu <- getGroups(fm, ~1|pop/mum, level=2)
>>>fm\$grp = as.factor(rep(1,nrow(fm)))
>>>fm\$pl <- getGroups(fm, ~1|plot)
>>>fm\$mo <- getGroups(fm, ~1|moist)
>>>fm\$su <- getGroups(fm, ~1|sub)
>>>
>>>
>>>>fm1 <- lme(sqrt(mass) ~ iheight + moist*sub*pop,
>>>
>>>data=fm,
>>
>>random=list(grp=pdBlocked(list(pdIdent(~pl -
>>
>>>1), pdIdent(~pmu - 1),  pdIdent(~pmu:su - 1),
>>>pdIdent(~pmu:mo - 1)))))
>>>Error in chol((value + t(value))/2) : non-positive
>>>definite matrix in chol
>>>
>>>I know the problem is with the random interaction
>>>terms, but I don't know how to overcome this.
>>>
>>>Any advice would be greatly appreciated. I'm new
>>
>>to R
>>
>>>and analysis such as this.
>>>
>>>Thank you,
>>>
>>>Sarah Mclean
>>>sarahmclean9 at yahoo.co.nz
>>>
>>>
>>>http://mobile.yahoo.com.au - Yahoo! Mobile
>>>- Check & compose your email via SMS on your
>>
>>Telstra or Vodafone mobile.
>>
>>>______________________________________________
>>>R-help at stat.math.ethz.ch mailing list
>>>
>>
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
>>
>
>
> http://mobile.yahoo.com.au - Yahoo! Mobile
> - Check & compose your email via SMS on your Telstra or Vodafone mobile.

```