[R-sig-ME] multiple random effects and correlation structure in nlme

[Thierry Onkelinx]

Dear Karl,

You have only 2 levels of cost. So it better to move that to the fixed
effects. Then you'll have only one random effect.

Best regards,

Thierry

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

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2015-11-04 23:50 GMT+01:00 Karl Jarvis <karljarvis op gmail.com>:

> Hi all,
> I am trying to build a model that includes two random effects while also
> using a correlation structure to account for spatial autocorrelation. It’s
> a full factorial study on simulations of wildlife where individuals are
> spread across landscapes, so one of the random effects (N) is crossed.
>
> If I use nlme I can do this by reusing creating a new group factor by
> pasting the three crossed factors together (would be land:barr:mort in
> lme4), which I call ‘lr'. The parameter estimates are similar, so it seems
> ok. (Link to the data frame:
> https://drive.google.com/open?id=0B096pYMrPnKAdC1FdWhCR3Z4bjg <
> https://drive.google.com/open?id=0B096pYMrPnKAdC1FdWhCR3Z4bjg> )
>         ibr4 <- read.csv(“~/ibr4.csv”)
>         m1 <- lme(A ~ barr + mort, random = list(~cost | land, ~N | lr),
> data=ibr4, method = “ML”)
>
> Once I try to do that along with a correlation structure, it complains
> that there are incompatible formulas for ‘random’ and ‘correlation’.
>         m2 <- lme(A ~ barr + mort, random = list(~cost | land, ~N | lr),
> data=ibr4, method = “ML”,
>         correlation = corExp(form = ~ x+y | lr))
>
> I think it’s because it doesn’t know how to relate lr to land, because it
> complains the same way when the only random effect is '~cost | land’.
> However, when one random effect is in the model with a correlation
> structure nested as ~x+y | land/barr/mort, it does work. But it doesn’t
> seem to ever accept multiple random effects together with a correlation
> structure. I know Pinheiro and Bates say in their book (p.163) that you can
> build a crossed random-effects structure with pdBlocked and pdIdent, but
> (1) it’s not clear to me how to do this for a single random effect, and (2)
> it’s not clear to me that you could include multiple random effects in such
> a structure. Am I misunderstanding how correlation structures and/or random
> effects work? Let me know if you need more information about my data.
>
> Thanks,
> Karl
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>
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