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http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg10849.html

<http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg10849.html>Kevin


On Mon, Oct 18, 2010 at 7:06 AM, anord <andreas.nord@zooekol.lu.se> wrote:

>
> Dear all,
>
> I am trying to fit a model with crossed random effects using lme. In this
> experiment, I have been measuring oxygen consumption (mlmin) in bird
> nestlings, originating from three different treatments (treat), in a
> respirometer with 7 different channels (ch). I have also measured body mass
> (mass) for these birds.
>
> id              nest    treat   year    mlmin                   mass    ch
>      hack
> 1EP51711        17      H       2008    1.401719138     10.7    4
> 2008:17
> 1EP51709        17      H       2008    1.257163112     9.7     5
> 2008:17
> 1EP51716        17      H       2008    1.050170714     10.2    6
> 2008:17
> 1EP51712        17      H       2008    1.330495314     9.6     7
> 2008:17
> 1EP51791        687     M       2008    1.07625708              9.7     3
>     2008:687
> 1EP51772        823     H       2008    1.336820232     10.2    4
> 2008:823
> 1EP51778        613     L       2008    1.300814516     10.7    5
> 2008:613
> 1EP52336        207     M       2008    1.071775936     10.7    3
> 2008:207
> 1EP52403        808     H       2008    1.142389688     10.3    5
> 2008:808
> 1ER17603        838     M       2009    0.984225217     9.6     3
> 2009:838
> 1ER17607        838     M       2009    1.045058894     9.3     4
> 2009:838
> 1ER17600        247     L       2009    1.047603048     9.2     5
> 2009:247
> 1ER17299        247     L       2009    0.974569658     9.2     6
> 2009:247
> 1ER17292        617     H       2009    1.271260094     10.5    7
> 2009:617
> 1ER17206        7009    M       2009    1.074791644     10.7    2
> 2009:7009
> 1ER17221        730     H       2009    1.423266177     10.2    4
> 2009:730
> 1ER17275        863     L       2009    1.433076022     10.7    4
> 2009:863
> 1ER17277        863     L       2009    1.165236024     9.7     5
> 2009:863
> 1ER17283        863     L       2009    1.139311895     10.4    6
> 2009:863
> 1ER17280        863     L       2009    1.056161196     10.4    7
> 2009:863
> CK59991 690     H       2010    0.994878996     9.5     2       2010:690
> CK59806 161     M       2010    1.070052025     9.7     6       2010:161
> CK59859 545     M       2010    1.456680579     9.9     4       2010:545
> CK59862 545     M       2010    1.350698793     9.9     5       2010:545
> CK59871 223     L       2010    0.830582186     8.3     6       2010:223
> CK59868 223     L       2010    0.776241825     8       7       2010:223
> CL77343 365     M       2010    1.352454484     10.3    4       2010:365
> CL77338 365     M       2010    1.327691628     9.6     5       2010:365
> CL77356 191     H       2010    1.212796979     11.3    1       2010:191
> CL77361 191     H       2010    0.882307732     11.4    2       2010:191
> CL77355 191     H       2010    1.137097586     10.9    3       2010:191
>
> I want to include both nesting attempt (hack) and respirometer channel (ch)
> as random factors in a model trying to explain variation in oxygen
> consumption. From Pinheiro & Bates (2000), I've gathered that this model
> could be fit making use of pdBlocked and pdIdent, so I've tried fitting the
> below model:
>
>
> m1.bmr<-with(bmred.df,lme(mlmin~treat*year+massout,random=pdBlocked(list(pdIdent(~hack-1),pdIdent(~ch-1)))
> ))
>
> However, my model fails with the following error message:
> Error in getGroups.data.frame(dataMix, groups) :
>  Invalid formula for groups
>
> I would much appreciate any input on this!
>
> Kind regards,
> Andreas Nord
> Sweden
>
>
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Crossed-random-effects-in-lme-tp3000101p3000101.html
> Sent from the R help mailing list archive at Nabble.com.
>
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Kevin Wright

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