[R-sig-eco] "random" lme syntax; related problem

Rafael Maia queirozrafaelmv at yahoo.com.br
Tue Jul 22 00:39:54 CEST 2008


Dear Maaike,

Again, I lack the mathematical foundations, but I'd try the following 
syntax:

lme(wing~treat,random=~1|nest/day/nstchk, data=wdata)

which seems more logical to me... I believe you probably have random intercepts and fixed slopes (thus, the ~1 | ), but I'm not sure if it'd be day/nest/nstchk or nest/day/nstchk which will adequately represent your hierarchical structure.

Let me know if it helps!

Best,
Rafael Maia




Maaike A Versteegh wrote:
> Dear Rafael and Kongston Jones (and others)
>
> I am also helping a colleague with quite similar data-set.
>
> He's interested in the effect of a lysozyme treatment on growth
> wing-lenght of chicks. He has has multiple chicks in nests but the
> treatment is on the nest level. So he has treated and untreated nests.
> He measured wing-length on day 2,4,8 and 15.
> He has a balanced design, with 40 treated and 40 untreated chicks, and
> 10 treated and 10 untreated nests.
>
> So he has chicks (who get an unique id: nstchk) nested in nests,
> measured on 4 days
> We tried the method Kingston Jones suggest (wing<-treat,
> random=~day|nest/nstchk). If we do an lme with only the first two days
> (day 2 and day 4) it works fine. But if we try to run a lme on the data
> of all 4 days we get an error message. The error message is:
>
> Error in lme.formula(wing ~ treat, random = ~day | *nest/nstchk*, data =
> wdata) :
>   nlminb problem, convergence error code = 1
>   message = iteration limit reached without convergence (9)
>
> If he does not include nstchk (the unique id of the chicks) in the
> random part of the equation (so: random = ~day| nest), lme works fine
> with the data from all 4 days, but doesn't with just the data from day 2
> and day 4. It gives the same error message as above
>
> Both of the methods work with day 4 and day 8. Day 2 and day 15 also
> works with both models.
> As you can see we tried a lot, and we don't understands what makes it
> sometimes give error message and sometimes not.
>
> Can anybody help? could the problem be that we have too little variation
> in winglength on day 2? or too little growth between day 2 and day 4?
> Ideally my colleague would like to include all the days.
>
> Any help would be appreciated
>
> Maaike
>
> The complete R-code:
>
> wdata=read.csv("f:\\r practice\\wingtest320.2.4.8.15.csv")
> attach(wdata)
> names(wdata)
> library(nlme)
>  
> model.with.nstchk<-lme(wing~treat,random=~day|nest/nstchk, data=wdata);
> summary(model.with.nstchk);
> model.no.nstchk<-lme(wing~treat,random=~day|nest, data=wdata);
> summary(model.no.nstchk)
>  
>
> (part of) the data-set:
>
>
>       treat     nest chick           nstchk day wing
> 1   LYS      209ward      1 209ward-1          2  9.0
> 2   LYS      209ward      1 209ward-1          4 13.5
> 3   LYS      209ward      1 209ward-1          8 34.0
> 4   LYS      209ward      1 209ward-1         15 64.0
> 5   LYS      209ward      2 209ward-2          2  9.0
> 6   LYS      209ward      2 209ward-2          4 13.0
> 7   LYS      209ward      2 209ward-2          8 32.0
> 8   LYS      209ward      2 209ward-2         15 63.0
> 9   LYS      209ward      3 209ward-3          2  8.5
> 10  LYS      209ward      3 209ward-3          4 13.5
> 11  LYS      209ward      3 209ward-3          8 32.5
> 12  LYS      209ward      3 209ward-3         15 63.0
> 13  LYS      209ward      4 209ward-4          2  8.5
> 14  LYS      209ward      4 209ward-4          4 12.5
> 15  LYS      209ward      4 209ward-4          8 34.0
> 16  LYS      209ward      4 209ward-4         15 61.0
> 17  LYS      209ward      5 209ward-5          2  9.0
> 18  LYS      209ward      5 209ward-5          4 13.0
> 19  LYS      209ward      5 209ward-5          8 34.0
> 20  LYS      209ward      5 209ward-5         15 62.5
> 21  LYS      b13          1 b13-1              2  9.5
> 22  LYS      b13          1 b13-1              4 14.0
> 23  LYS      b13          1 b13-1              8 34.0
> 24  LYS      b13          1 b13-1             15 65.0
> 25  LYS      b13          2 b13-2              2  9.5
> 26  LYS      b13          2 b13-2              4 14.5
> 27  LYS      b13          2 b13-2              8 34.5
> 28  LYS      b13          2 b13-2             15 64.0
> 29  LYS      b40          1 b40-1              2 10.0
> 30  LYS      b40          1 b40-1              4 13.5
> 31  LYS      b40          1 b40-1              8 32.5
> 32  LYS      b40          1 b40-1             15 65.5
> 33  LYS      b40          2 b40-2              2 10.0
> 34  LYS      b40          2 b40-2              4 14.5
> 35  LYS      b40          2 b40-2              8 34.0
> 36  LYS      b40          2 b40-2             15 66.0
> 37  LYS      b40          3 b40-3              2  9.5
> 38  LYS      b40          3 b40-3              4 14.0
> 39  LYS      b40          3 b40-3              8 32.5
> 40  LYS      b40          3 b40-3             15 64.5
> ....
> 161 PBS      b1           1 b1-1               2  9.0
> 162 PBS      b1           1 b1-1               4 12.5
> 163 PBS      b1           1 b1-1               8 30.0
> 164 PBS      b1           1 b1-1              15 57.5
> 165 PBS      b1           2 b1-2               2  9.0
> 166 PBS      b1           2 b1-2               4 14.5
> 167 PBS      b1           2 b1-2               8 33.0
> 168 PBS      b1           2 b1-2              15 59.0
> 169 PBS      b1           4 b1-4               2  9.5
> 170 PBS      b1           4 b1-4               4 14.0
> 171 PBS      b1           4 b1-4               8 30.5
> 172 PBS      b1           4 b1-4              15 58.0
> 173 PBS      b1           5 b1-5               2  8.5
> 174 PBS      b1           5 b1-5               4 12.5
> 175 PBS      b1           5 b1-5               8 23.5
> 176 PBS      b1           5 b1-5              15 55.0
> 177 PBS      b18          1 b18-1              2  8.5
> 178 PBS      b18          1 b18-1              4 13.0
> 179 PBS      b18          1 b18-1              8 30.0
> 180 PBS      b18          1 b18-1             15 63.5
> 181 PBS      b18          2 b18-2              2  8.5
> 182 PBS      b18          2 b18-2              4 12.0
> 183 PBS      b18          2 b18-2              8 28.0
> 184 PBS      b18          2 b18-2             15 65.0
> 185 PBS      b18          3 b18-3              2  8.5
> 186 PBS      b18          3 b18-3              4 13.5
> 187 PBS      b18          3 b18-3              8 30.0
> 188 PBS      b18          3 b18-3             15 64.0
> 189 PBS      b19          1 b19-1              2  8.5
> 190 PBS      b19          1 b19-1              4 13.0
> 191 PBS      b19          1 b19-1              8 32.5
> 192 PBS      b19          1 b19-1             15 64.0
> 193 PBS      b19          2 b19-2              2  9.5
> 194 PBS      b19          2 b19-2              4 14.0
> 195 PBS      b19          2 b19-2              8 33.0
> 196 PBS      b19          2 b19-2             15 68.0
> 197 PBS      b19          3 b19-3              2  9.5
> 198 PBS      b19          3 b19-3              4 13.0
> 199 PBS      b19          3 b19-3              8 30.5
> 200 PBS      b19          3 b19-3             15 63.5
> 201 PBS      b19          4 b19-4              2  8.5
> 202 PBS      b19          4 b19-4              4 13.5
> 203 PBS      b19          4 b19-4              8 32.0
> 204 PBS      b19          4 b19-4             15 66.0
> 205 PBS      b19          5 b19-5              2  8.5
> 206 PBS      b19          5 b19-5              4 11.0
> 207 PBS      b19          5 b19-5              8 29.0
> 208 PBS      b19          5 b19-5             15 61.5
> 209 PBS      b42          1 b42-1              2  8.0
> 210 PBS      b42          1 b42-1              4 13.0
> 211 PBS      b42          1 b42-1              8 29.0
> 212 PBS      b42          1 b42-1             15 63.0
> 213 PBS      b42          2 b42-2              2  7.5
> 214 PBS      b42          2 b42-2              4 11.5
> 215 PBS      b42          2 b42-2              8 26.0
> 216 PBS      b42          2 b42-2             15 58.0
> 217 PBS      b42          3 b42-3              2  9.5
> 218 PBS      b42          3 b42-3              4 14.5
> 219 PBS      b42          3 b42-3              8 31.0
> 220 PBS      b42          3 b42-3             15 65.0
> 221 PBS      b42          4 b42-4              2  8.0
> 222 PBS      b42          4 b42-4              4 12.0
> 223 PBS      b42          4 b42-4              8 27.0
> 224 PBS      b42          4 b42-4             15 62.5
> 225 PBS      b42          5 b42-5              2  8.0
> 226 PBS      b42          5 b42-5              4 11.0
> 227 PBS      b42          5 b42-5              8 27.5
> 228 PBS      b42          5 b42-5             15 65.0
>
>
>
>
>
>
> -- Maaike Versteegh Animal Ecology Group University of Groningen PO Box
> 14 9750 AA Haren The Netherlands phone +31 50 363 3408 fax +31 50 363
> 5205 e-mail m.a.versteegh at rug.nl
>
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>
>



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