[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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