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

Maaike A Versteegh M.A.Versteegh at rug.nl
Mon Jul 21 11:36:09 CEST 2008


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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