Dear R Friends,
I need help with an error associated with corCompSymm in an lme fit.
I am using a mixed effects model to analyze a split-plot with
repeated measures and would like to fit with the compound symmetry
correlation structure. This problem doesn't occur when using
corAR1 or any of the other structures. I would greatly appreciate
help on how to solve this issue.
Here's my data, code lines, and error messages:
> PhotoRed
TreeID Block M D Time y
1 1 Dgl s1 0.5m june 2.91130232
2 1 Dgl s1 1.0m june 4.92232779
3 1 Dgl s1 2.5m june 6.17724409
4 1 Dgl s1 5.0m june 3.34278032
5 1 Dgl s1 0.5m july 6.30782170
6 1 Dgl s1 1.0m july 6.98652976
7 1 Dgl s1 2.5m july 8.80715989
8 1 Dgl s1 5.0m july 7.19424460
9 1 Dgl s1 0.5m august 4.46399690
10 1 Dgl s1 1.0m august 10.63857941
11 1 Dgl s1 2.5m august 9.84689405
12 1 Dgl s1 5.0m august 13.15311387
13 2 Dgl s4 0.5m june 5.37380975
14 2 Dgl s4 1.0m june 4.05953992
15 2 Dgl s4 2.5m june 6.53184737
16 2 Dgl s4 5.0m june 4.85340448
17 2 Dgl s4 0.5m july 3.77109456
18 2 Dgl s4 1.0m july 6.64288350
19 2 Dgl s4 2.5m july 9.74241641
20 2 Dgl s4 5.0m july 5.10884682
21 2 Dgl s4 0.5m august 8.01357594
22 2 Dgl s4 1.0m august 5.31430680
23 2 Dgl s4 2.5m august 10.62809063
24 2 Dgl s4 5.0m august 10.30284109
25 3 Dog s1 0.5m june NA
26 3 Dog s1 1.0m june 3.29442388
27 3 Dog s1 2.5m june 1.02478107
28 3 Dog s1 5.0m june NA
29 3 Dog s1 0.5m july NA
30 3 Dog s1 1.0m july 2.19628259
31 3 Dog s1 2.5m july 1.11794299
32 3 Dog s1 5.0m july NA
33 3 Dog s1 0.5m august NA
34 3 Dog s1 1.0m august 2.44031399
35 3 Dog s1 2.5m august 0.37264766
36 3 Dog s1 5.0m august NA
37 4 Dog s4 0.5m june 4.33381487
38 4 Dog s4 1.0m june 1.34196737
39 4 Dog s4 2.5m june 0.12930756
40 4 Dog s4 5.0m june 6.51695980
41 4 Dog s4 0.5m july 1.33348150
42 4 Dog s4 1.0m july 2.81174115
43 4 Dog s4 2.5m july 7.69379970
44 4 Dog s4 5.0m july 6.35992462
45 4 Dog s4 0.5m august 3.66707412
46 4 Dog s4 1.0m august 0.44732246
47 4 Dog s4 2.5m august 7.75845348
48 4 Dog s4 5.0m august 5.96733668
49 6 F s1 0.5m june 6.98640483
50 6 F s1 1.0m june 8.14953755
51 6 F s1 2.5m june 4.50763794
52 6 F s1 5.0m june 6.62297344
53 6 F s1 0.5m july 13.59516616
54 6 F s1 1.0m july 9.31375720
55 6 F s1 2.5m july 8.01357856
56 6 F s1 5.0m july 3.72542256
57 6 F s1 0.5m august 2.45468278
58 6 F s1 1.0m august 2.13440269
59 6 F s1 2.5m august 0.08347478
60 6 F s1 5.0m august NA
61 7 F s4 0.5m june NA
62 7 F s4 1.0m june NA
63 7 F s4 2.5m june 6.03948199
64 7 F s4 5.0m june 5.73051868
65 7 F s4 0.5m july NA
66 7 F s4 1.0m july NA
67 7 F s4 2.5m july 10.27613353
68 7 F s4 5.0m july 8.00803252
69 7 F s4 0.5m august NA
70 7 F s4 1.0m august NA
71 7 F s4 2.5m august 10.27613353
72 7 F s4 5.0m august 7.34681883
> lme1 = lme(y ~ M*D*Time, random=~1|Block/M/D/Time, data=PhotoRed,
> na.action=na.omit)
> lme2 = update(lme1, correlation=corAR1())
> lme3 = update(lme1, correlation=corCompSymm())
Error in corMatrix.corCompSymm(object) : NA/NaN/Inf in foreign function call
(arg 1)
> cs = corCompSymm(value=0.5,form=~1|TreeID)
> lme3 = update(lme1, correlation=cs)
Error in lme.formula(fixed = y ~ M * D * Time, data = PhotoRed, random = ~1 |
:
Incompatible formulas for groups in "random" and "correlation"
>
--
Francois Teste (Ph.D. candidate)
The University of British Columbia
Department of Forest Sciences
3041-2424 Main Mall
Vancouver, B.C., Canada, V6T 1Z4
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
