Hi
I am having problems with an error message in MCMCglmm. I am trying
to partition the variance in the model so that each group has its
own estimated variance. Originally I had a more complicated model
but I have simplified it below to show the source of the problem (so
the prior is not optimised for this model and only part of the data
set is given). If I fit random = ~GroupA, it runs ok, but if I add
in ~us (GroupA):units it gives the error:
Error in `[.data.frame`(data, , components$rterms[select.terms]) :
undefined columns selected
Previous posts have suggested it may be because the variables do not
exist but it is not this. I have tried other variants but I keep
getting the same error. I have changed all the variable names in
case there was a double with a function but still no luck.
Does anyone have any ideas? The same error occurs if you just try to
fit the rcov statement (with units). I thought there could be a
problem estimating the units term perhaps and so it can not find the
residual variance. But if I try other terms in its place I get the
same error
Thanks
Sam
Script
library(MCMCglmm)
prior2.1 <- list(R = list(V= 1, nu =0.002), G = list(G1 = list(V
=diag(4), nu = 1.002)))
mod2.1<- MCMCglmm(DistanceA ~FixedA, random = ~us(GroupA):units,
# rcov = ~idh(GroupA):units,
prior = prior2.1,
data=h,
pr=TRUE, burnin = 200, nitt = 5000000, thin = 200)
Data
IDA DistanceA FixedA GroupA
1 35.76203413 12 A
1 353.8044206 26 A
1 28.6894637 14 A
1 302.9190056 16 A
1 308.7219701 23 A
2 173.9284996 111 B
2 231.2895313 37 B
2 223.0156577 11 B
2 257.7869899 27 B
3 308.3258686 110 A
3 178.3784977 37 A
3 218.3712172 15 A
4 288.5865862 65 B
5 54.62104181 20 A
5 310.5786671 118 A
5 185.3627266 18 A
5 300.8304258 51 A
6 461.4315924 75 B
6 496.403949 52 B
7 708.2367263 181 B
7 214.8704587 35 B
8 183.6161529 44 A
8 183.326292 21 A
8 319.0479119 39 A
9 269.6319359 79 B
9 325.1318986 98 B
9 399.208417 99 B
10 135.2138385 50 B
10 162.9959776 67 B
11 49.05385099 17 A
11 80.92750054 26 A
11 184.7205464 16 A
12 327.6768626 47 A
29 240.6830677 85 C
29 126.9140906 23 C
29 216.4021125 29 C
29 168.8125168 52 C
30 230.8613452 25 D
30 134.8893388 38 D
30 164.2181205 48 D
30 140.8627105 55 D
31 15.51295239 6 D
31 42.45851533 3 D
31 16.30773693 4 D
31 89.57289202 20 D
31 108.0256345 115 D
32 118.2199077 12 D
32 247.9492249 26 D
32 18.20298953 15 D
32 70.97933919 20 D
32 109.7264855 36 D
32 101.8653273 19 D
32 68.54583069 7 D
33 24.1465819 7 C
33 67.33233486 75 C
33 64.92951246 31 C
33 94.90538004 53 C
34 474.3625341 171 C
54 150.6926733 43 D
54 191.6157478 58 D
54 127.1248342 14 D
55 385.2042737 42 D
55 202.8058375 23 D
55 144.4546654 44 D
56 194.0171206 81 D
56 163.6960289 40 D
57 122.5337279 89 D
57 172.2405156 44 D
57 206.4998878 79 D
57 122.677563 19 D
58 147.3699167 31 D
59 140.7191172 84 D
59 241.2723386 50 D
59 230.1874477 83 D
60 130.6675375 101 D
60 104.4518299 9 D
60 134.473374 56 D
61 135.7597774 17 D
61 232.3798885 40 D
62 164.1352534 65 D
62 259.1312989 28 D
63 177.8687393 145 C
63 121.3886107 43 C
64 202.009693 43 D
64 218.7044853 41 D
Dr Samantha Patrick
Research Fellow
Biosciences QU116
Francis Close Hall Campus
University of Gloucestershire
Cheltenham
GL50 4AZ
UK
Research Associate: ABRG, University of Oxford
Tel : +44 1242 714 668
Skype: sammy_patrick