[R-sig-ME] MCMCglmm error message:Error in `[.data.frame undefined columns selected
Jarrod Hadfield
j.hadfield at ed.ac.uk
Tue Jun 24 15:25:36 CEST 2014
Hi Sam,
Which version of MCMCglmm are you using, and do you get the same error
with the newest version?
Also, the covariances in us(GroupA):units cannot be estimated - so
idh(GroupA):units is more appropriate (as an rcov term).
Cheers,
Jarrod
Quoting "PATRICK, Samantha" <spatrick at glos.ac.uk> on Tue, 24 Jun 2014
11:51:53 +0000:
> 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
>
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