[R-sig-ME] MCMCglmm error message - data.frame subscripts

[Liz Hare]

Hello,

I'm getting an error message with MCMCglmm that I can't figure out.

The data:

Pedigree

> head(ped)
    animal sire dam
1 1001001   NA  NA
2 1001002   NA  NA
3 1001003   NA  NA
4 1001004   NA  NA
5 1001005   NA  NA
6 1001006   NA  NA

Phenotype

> head(pp9)
      animal  PP
36 20020999 4.0
38 20021000 2.5
43 20021001 3.5
46 20021002 3.5
52 20021003 4.0
53 20021004 5.0

(I have more animals in the pedigree than I have phenotypes for)


> m3 <- MCMCglmm(pp9$PP ~ 1, random=~animal, family="gaussian",
pedigree=ped, data=pp9, nitt=100000, burnin=10000, thin=10)
Error in `[<-.data.frame`(`*tmp*`, , response.names, value = c(4, 2.5,  :
   missing values are not allowed in subscripted assignments of data frames


Which data.frame subscripts does this refer to? Am I neglecting to set 
some parameter? I have removed all the NAs from the phenotype 
data.frame. I ran MCMCglmm with very small trial data, so I think the 
problem is with my data but I can't find where.



> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] MCMCglmm_2.17   corpcor_1.6.4   ape_3.0-7       coda_0.16-1
[5] Matrix_1.0-10   lattice_0.20-13 tensorA_0.36

loaded via a namespace (and not attached):
[1] compiler_2.15.1 gee_4.13-18     grid_2.15.1     nlme_3.1-108
[5] tools_2.15.1


I'd appreciate any suggestions,
Liz


-- 
Liz Hare PhD
Dog Genetics LLC
doggene at earthlink.net
http://www.doggenetics.com