[R-sig-ME] binary trait

[Jarrod Hadfield]

Hi,

It looks like you might have complete separation in the fixed effects, 
and therefore under/overflow. Are there some years or farms where all 
animals have a zero or one? Treating them as random effects might 
alleviate the problem, and be a sensible option anyway given the number 
of levels.

Cheers,

Jarrod


On 01/12/2016 15:29, Mohamed Salem wrote:
> Dears,
> I am trying to use MCMCglmm to estimate heritability for binary trait.
> I used this model
> "
>
> prior <- list(R = list(V = 1, fix = 1), G = list(G1 =
>
> list(V = 1, nu = 1000, alpha.mu = 0, alpha.V = 1)))
>
>
>
> model1 <- MCMCglmm(SB ~ 1 + Farm +year, random = ~animal, family =
> "ordinal",
>
> prior = prior, pedigree = Ped, data = Data, nitt = 1e+06,burnin = 10000,
> thin = 100)
> and when I diagnosed the MCMC work by autocorr.diag(model1$VCV)
> I found this results
>           animal units
> Lag 0    1.0000000   NaN
> Lag 100  0.9786790   NaN
> Lag 500  0.9092071   NaN
> Lag 1000 0.8360430   NaN
> Lag 5000 0.4860764   NaN
>
> the total number of animals is 2800 animal
>
> the summary of the analysis are
> Iterations = 10001:999901
>   Thinning interval  = 100
>   Sample size  = 9900
>
>   DIC: 1347.1
>
>   G-structure:  ~animal
>
>         post.mean  l-95% CI u-95% CI eff.samp
> animal     1.433 8.014e-08    4.598    64.81
>
>   R-structure:  ~units
>
>        post.mean l-95% CI u-95% CI eff.samp
> units         1        1        1        0
>
>   Location effects: SB ~ 1 + Farm + year
>
>               post.mean   l-95% CI   u-95% CI eff.samp    pMCMC
> (Intercept) -5.836e+02 -1.003e+03 -4.714e+00    2.632 0.000404 ***
> Farm2       -7.124e-02 -6.184e-01  4.535e-01 3785.279 0.803636
> Farm3       -2.997e-01 -8.896e-01  2.803e-01  886.117 0.288889
> Farm4       -1.194e-01 -1.213e+00  9.619e-01 7819.001 0.836162
> Farm5        5.514e-01 -9.988e-02  1.279e+00  652.534 0.071919 .
> Farm6        4.886e-01 -1.597e-01  1.149e+00  655.714 0.097172 .
> year1978     3.215e+02 -4.543e+02  8.054e+02    3.190 0.353535
> year1979     1.188e+03  1.480e+02  2.099e+03    1.665  < 1e-04 ***
> year1980     1.952e+02 -1.496e+02  6.365e+02    5.395 0.394343
> year1981     5.817e+02 -1.770e+00  9.969e+02    2.623 0.001818 **
> year1982     3.986e+02 -3.734e+02  9.482e+02    2.515 0.356768
> year1983     4.984e+02 -6.546e+01  1.014e+03    2.381 0.167071
> year1984     5.007e+02 -8.501e+01  9.976e+02    2.620 0.193535
> year1985     2.057e+02 -1.166e+02  6.239e+02    5.649 0.350505
> year1986     5.812e+02  1.908e+00  1.000e+03    2.619 0.002424 **
> year1987     5.809e+02  2.574e+00  1.001e+03    2.627 0.002222 **
> year1988     5.816e+02  2.922e+00  1.001e+03    2.557 0.001616 **
> year1989     5.800e+02  1.863e+00  1.000e+03    2.623 0.002828 **
> year1990     5.807e+02  1.117e+00  9.997e+02    2.558 0.002020 **
> year1991     5.811e+02  2.930e+00  1.002e+03    2.549 0.001818 **
> year1992     5.800e+02  1.759e+00  1.000e+03    2.626 0.002222 **
> year1993     5.812e+02  2.556e+00  1.002e+03    2.629 0.001818 **
> year1994     5.035e+02 -3.250e+00  8.543e+02    3.221 0.013939 *
> year1995     5.809e+02  2.055e+00  1.001e+03    2.626 0.002222 **
> year1996     5.801e+02 -1.762e+00  9.969e+02    2.627 0.002424 **
> year1997     5.808e+02  1.968e+00  1.001e+03    2.554 0.001818 **
> year1998     5.805e+02  2.003e+00  1.000e+03    2.627 0.002020 **
> year1999     5.803e+02 -1.759e+00  9.969e+02    2.622 0.002828 **
> year2000     5.814e+02  2.903e+00  1.001e+03    2.627 0.001818 **
> year2001     5.809e+02  2.474e+00  1.001e+03    2.628 0.002020 **
> year2002     5.813e+02  2.494e+00  1.001e+03    2.557 0.001818 **
> year2003     5.815e+02  3.182e+00  1.002e+03    2.627 0.001818 **
> year2004     5.813e+02  2.462e+00  1.001e+03    2.628 0.001818 **
> year2005     5.815e+02  2.719e+00  1.002e+03    2.629 0.001818 **
> year2006     5.820e+02  3.711e+00  1.002e+03    2.628 0.001414 **
> year2007     5.821e+02  3.275e+00  1.002e+03    2.631 0.001616 **
> year2008     5.818e+02  3.401e+00  1.002e+03    2.556 0.001414 **
> year2009     5.815e+02  2.774e+00  1.001e+03    2.626 0.001818 **
> year2010     5.822e+02  3.230e+00  1.002e+03    2.559 0.001010 **
> year2011     5.815e+02  2.777e+00  1.001e+03    2.625 0.002020 **
> year2012     5.817e+02  2.849e+00  1.001e+03    2.628 0.001818 **
> year2013     5.812e+02  2.790e+00  1.001e+03    2.550 0.002020 **
> year2014     1.103e+02 -3.772e+02  4.805e+02    3.673 0.673737
>
>


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