[R-sig-ME] binary trait

[Mohamed Salem]

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


-- 
*Mohamed M. I. Salem*

Lecturer
Department of Animal Production
Faculty of Agriculture, Alexandria University
Aflaton St., El-Shatby, P. O. Box 21545
Alexandria, Egypt
Tel: (+203) 5915427, (+203) 5924391
Fax (+203)5922780
e-mail: mmisalem at gmail.com
           mohamed.salim at alexu.edu.eg
skype: mmisalem

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