Checking phenotypes...
Individual IDs (strings) are provided in the first column of the phenotypic data.
Phenotypes for all traits included in the model for individual a7 in the row 5 are missing. This record is deleted.
The number of observations with both genotypes and phenotypes used in the analysis is 4.
The number of observations with both phenotype and pedigree information used in the analysis is 4.
Prior information for genomic variance is not provided and is generated from the data.
Prior information for residual variance is not provided and is generated from the data.
Prior information for random effect variance is not provided and is generated from the data.
Prior information for random effect variance is not provided and is generated from the data.
Missing values are found in independent variables: dam.
Pi (Π) is not provided.
Pi (Π) is generated assuming all markers have effects on all traits.
The prior for marker effects covariance matrix is calculated from genetic covariance matrix and Π.
The mean of the prior for the marker effects covariance matrix is:
0.617255 0.0 0.0
0.0 0.532118 0.0
0.0 0.0 0.155597
A Linear Mixed Model was build using model equations:
y1 = intercept + x1 + x3 + ID + dam
y2 = intercept + x1 + x2 + x3 + ID
y3 = intercept + x1 + x1*x3 + x2 + ID
Model Information:
Term C/F F/R nLevels
intercept factor fixed 1
x1 covariate fixed 1
x3 factor fixed 2
ID factor random 12
dam factor random 12
x2 factor random 2
x1*x3 interaction fixed 2
MCMC Information:
methods BayesC
complete genomic data
(i.e., non-single-step analysis)
chain_length 100
burnin 0
estimatePi true
estimateScale false
starting_value false
printout_frequency 101
output_samples_frequency 1
constraint false
missing_phenotypes true
update_priors_frequency 0
seed false
Hyper-parameters Information:
random effect variances (y2:x2,y3:x2):
1.081 0.0
0.0 0.316
random effect variances (y1:ID,y2:ID,y3:ID,y1:dam):
1.253 0.0 0.0 0.0
0.0 1.081 0.0 0.0
0.0 0.0 0.316 0.0
0.0 0.0 0.0 1.253
residual variances:
1.253 0.0 0.0
0.0 1.081 0.0
0.0 0.0 0.316
genetic variances (polygenic):
1.253 0.0 0.0 0.0
0.0 1.081 0.0 0.0
0.0 0.0 0.316 0.0
0.0 0.0 0.0 1.253
genetic variances (genomic):
1.253 0.0 0.0
0.0 1.081 0.0
0.0 0.0 0.316
marker effect variances:
0.617 0.0 0.0
0.0 0.532 0.0
0.0 0.0 0.156
Π: (Y(yes):included; N(no):excluded)
["y1", "y2", "y3"] probability
["Y", "Y", "N"] 0.0
["N", "N", "N"] 0.0
["Y", "N", "N"] 0.0
["N", "Y", "Y"] 0.0
["Y", "N", "Y"] 0.0
["N", "N", "Y"] 0.0
["Y", "Y", "Y"] 1.0
["N", "Y", "N"] 0.0
Degree of freedom for hyper-parameters:
residual variances: 7.000
random effect variances: 6.000
polygenic effect variances: 8.000
marker effect variances: 7.000
The file MCMC_samples_residual_variance.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_polygenic_effects_variance.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_marker_effects_y1.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_marker_effects_y2.txt is created to save MCMC samples for marker_effects_y2.
The file MCMC_samples_marker_effects_y3.txt is created to save MCMC samples for marker_effects_y3.
The file MCMC_samples_marker_effects_variances.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_pi.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_y2.x2_y3.x2_variances.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_y1.ID_y2.ID_y3.ID_y1.dam_variances.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_EBV_y1.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_EBV_y2.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_EBV_y3.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_genetic_variance.txt already exists!!! It is overwritten by the new output.
The file MCMC_samples_heritability.txt already exists!!! It is overwritten by the new output.