Repeat records of single trait model

Running repeat records model is nearly the same with fitting single trait model, the only difference is that repeat records model can fit the permanent environment effect, which can be achieved by assigning individual id at the first column of phenotype file to environmental random effect, take GBLUP model for an example:

./hiblup --single-trait 
         --pheno demo.repeat.phe
         --pheno-pos 2
         --rand 1
         --bfile demo
         --threads 32
         --out demo

It should be noted that HIBLUP uses the variance-covariance matrix of phenotype records in genetic parameter estimation, thus if there are low-replications (e.g., 2000 records from 1000 individuals replicated twice), HIBLUP will be faster than MME-based software. But if the analyzed trait are highly replicated (e.g., 2000 records from 200 individuals replicated 10 times), the BLUPF90, ASreml or other MME-based algorithms will be much faster and we recommend you to use that software.