A method for partitioning trends in genetic mean and variance to understand breeding practices

Authors: Oliveira, T. P., Obšteter, J., Pocrnic, I., Heslot, N., Gorjanc, G.

Genetics Selection Evolution

https://gsejournal.biomedcentral.com/articles/10.1186/s12711-023-00804-3

Code Structure

The code can be executed at once by following the RunME.R script. However, I am pointing out below a step-by-step on the order the script should be executed.

1. Generating the Cattle Breeding Programme
   1. Go to the folder simulation5Males and open the script breedingProgrammeScheme.R.
   2. The script breedingProgrammeScheme.R calls the following scripts:
   3. globalParameters.R - Global Parameter of the simulation
   4. CreateFounders.R - Create Parents
   5. burnin.R - to run the Burnin phase
   6. Scenario1.R - to run the Medium-accuracy scenario
   7. Scenario2.R - to run the high-accuracy scenario
2. Analysis of true trends in genetic mean and variance
   1. Go to the folder Analysis
   2. Analysis of true breeding value
      1. AlphaPart_TruePartition.R - for 1 replicate
      2. AlphaPart_TruePartition30reps.R - for 30 replicate
3. Using MCMC approach to get samples from the posterior distribution of $p(a|y)$ - 1 replicate
   1. Model and Samples
      1. gibbs1f90.R - run blupf90 family of programmes (it is assumed the programmes are already installed in the path $HOME/bin/)
      2. gibbs1f90NoInb.R - run blupf90 family of programmes without considering inbreeding
   2. AlphaPart analysis
      1. AlphaPart_Gibbs_Pheno_Validation.R - analysis of medium-accuracy scenario
      2. AlphaPart_Gibbs_Pheno_ValidationNoInb.R - analysis of medium-accuracy scenario without considering inbreeding
      3. AlphaPart_Gibbs_TBV_Validation.R - analysis of high-accuracy scenario
      4. AlphaPart_Gibbs_TBV_ValidationNoInb.R - analysis of high-accuracy scenario without considering inbreeding
4. Using MCMC approach to get samples from the posterior distribution of $p(a|y)$ - 30 replicate
   1. Go to the folder ./Analysis/Supplementary/30_Replicates
   2. You can run the script RUNME.R
   3. The script AlphaPart_Results.R can be used to visualise and generate the outputs.