Preservation of genetic variation in a breeding population for long-term genetic gain

Running the code

Install the package hypred (zip file included)
Install the package GSSimTPUpdate (zip file included)
Open the R project Article_files.Rproj
Run Create_directory.R
Run MakeGenome_File.R
Run one of the 'run_experiment' files in the main directory
Transfer the simulation results from the 'own_results' directory to the 'data' directory
Run the correct 'make_figure' script

data

This directory contains the original base population used for each simulation study and several directories where the simulation results can be stored.

Figures

This directory contains the original figures used for the article.

make_figures

This directory contains the R scripts used to make the figures. The simulated data should be put in the data/<method> directory.

own_results

Empty directory where simulation results will be saved. This directory is creating by running the script Create_directory.R.

MakeGenome_File

Makes a list of n different genomes that can be used in the run_experiment files. At each iteration, each method will use the same genome, making it possible to compare the different methods.

Genome

Directory containing an example files of genomes that can be used in the run_experiment files.

run_experiment files

R scripts used to simulate a population following the oracle, baseline, backcrossing, scoping or combined selection method. The results will be saved in the directory 'own_results'. The user will have to load the correct genome from the genome directory and choose the number of nodes that are available for calculation.

Supplementary data

Directory containing the supplementary figures and tables.

R

Directory containing functions that are used in the run_experiment files.

biointec/scoping