Manual on general management principles for breeding seed orchards (BSOs):Part II: data analysis

This guide provides a manual for analysis of data from breeding seed orchards in the statistical program R mainly based on BreedR (Muñoz and Sanchez 2020) aiming at the highest possible genetic gains while considering genetic diversity and providing knowledge on provenances as well. The guide gives some of the theoretical backgrounds for quantitative genetic analysis at the start. However, it is possible to go directly to the chapter on “Data files” and continue from there and modify the R program made for a Cordia africana case to obtain tables with breeding values, which can be used to make the thinning decisions for the BSOs. It is recommended to print out the tables and figures attached at the end of this guide, and at the same time copy the program and paste it into a text editor like “Context” or the Windows editor making it possible to search for the references made in this guide to program steps in the R-program