GxE Analysis in R Workshop hosted by CIAT Arusha. Updated 2022-10-12
My name is Ellena Girma and I am a breeding data systems and analytics specialist at the Alliance Bioversity International - CIAT.
The goal of this workshop is to give CIAT Bean Program scientists and technicians an overview of how to use the metan pacakge in R to run GxE Interaction and Stability Analysis.
Below are the materials you need to follow the workshop:
You will need to install R/RStudio* as well as the following packages:
Check out my resources page for video instructions on how to download R and RStudio.
It’s best to organize your R code using R Projects. This way, all the materials related to an analysis/project will be under one parent folder but will be separated by content type (ex: data, scripts, outputs, reports, notes). All folders in this parent folder are easily accessed by the RProject.
Some resources on project oriented workflows in R:
Feel free to use your own data if you have data available.
If you need data to practice on, I suggest using data from this paper. 1 The data contains information about the seed yield, 100 seed weight, number of seeds/pod, number of pods/plant and days to 75% flowering for 99 common bean variants grown in 3 locations. The data is listed under Appendix A. Supplementary data.
‘’Philipo M, Ndakidemi PA, Mbega ER. Environmentally stable common bean genotypes for production in different agro-ecological zones of Tanzania. Heliyon. 2021 Jan 19;7(1):e05973. doi: 10.1016/j.heliyon.2021.e05973’’↩︎