This document contains the code that takes the raw phenotypic data from the Cooperative Dry Bean Nursery that was digitized by Jeff White, and generates the phenotypes used for Best Linear Unbiased Prediction. It standardizes the scales these phenotypes are measured on, and removes outliers, primarily by location and year.

Analysis of the 2018 yield data for 10 older CDBN germplasm entries, trying to see if a Finlay-Wilkinson model of GxE had predictive power in determining the type of GxE that different entries had. Tl;dr: This isn't a good enough model to predict differences in GxE in common bean.

Data Processing of the raw Cooperative Dry Bean Nursery phenotypic dataset to generate 22 cleaned phenotypes.

Finlay Wilkinson Predictions and varieties to grow at five CDBN locations to test these predictions. Varieties with high GxE, low GxE, high yield, and low yield at these sites are indicated.

This document contains some of the yield predictions made using the CDBN dataset and a Finlay-Wilkinson model. These predictions are based on a Finlay-Wilkinson (FW) model fitted using a Bayesian Gibbs sampler and a matrix of variety relatedness (A). The Gibbs sampler shrinks estimates for each variety towards the average performance of the model, and generally gives better predictive power than an ordinary least squares model. The A matrix was calculated in Tassel using the recommended methodology (centered IBS). The SNP matrix used in Tassel was generated from the GBS data collected by Phil McClean and myself using the ApeKI enzyme, aligned using bwa mem to the P. vulgaris genome V 2.0, and with SNP calls using NGSEP.

What is the variation in daylength during the growing season for sites in the CDBN? And what is the relationship between cumulative growing degree days and days to flowering? Does this relationship vary by site?

Cleaning up Jeff's V1.5 data to make my version V1.5.1 with revised location and germplasm data and estimated planting dates.

Here are histograms that compare population genetic summary statistics for Rpp8, a duplicated R-gene, with singleton R-genes that were sequenced in Erika Bakker's 2006 Plant Cell paper.

Rarefaction analysis by allele to make sure that our sample size of alleles is large enough to do the kinds of analyses we want to do in the Rpp8 paper.

Taking Jeff's All_experiments file and adding my germplasm data and Climate_bin information to make an updated dataset.

A small mapping tutorial to get you started mapping with ggplot.

How much heterozygousity is there in the bean samples, and how much does heterozygousity vary by bean variety?