Explores trial and germplasm data. For a trial with one row per plot: analysis of variance for one or two treatment factors, completely randomized or in complete blocks, with Tukey HSD, Fisher LSD or Duncan mean comparison letters, Shapiro-Wilk and Levene assumption checks, means plots, and a summary table across several traits at once giving each treatment mean with its letter, the LSD and the CV. For a genotype × trait table: data overview and validation, correlation analysis between traits, PCA and hierarchical clustering (via FactoMineR/factoextra), and multi-trait genotype selection with the MGIDI index (via the metan package).
R analysis pipeline
Stage-3 dosage-aware genomic selection pipeline for hexaploid sweetpotato
Reference R implementation of the Stage-3 pilot genomic-selection workflow in Table 5 of the Ecological Genetics and Genomics review on AI-assisted breeding in sweetpotato. The pipeline calls dosage-uncertain genotypes with polyRAD, builds a hexaploid additive relationship matrix with AGHmatrix (VanRaden extended to ploidy 6), fits dosage-aware GBLUP for five target traits under five-fold cross-validation with sommer, computes a classical MGIDI Stage-1 baseline on the same traits with metan, and tests the accuracy difference between them with a 10,000-resample bootstrap confidence interval. No genotyping-by-sequencing data yet exist for the sweetpotato panel, so all genotypes and phenotypes in the repository are simulated (a 315-progeny biparental hexaploid population); only the data-loading step changes when real genotyping data become available.