Per-Environment BLUEs for Stability Analysis Examples

Simulated pre-adjusted phenotype means (BLUEs) for 120 individuals across two environments, formatted as a named list for use with run_haplotype_stability and cv_haplotype_prediction. Each element is a named numeric vector (names = individual IDs, values = BLUEs) representing adjusted means from one environment or growing season.

In a real analysis these would come from fitting environment-specific mixed models. Here they are generated from the same polygenic trait values as ldx_blues with environment-specific offsets and noise.

Usage

ldx_blues_list

Format

A named list with 2 elements:

env1

Named numeric vector of length 120. BLUEs for environment 1 (base yield values with small noise).

env2

Named numeric vector of length 120. BLUEs for environment 2 (mean shift of 0.4 units above env1, simulating a more favourable environment).

Names of each vector match rownames(ldx_geno) (ind001 to ind120).

Source

Generated by data-raw/generate_example_data.R. Seed: set.seed(20250409).

See also

run_haplotype_stability, cv_haplotype_prediction, ldx_blues, ldx_geno

Examples

data(ldx_blues_list)
names(ldx_blues_list)          # "env1" "env2"
#> [1] "env1" "env2"
length(ldx_blues_list$env1)    # 120
#> [1] 120
head(ldx_blues_list$env1)
#>  ind001  ind002  ind003  ind004  ind005  ind006 
#> -0.3923  0.6664 -1.4078 -1.4531  1.3324  1.1296 

# Mean BLUE difference between environments (expected ~0.4)
mean(ldx_blues_list$env2 - ldx_blues_list$env1)
#> [1] 0.3960925

# \donttest{
# Finlay-Wilkinson stability analysis across two environments
data(ldx_geno, ldx_snp_info, ldx_blocks)
stab <- run_haplotype_stability(
  geno_matrix = ldx_geno,
  snp_info    = ldx_snp_info,
  blocks      = ldx_blocks,
  blues_list  = ldx_blues_list,
  verbose     = FALSE
)
# Stable blocks (regression slope b not significantly different from 1)
head(stab[stab$stable, c("block_id","b","b_se","r2_fw")])
#> [1] block_id b        b_se     r2_fw   
#> <0 rows> (or 0-length row.names)
# }