Fix AnimalBreeding Project.toml metadata - #13
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| rename_map = Dict{String,String}() | ||
| for (std_name, aliases) in required_cols | ||
| col_found = findfirst(name -> name in names(pedigree), aliases) | ||
| if isnothing(col_found) | ||
| error("谱系文件 '$filepath' 缺少必需列: $(first(aliases))") | ||
| end | ||
| rename_map[aliases[col_found]] = String(std_name) | ||
| end |
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The loop that verifies and renames the animal, sire, and dam columns searches names(pedigree) using raw strings (findfirst(name -> name in names(pedigree), aliases)). DataFrames names are Symbols by default, so this lookup never succeeds and the function always errors even when the CSV contains the expected headers. Converting aliases to Symbol before comparing (or converting names(pedigree) to strings) is required for load_pedigree to accept any real input.
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| # 更新残差方差 | ||
| residuals = y - X * solutions[1:n_fixed] - sum(Z * solutions[n_fixed+1:end] for (name, Z) in Z_dict) | ||
| s_y = dot(residuals, residuals) | ||
| tr_term = tr(C_inv[1:n_fixed, 1:n_fixed] * (X' * X)) # 简化 | ||
| variances_new["residual"] = (s_y + tr_term) / n_obs | ||
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| # 更新随机效应方差 | ||
| current_pos = n_fixed | ||
| for effect in model.random_effects | ||
| name = effect.name | ||
| dim = size(Z_dict[name], 2) | ||
| u = solutions[current_pos+1 : current_pos+dim] | ||
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| if effect.type == :additive && !isnothing(dm.A_inv_matrix) | ||
| u_Ainv_u = dot(u, dm.A_inv_matrix * u) | ||
| tr_term_u = tr(C_inv[current_pos+1:end, current_pos+1:end] * dm.A_inv_matrix) # 简化 | ||
| variances_new[name] = (u_Ainv_u + tr_term_u) / dim |
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The REML M‑step computes residuals and trace terms by multiplying each Z matrix with solutions[n_fixed+1:end] and by using C_inv[current_pos+1:end, current_pos+1:end] for every random effect. When more than one random effect is defined, this uses the entire concatenated random-effect vector for every effect and mis-sized submatrices, causing dimension mismatches or incorrect variance updates. The random-effect blocks need to be sliced per effect (as is already done later for u) before multiplying with each Z and when forming the trace terms.
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Summary
Testing
https://chatgpt.com/codex/tasks/task_e_68de471a61a08321a08031b35c9b9e94