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CDmean(v2)

Source: vignettes/articles/criterion-cdmean2.Rmd
criterion-cdmean2.Rmd

The heuristic form of CDmean from Chen et al. (2024): the contrast is replaced by the individual itself.

Type Model-based
Direction Larger is better
Uses a test set yes; without a test set, all candidates
Score a given set cdmean2_score()
Search with it optTrain(method = "CDmeanV2")

Definition

Mean of diag(KPTWKTP)/diag(KPP)\mathrm{diag}(K_{PT}WK_{TP})/\mathrm{diag}(K_{PP}). TSODBG sums instead of averaging; the optimum is the same for a fixed target.

Use in TSDFGS 

library(TSDFGS)
data(geno)
cdmean2_score(geno[1:50, ], geno[51:100, ])
## [1] 0.6036041
fit <- optTrain(geno, cand = 1:404, n.train = 50, method = "CDmeanV2",
                 min.iter = 300, console = FALSE, seed = 1)
fit$OPTtrain
##  [1] 181 312 119 184 178 170 251 256 277   5 330 263  32  79 158 135 105 217 199
## [20]  73 391 287 373  89 289 370 153 394  42 237  20  44 308  92 121 247 205 389
## [39] 262 221  62 298 165 160  38  15 183 196 206 230
# targeted: the test set is known
fit2 <- optTrain(geno, cand = 1:300, n.train = 50, test = 301:404,
                  method = "CDmeanV2", min.iter = 300, console = FALSE, seed = 1)
fit2$OPTtrain
##  [1] 162 129 102 183  85 293  65 147 298  43 163 217 165  89 261  34 199  44 168
## [20]  76  99 172  71 186 220 216 160  12 130 133 116 118  60 193  70  67 300  16
## [39] 151 289  93  31  15  48 245 252 180 221 247  97

The search is a random-start exchange (hill-climbing) search; see How the scores are computed. Use min.iter larger than 300 on real data and check fit$converged.

Original work

Chen, S.-P., Sung, W.-H., & Liao, C.-T. (2024). Constructing training sets for genomic selection to identify superior genotypes in candidate populations. Theoretical and Applied Genetics, 137, 270. https://doi.org/10.1007/s00122-024-04766-y

Repository or website of the original authors: R package TSODBG of Chen et al. (2024): github.com/spcspin/TSODBG (GPL >= 3).

License review

Formulas and algorithms are ideas and methods, which copyright does not protect. Where an original package is under a GPL license, we read it to check our results and credit it; TSDFGS is GPL-3, which is compatible with GPL-3 and GPL (>= 3) code. This is our reading of the public record, not legal advice; see the license review.

  • Original software: TSODBG, GPL (>= 3); compared, not copied.
  • Article license: CC BY-NC-ND 4.0.
  • Verdict: included.

Reviewed 2026-11-04. All criteria and the ones left out.