D-optimality • TSDFGS

D-optimality maximizes the information content of the training set, the determinant of the ridge information matrix.

Type	Optimal design
Direction	Larger is better
Uses a test set	no (a test set given to `optTrain()` is ignored)
Score a given set	`dopt_score()`
Search with it	`optTrain(method = "DOpt")`

Definition

$\mathrm{D} = \log\det(X'X + \lambda I)$ , $\lambda = 1/p$ , to be maximized. STPGA returns the negative, to be minimized.

Use in TSDFGS

library(TSDFGS)
data(geno)
dopt_score(geno[1:50, ])

## [1] -1654.586

fit <- optTrain(geno, cand = 1:404, n.train = 50, method = "DOpt",
                 min.iter = 300, console = FALSE, seed = 1)
fit$OPTtrain

##  [1] 324 244 314 299 402 315 321 253 216 185 398  49 103 328 262 278 296  20 392
## [20] 388 297 168 196  27 282 260 325 399 369 227 131 128 197 245  10 312  77 389
## [39] 256  16 135 268 149  60 152  62 350 316 298 138

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

Akdemir, D., & Isidro-Sánchez, J. (2019). Design of training populations for selective phenotyping in genomic prediction. Scientific Reports, 9, 1446. https://doi.org/10.1038/s41598-018-38081-6

Akdemir, D., Sanchez, J. I., & Jannink, J.-L. (2015). Optimization of genomic selection training populations with a genetic algorithm. Genetics Selection Evolution, 47, 38. https://doi.org/10.1186/s12711-015-0116-6

Repository or website of the original authors: R package STPGA by Akdemir and colleagues: CRAN.R-project.org/package=STPGA (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: STPGA, GPL-3 (DOPT); compared, not copied.
Verdict: included.

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