A new version (2.4.2) of my R-package CEGO was recently uploaded to CRAN.
This update contained an important fix to one of the distance functions: distancePermutationSwap. As kindly reported by Manuel López-Ibáñez, that distance was previously computing the swap distance on the inverse of the provided permutations. This is now corrected. The original behavior can be reproduced via distancePermutationSwapInv.
This issue and the impact it can have on the results with CEGO in optimization runs is discussed in an article by Irurozki and López-Ibáñez, which also covers an interesting modeling approach based on Mallows models, see:
Ekhine Irurozki and Manuel López-Ibáñez. Unbalanced Mallows Models for Optimizing Expensive Black-Box Permutation Problems. In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO 2021. ACM Press, New York, NY, 2021. doi: 10.1145/3449639.3459366
For the updated CEGO Package see also (external link) https://cran.r-project.org/package=CEGO.