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updated JOSS draft
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cicirello committed Sep 1, 2018
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Expand Up @@ -51,8 +51,7 @@ pool is important to evolutionary computation. In later generations, if variati
the members of the population declines, then the evolutionary search can stagnate. Approaches
to population management [@sevaux2005], such as in scatter search [@campos2005; @marti2005],
attempt to maintain diversity among the population of solutions. They require a means of
measuring distance between population members. And if the problem is one in which solutions are
represented as permutations, then a permutation distance metric is required.
measuring distance between population members.

The second application of permutation distance for evolutionary computation is that of search
landscape analysis. A fitness (or search) landscape [@mitchell] is the space of possible
Expand Down Expand Up @@ -95,6 +94,17 @@ reinsertion distance | $O(n \lg n)$ | yes | [@cicirello2016; @cicirello2013]
reversal distance | Init: $O(n!n^3)$ Compute: $O(n^2)$ | yes | [@cicirello2016; @caprara1997]
squared deviation distance | $O(n)$ | yes | [@sevaux2005]

The library also provides distance metrics on sequences (Strings and arrays of various types), where unlike
a permutation, a sequence may contain multiple copies of the same element. The following table lists the metrics on
sequences that are provided ($n \leq m$ are the lengths of the compared sequences).

Distance | Runtime | Metric? | Citations
-------- | ------- | ------- | ---------
edit distance | $O(n*m)$ | yes | [@wagner74]
exact match distance | $O(n)$ | yes | [@ronald1998]
Kendall tau distance | $O(n \lg n)$ | yes | [@kendall1938]
longest common subsequence distance | $O(n*m)$ | yes | [@wagner74]

The source repository (https://github.com/cicirello/JavaPermutationTools)
contains source code of the library, programs that provide example
usage of key functionality, as well as programs that reproduce results from papers that
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