permute: version 0.9-0

Changes in version 0.9-0 General

This is small update to permute, focused mainly on ensuring the many combinations of restrictions on permutations allowed by the package work. An extensive test suite has been written which covers ~87% of the package's codebase at the time of release.

• Permutation matrices produced by shuffleSet() are now printed in a more compact form.

• Better heuristics in check() allow for more reliable permutations (i.e. fewer duplicate permutations) when the set is small. This has increased the minperms setting. Consequently we generate all possible permutations up to ~500,000 more often as we now randomly sample from the entirely generated set rather than randomly generate permutations. This provides a small performance hit in some rare cases.

• shuffleSet() has a new argument quietly = FALSE which is passed on to check().

• A number of bugs were fixed. See the Changelog and the Bug reports on github for details.

• permControl() and permuplot() are defunct and have been removed from the package.