permute 0.9-7 released

Version 0.9-7 of permute is now on CRAN. This version fixed an error caught in r-devel (to be 4.2 I think).

• The documented behaviour of shuffleFree() allowed shuffleFree(x = 1:10),
  with x passed immediately to sample.int(), which is incorrect and raises
  an error in the development version of R (at the time of writing).
  Reported by Brian Ripley.

I had previously drafted version 0.9-6 for release but for some reason it never got released. That version fixed a bug in allPerms()

• allPerms() was calling allSeries() with the incorrect number of
  permutations, leading to problems with shuffleSet() also.
  #28 reported by Cajo ter Braak

This fix is contained with 0.9-7.

permute 0.9-5 on CRAN

This release is a minor update prompted by changes to the random number generator in r-devel (what will become the R 3.6.x branch).

As a result a bug related to user-selected complete enumeration failing to modify the nperm component of the object returned by how() has also been fixed. #23

permute version 0.9-4

This release was generated by a snafu in building the tarball that I sent to CRAN. This didn't have the updated example reference materials and thus reference an out of date vegan release. 0.9-4 fixes this forever as we now suppress package startup messages in ?check, the one place in permute than any external package is loaded.

permute version 0.9-3

This release fixes a problem with canonical forms of URLs for CRAN

permute version 0.9-2

Minor change to v0.9-1 updating reference materials that were built using vegan 2.4-0 whilst 2.4-1 was just released to CRAN.

Minor bug-fix release

This release fixes a single bug:

• shuffleSet() wasn't returning a matrix if nset = 1 and allPerms was invoked because of a low set of possible permutations. Now shuffleSet() can be relied upon to always return a matrix of permutations. GitHub Issue #19

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.

New features

• 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.

Defunct

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

Permute Version 0.8-4

update the Description field to match latest requirements in WRE