$Date: 2012-04-04 21:14:12 +0100 (Wed, 04 Apr 2012) $

permute ChangeLog

Version 0.7-0

	* Vignette: silly typo is example code illustrating shuffle().
	New section on `shuffleSet()`.

	The Vignette is now in `vignettes` not `inst/doc`.

	* check.Rd: undo the hack needed to pass checks prior to
	vegan 2.0 being on CRAN.

	* Suggests: now needs vegan >= 2.0-0

	* shuffleGrid: was doing random flipping of permutations even
	if `mirror = FALSE` for the `constant = TRUE` case.

	* shuffleStrata: assumed that the samples were in contiguous
	blocks. Reported by Cajo ter Braak.

	* .Internal: removed all instances of .Internal calls in the
	code.

	* Package is now byte-compiled.

Version 0.6-1 (released to CRAN on September 7, 2011)

	* NAMESPACE: export(permuplot)

	* check.Rd: temporarily supress some of the examples to run
	only on vegan >= 2.0-0. Needed during transition to pass
	checks on CRAN until version 2.0-0 is released.

Version 0.6-0 (closed September 7, 2011)

	* allPerms: added warning regarding current need for samples
	to be arranged in order of any strata.

	* Release: Pushed to CRAN. First beta release.

Version 0.5-4 (opened August 31, 2011)

	* permCheck: deprecate `permCheck()` in favour of `check()`.

	* allPerms: code clean-up

	* preparing for first release to CRAN.

Version 0.5-3 (closed August 31, 2011)

	* shuffleSet: now handles all permutation types that are
	available in shuffle().

	* nobs.Rd: fixed an example which created a numeric vector of
	zeros instead of changing sampled vector to numeric. The example
	yielded an error in R 2.14.0 (under development) where only one
	argument was accepted for numeric() and two or more args cause an
	error. The two isTRUE() cases should be true only exceptionally,
	and may call for a fix.

	* NAMESPACE, nobs-methods.R: The package relied on import(stats,
	nobs), but that works only in R 2.13 and failed in R 2.12.2. Now
	we define and export nobs() generic in permute package for older
	R. The help file still gives a warning for missing documentation
	of nobs in R 2.12.2 and prior, but there is no obvious fix to
	this.

Version 0.5-2 (closed August 23, 2011)

	* shuffelSet: new function to generate a set of `n`
	permutations without the overhead of `n` repeated calls to
	`shuffle()`. Currently only for designs without
	strata/blocks.

Version 0.5-1 (closed July 5, 2011)

	* shuffle: now returns seq_len(n) for no permutation within
	blocks or of blocks.

	* tests: testing using the `testthat` package. Initial
	infrasctructure.

Version 0.5-0 (closed June 28, 2011)

	* shuffle: renamed permuted.index() to shuffle()
	* Vignette: the package has a vignette, which is very much
	a work-in-progress.

Version 0.0-3 (closed June 17, 2011)

	* NAMESPACE: permute gets a NAMESPACE. Needed to shield
	functions form ones of similar name in vegan.

Version 0.0-2 (closed December 09, 2010)

	* allPerms: Large update. allPerms now works for all
	permutation designs *except* when permuting both blocks
	and within blocks. This exception is handled with
	.NotYetImplemented().

	* numPerms: Wasn't returning the correct number of
	permutations when WITHIN == "none" and BLOCK != "none",
	i.e. permuting strata.

	* Utils: Utility functions defined inline within allPerms
	moved to new proper functions and renamed; allFree, allSeries
	allGrid, allStrata.

Version 0.0-1 (closed February 28, 2010)

	* SVN: Uploaded code to r-forge within vegan source tree.
	This code base represents my working version as of today,
	*not* the version in vegan at that time.