Cocorresp Change Log

Version 0.4-4

    * Suggests: {pls} is now explicitly a suggested package.

Version 0.4-3

    * Suggests: {rmarkdown} is now explicitly a suggested package following
    changes to the {knitr} dependencies.

Version 0.4-2

	* eigenvals: Methods now return an object of class "eigenvals".

	* print.predcoca: The labels for predictor and response matrices were in
	the reverse order. The total variances for preditors and responses were
	correct, but the object names were back-to-front.

	* print.crossval, print.summary.crossval: Tweak to order of response and
	predictor matrices in a printed message. Suggested by Cajo ter Braak.

Version 0.4-1

	* envfit.coca: Don't test the output from example in `envfit.coca`
	during `R CMD check`. Issue using ATLAS BLAS reported by Brian
	Ripley. Issue #11

Version 0.3-0

	* screeplot: a new `screeplot()` for symmetric Co-CA analyses.

	* Vignette: a new HTML vignette is provided as an introduction
	to the co-correspondence analsysi.

Version 0.2-3

	* Corrected a typo in the package DESCRIPTION.  Reported by
	Prof. Ripley.

	* Switched to title case in DESCRIPTION Title field.  Reported by
	Uwe Ligges.

Version 0.2-2

	Development is now done on Github:
	https://github.com/gavinsimpson/cocorresp

	* envfit.coca: fixed to work with new vegan permutation
	interface in `envfit.default`. Reported & fixed by Jari Oksanen

	* NAMESPACE: import `factorfit` and `vectorfit` as we use these
	directly. Reported & fixed by Jari Oksanen

Version 0.2-1

	* envfit.coca: now does weighted correlations in common with
	`envfit.default` for weighted ordinations.

	* weights: new methods for objects of classes "symcoca" and
	"predcoca".

	* fitted.symcoca: was not preserving the names of the `X`
	and `Y` community matrices. The `print` method now squishes
	very small variations in the results resulting from floating
	point computations.

	* Tests: The package Examples are now checked against known
	good runs as part of new package checks in `./tests/`.

Version 0.2-0

	* NAMESPACE: cocorresp now has a namespace and imports from
	package vegan's namespace. Hence we now depend on vegan version
	1.17-12 or greater.

	* coca: now returns an object with class "coca" as well as a
	class from the fitting function ("predcoca" or "symcoca").

	* scores.symcoca: Now always returns a nested list even if only
	a single type of scores is requested. Individual scores
	components are named consistently `X` and `Y` rather than `U1`,
	`U2` etc.

	* scores.predcoca: Now always returns a nested list even if only
	a single type of scores is requested. Individual scores
	components are named consistently `X` and `Y` rather than `U1`,
	`U2` etc.

	* plot.symcoca, plot.predcoca: Plot method changed to plot
	only one of the	response or predictor results. Now also returns
	an object of class "ordiplot" which should be able to be used
	with all of Vegan's ordiplot code.

	* predcoca.eigen, predcoca.simpls, symcoca: These are now non-
	visible and not exported. Original intention was that the user
	would not call these functions.

	* envfit.coca: a method for the vegan envfit() function for
	vector and factor fitting external data to Co-CA fits.

	* eigenvals.coca: a method for the vegan eigenvals() function,
	which extracts Eigenvalues from Co-CA models.

	* points.coca: a points method for all types of Co-CA fitted by
	coca().

	* coinertia: this is now a fully user-visible function. The old
	function is now named fitCoinertia().

Version 0.1-9

	* CITATION: Updated citation file.

	* DESCRIPTION: Updated to latest version - updates were
	missed from previous version.

Version 0.1-8

	* CITATION: updated citation file to match CRAN requirements.

Version 0.1-7 (opened June 25th 2008)

	* permutest.coca: Correct markup for S3 method now
	that permutest is generic in vegan.

	* pasteCall: This function was added to vegan as a
	helper. As cocorresp depends on vegan there is no
	need for it in cocorresp.

Version 0.1-6

	* Removed Encoding: UTF-8 from package DESCRIPTION file.

	* Fixed a bug in print method for fitted.predcoca

	* Added scaleLin and mcLin to internal functions.

	* Updated Version: field in DESCRIPTION to match new
	requirements in R 2.6.0.

Version 0.1-5

	* Added 'stats' and 'graphics' to Depends field.

Version 0.1-4

	* Completely rewrote plot.predcoca() and plot.symcoca()
	from the ground up. These methods are far more
	flexible and modular than before and most options are
	user-configurable. Methods default to a 1x2 display
	showing both biplots, setting 'oneFig = FALSE' overides
	this behaviour and each biplot is plotted in turn on
	the active device. New argument 'ask' controls whether
	the user is prompted to display the next plot or not
	like plot.lm() does. 'ask' tries to work out whether
	prompting is required (it is not if the user has already
	set up a 1x2 or greater plotting region). This feature is
	based on code in plot.lm().

	Still need to work out the most intuitive way of
	handlings set of graphical parameters for the
	predictor and response for total customisation.

	* Minor documentation fix

Version 0.1-3

	* scores.symcoca() incorrectly returned the wrong site
	scores for matrix X. Reported by S. Juggins.

	* corAxis.symcoca() incorrectly called scores with
	argument ''extract'' instead of ''display''. Reported
	by S. Juggins.

	* Added flush.console() calls to crossval() and
	permutest.coca() to make sure the progress is
	printed to the console in Mac OSx and Windows. Suggested
	by S. Juggins.

	* Added argument n.axes to permutest.coca to control the
	number of axes tested. Defaults to x$n.axes to maintain
	backwards compatibility. Suggested by S. Juggins.

	* Minor typos in documentation fixed, and removed
	\dQuote{} from within \code{} chunks as it was not being
	processed as I expected.

Version 0.1-2

	* First Public Release

