2008-07-08 11:08  kingaa

	* ouch/tests/: boot.R, boot.Rout.save: use 'bootstrap' method

2008-07-08 10:58  kingaa

	* ouch/: NAMESPACE, R/aaa.R, R/brown.R, man/browntree-class.Rd,
	  man/hansentree-methods.Rd, R/hansen.R: add 'bootstrap' method for confidence intervals by parametric bootstrap

2008-06-25 13:05  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: improved documentation

2008-06-25 12:46  kingaa

	* ouch/R/: brown.R, hansen.R: fix rownames for simulate output

2008-06-25 12:46  kingaa

	* ouch/tests/simtree.Rout.save: faster

2008-06-25 12:45  kingaa

	* ouch/tests/: boot.R, boot.Rout.save: bootstrap tests

2008-06-24 14:27  kingaa

	* ouch/: R/hansen.R, man/hansen.Rd: bug fix

2008-06-24 13:15  kingaa

	* ouch/R/hansen.R: bug fix

2008-06-24 13:15  kingaa

	* ouch/tests/: exacttree.R, exacttree.Rout.save: add a 3-character test

2008-06-24 10:42  kingaa

	* ouch/: src/covar-matrix.c, src/ouch.h, src/weight-matrix.c,
	  NAMESPACE, R/hansen.R, DESCRIPTION: .Call interface for weight and covariance matrices

2008-06-24 10:40  kingaa

	* ouch/tests/: bigtree.R, bigtree.Rout.save, exacttree.R,
	  exacttree.Rout.save, simtree.R, simtree.Rout.save, smalltree.R,
	  smalltree.Rout.save: change names (and order) of tests

2008-06-24 08:39  kingaa

	* ouch/: R/paint.R, man/paint.Rd: fix paint

2008-06-24 08:06  kingaa

	* ouch/src/covar-matrix.c: put covariance matrix calculation into C

2008-06-24 08:03  kingaa

	* ouch/: NAMESPACE, src/covar-matrix.c: put covariance matrix calculation into C

2008-06-24 07:54  kingaa

	* ouch/R/hansen.R: put covariance matrix calculation into C

2008-06-24 00:10  kingaa

	* ouch/: R/brown.R, R/hansen.R, man/browntree-class.Rd,
	  man/hansentree-methods.Rd, tests/bigtree.R,
	  tests/bigtree.Rout.save, tests/smalltree.R,
	  tests/smalltree.Rout.save, DESCRIPTION: change update method to make it more useful

2008-06-23 11:30  kingaa

	* ouch/tests/: bigtree.R, bigtree.Rout.save, snizard.R,
	  snizard.Rout.save: add some timing functions

2008-06-23 11:29  kingaa

	* ouch/R/ouchtree.R: improve the recursive lineage building

2008-06-23 11:29  kingaa

	* ouch/R/deprecated.R: pedigree -> pedigree.deprec

2008-06-15 12:28  kingaa

	* ouch/R/ouchtree.R: revert to using 'pedigree' in build.lineages

2008-06-15 12:27  kingaa

	* ouch/R/ape2ouch.R: minor change

2008-06-12 16:24  kingaa

	* ouch/DESCRIPTION: bug fix!

2008-06-12 16:11  kingaa

	* ouch/tests/bigtree.R: test using big artificial tree

2008-06-12 16:06  kingaa

	* ouch/R/hansen.R: remove old code

2008-06-12 14:29  kingaa

	* ouch/R/hansen.R: get rid of 'utimes'

	fix bug in weight matrix

2008-06-12 14:28  kingaa

	* ouch/R/: aaa.R, brown.R, ouchtree.R: get rid of utimes

2008-06-12 14:27  kingaa

	* ouch/tests/: smalltree.R, smalltree.Rout.save: exact test

2008-06-11 11:38  kingaa

	* ouch/R/: brown.R, hansen.R: better error message for missing data

2008-06-11 11:33  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: oops

2008-06-11 11:24  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: minor change

2008-06-11 11:20  kingaa

	* ouch/R/hansen.R: replace 'pedigree' with a new slot, 'lineages', constructed by a more efficient algorithm

	remove 'mvou.quants': no longer needed

2008-06-11 11:20  kingaa

	* ouch/R/: aaa.R, ouchtree.R: replace 'pedigree' with a new slot, 'lineages', constructed by a more efficient algorithm

	pedigree is now only used in the deprecated functions

2008-06-11 11:17  kingaa

	* ouch/R/deprecated.R: pedigree is now only used in the deprecated functions

2008-06-11 10:06  kingaa

	* ouch/: R/hansen.R, DESCRIPTION: use different algorithm for computing weight and covariance matrices:
	compute eigendecomposition once in 'ou.lik.fn'
	then compute matrices in such a way that only -lambda t for lambda, t > 0 gets exponentiated

	when given a hansentree object and regimes are not specified, re-use regimes

	use 'is' not 'inherits' for S4

2008-06-11 10:02  kingaa

	* ouch/R/brown.R: use 'is' not 'inherits' for S4 objects

2008-06-11 10:02  kingaa

	* ouch/tests/: bimactest.R, outest.R: test scripts

2008-06-11 10:01  kingaa

	* ouch/tests/outest.R: test script

2008-05-30 09:52  kingaa

	* ouch/R/hansen.R: streamlining

2008-05-30 09:48  kingaa

	* ouch/man/: hansentree-class.Rd, hansentree-methods.Rd: change organization of methods documentation

2008-05-29 12:18  kingaa

	* ouch/R/: aaa.R, methods.R: get rid of alpha.fn and sigma.fn slots altogether
	replace by sym.par and sym.unpar functions

2008-05-29 12:17  kingaa

	* ouch/: NAMESPACE, R/hansen.R, R/mvouode.R, src/mvouode.c: no longer need mvouode

2008-05-29 10:24  kingaa

	* ouch/R/hansen.R: take canonical branch of parameterization at the outset

2008-05-28 17:34  kingaa

	* ouch/man/: browntree-class.Rd, hansentree-class.Rd: get rid of special methods for deviance, sic, aic, aic.c: replace with one "summary" method

2008-05-28 17:14  kingaa

	* ouch/: ChangeLog, inst/ChangeLog: move ChangeLog

2008-05-28 17:12  kingaa

	* ouch/DESCRIPTION: bug fixes
	new summary method

2008-05-28 17:12  kingaa

	* ouch/R/methods.R: fix print method

2008-05-28 16:54  kingaa

	* ouch/: NAMESPACE, R/aaa.R, R/methods.R, man/generics.Rd: get rid of special methods for deviance, sic, aic, aic.c: replace with one "summary" method

2008-05-28 16:42  kingaa

	* ouch/man/hansen.Rd: fix broken link

2008-05-28 16:39  kingaa

	* ouch/: man/browntree-class.Rd, man/hansentree-class.Rd,
	  R/methods.R: add summary methods

2008-05-27 22:06  kingaa

	* ouch/man/: browntree-class.Rd, hansentree-class.Rd: change print method
	display sigma^2

2008-05-27 22:06  kingaa

	* ouch/R/methods.R: change print method
	display sigma^2 and aic.c

2008-05-27 21:24  kingaa

	* ouch/DESCRIPTION: bugfix

2008-05-27 21:22  kingaa

	* ouch/R/hansen.R: return beta to its previous shape
	make sure root regime is included

2008-05-27 21:09  kingaa

	* ouch/: R/aaa.R, R/methods.R, man/browntree-class.Rd,
	  man/generics.Rd, man/hansentree-class.Rd: add aic.c method (God help us)

2008-05-27 10:50  kingaa

	* ouch/: R/hansen.R, DESCRIPTION: complete reworking of calculations
	now from root to tips instead of tips to roots
	no assumption is made about ultrametricity

2008-05-27 10:47  kingaa

	* ouch/man/hansentree-class.Rd: corrections

2008-05-27 10:45  kingaa

	* ouch/: R/mvouode.R, src/mvouode.c: change the quantities computed.

	since the old Z = Id - Y, it isn't necessary to compute it.
	however, we do need Y^(-1).  Now we compute this.

2008-05-27 09:23  kingaa

	* ouch/R/: brown.R, ouchtree.R, aaa.R: add vector of unique times (utimes) to ouchtree object
	reformulate branch.times and epochs times as indices in utimes

2008-05-26 12:51  kingaa

	* ouch/R/: hansen.R, ouchtree.R: minor changes

2008-05-23 12:06  kingaa

	* ouch/R/print.R: move print codes to methods.R

2008-05-23 12:06  kingaa

	* ouch/R/methods.R: fix bug in coef

2008-05-23 11:05  kingaa

	* ouch/: R/hansen.R, DESCRIPTION: enforce assumption that alpha is symmetric and positive definite by setting alpha <- alpha%*%t(alpha)

	remove alpha.fn and sigma.fn arguments

	assume that root state is a random variable drawn from the stationary distribution of the process in the regime that the root node occupies

	the latter involves changes to the weight matrix, to the covariance matrix, and to the regime.spec routine

2008-05-23 11:03  kingaa

	* ouch/man/hansen.Rd: remove alpha.fn and sigma.fn arguments

2008-05-23 11:03  kingaa

	* ouch/R/print.R: enforce assumption that alpha is symmetric and positive definite by setting alpha <- alpha%*%t(alpha)

2008-05-23 11:02  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: minor changes

2008-05-23 09:34  kingaa

	* ouch/R/glssoln.R: clean up error handling

2008-02-04 10:36  kingaa

	* ouch/: man/generics.Rd, DESCRIPTION: bug fix

2008-02-04 10:36  kingaa

	* ouch/R/hansen.R: bug fix: det -> determinant

2008-01-15 17:27  kingaa

	* ouch/man/hansen.Rd: fix documentation inaccuracy

2007-10-24 14:01  kingaa

	* ouch/DESCRIPTION: bug fix

2007-10-24 14:01  kingaa

	* ouch/R/: hansen.R, print.R: must accommodate the lack of information in optim.diagn (in hansentree object) when hansen is called with fit=FALSE

2007-10-24 14:00  kingaa

	* ouch/man/bimac.Rd: don't run the subplex example at check time

2007-09-25 08:33  kingaa

	* ouch/: DESCRIPTION, R/hansen.R: bug fix

2007-09-13 13:43  kingaa

	* ouch/: DESCRIPTION, R/hansen.R: by default, both alpha and sigma are full matrices

2007-09-11 11:41  kingaa

	* ouch/: DESCRIPTION, R/hansen.R, man/bimac.Rd, man/hansen.Rd: include support for 'subplex' optimizer

2007-08-29 14:35  kingaa

	* ouch/data/: anolis.ssd.csv, anolis.ssd.rda, bimac.csv, bimac.rda: Move the data to human-readable CSV format

2007-07-23 17:32  kingaa

	* ouch/R/zzz.R: not needed

2007-07-11 12:30  kingaa

	* ouch/R/: ape2ouch.R, paint.R: bug fix

2007-07-11 12:06  kingaa

	* ouch/: DESCRIPTION, NAMESPACE, R/paint.R, man/paint.Rd: add a new facility to 'paint' regimes onto trees

2007-07-11 12:06  kingaa

	* ouch/R/plot.R: if the root has a regime all its own (which would be irrelevant anyway, and not plotted), remove it from the palette of colors before plotting

2007-07-11 12:05  kingaa

	* ouch/R/: brown.R, hansen.R: fix bug with naming data & regimes

2007-07-11 11:42  kingaa

	* ouch/: R/ape2ouch.R, man/ape2ouch.Rd: modify 'scale' option so that it can scale by a specified numerical factor

2007-07-11 11:35  kingaa

	* ouch/: R/methods.R, R/plot.R, man/ouchtree-class.Rd: add rownames to data.frame produced by coercion from ouchtree
	add node.names option to ouchtree-plot
	add legend to ouchtree-plot

2007-07-03 08:11  kingaa

	* ouch/: DESCRIPTION, R/aaa.R, R/ape2ouch.R, R/brown.R, R/hansen.R,
	  man/anolis.ssd.Rd, man/ape2ouch.Rd, man/bimac.Rd,
	  man/ouchtree-class.Rd, R/methods.R, R/ouchtree.R, R/plot.R: regimes and data must now have names
	if a data.frame is used, the rownames are taken for this purpose
	the slot 'nodenames' has been changed to 'nodelabels'
	ape2ouch now has an option 'scale'

2007-06-26 21:27  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: the data must now have names

2007-06-26 21:26  kingaa

	* ouch/man/: browntree-class.Rd, hansentree-class.Rd,
	  ouchtree-class.Rd: add method to coerce to a data.frame

2007-06-26 21:26  kingaa

	* ouch/R/: methods.R, plot.R, print.R: add a new method to coerce an ouchtree (or hansentree, or browntree) to a data.frame

2007-06-26 21:25  kingaa

	* ouch/R/: brown.R, hansen.R: the data must now have names corresponding to those of the nodes

2007-06-13 10:21  kingaa

	* ouch/man/ape2ouch.Rd: minor changes

2007-06-12 18:35  kingaa

	* ouch/man/hansen.Rd: corrected, improved

2007-06-12 18:26  kingaa

	* ouch/DESCRIPTION: 2.1-1

2007-06-12 18:23  kingaa

	* ouch/man/generics.Rd: documentation of new generics

2007-06-12 18:21  kingaa

	* ouch/man/: ouchtree-class.Rd, ouchtree.Rd: improved
	ouchtree.Rd now merged with ouchtree-class.Rd

2007-06-12 18:20  kingaa

	* ouch/man/ouch-package.Rd: improved

2007-06-12 18:20  kingaa

	* ouch/man/: ape2ouch.Rd, brown.Rd, browntree-class.Rd, hansen.Rd,
	  hansentree-class.Rd: improved documentation

2007-06-12 18:20  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: correct the references

2007-06-12 18:19  kingaa

	* ouch/R/brown.R: add 'evaluate' option to 'update' method

2007-06-12 18:18  kingaa

	* ouch/R/plot.R: dispense with 'tree.layout'

2007-06-12 18:18  kingaa

	* ouch/R/print.R: 'optim' messages are now printed as part of the default print method for 'hansentree' objects

2007-06-12 18:18  kingaa

	* ouch/R/methods.R: generics are now defined in aaa.R

2007-06-12 18:17  kingaa

	* ouch/R/hansen.R: better handling of 'optim' messages

	implement standard functions for alpha.fn and sigma.fn (3 functions are now implemented but are not yet incorporated into 'hansen'.  Some questions remain as to how to do this properly

	improved 'update' method: 'evaluate' option

2007-06-12 18:15  kingaa

	* ouch/R/deprecated.R: dispense with 'tree.layout'

2007-06-12 18:14  kingaa

	* ouch/R/zzz.R: cosmetic

2007-06-12 18:14  kingaa

	* ouch/R/aaa.R: all generics are now defined here

2007-06-12 15:07  kingaa

	* ouch/man/ouchtree-class.Rd: improved documentation

2007-06-12 08:20  kingaa

	* ouch/data/: anolis.ssd.rda, bimac.rda: remove and add in binary format

2007-06-12 06:59  kingaa

	* ouch/R/: brown.R, hansen.R: replace argument 'x' with 'data'

2007-06-12 06:58  kingaa

	* ouch/man/: ouch-deprecated.Rd, ouch-package.Rd, brown.Rd,
	  hansen.Rd: Improved documentation.

2007-06-11 22:17  kingaa

	* ouch/man/anolis.ssd.Rd: minor change

2007-06-11 21:18  kingaa

	* ouch/NAMESPACE: added deprecated functions from ouch v. 1.X-X

2007-06-11 21:18  kingaa

	* ouch/DESCRIPTION: new version

2007-06-11 21:17  kingaa

	* ouch/CITATION: original Butler & King paper

2007-06-11 21:16  kingaa

	* ouch/man/: brown.Rd, browntree-class.Rd, hansen.Rd,
	  hansentree-class.Rd, ouch-deprecated.Rd, ouch-package.Rd,
	  ouchtree-class.Rd: changed the file structure
	incorporate the deprecated functions from ouch v. 1.X-X

2007-06-11 21:15  kingaa

	* ouch/R/mvouode.R: rename package 'ouch'

2007-06-11 21:15  kingaa

	* ouch/R/plot.R: tree.plot -> tree.plot.internal

2007-06-11 21:14  kingaa

	* ouch/R/deprecated.R: deprecated functions from ouch v 1.X-X

2007-06-11 21:14  kingaa

	* ouch/R/hansen.R: hansen.dev -> hansen.deviate

2007-06-11 21:13  kingaa

	* ouch/R/brown.R: brown.dev -> brown.deviate

2007-05-22 14:11  kingaa

	* ouch/man/hansen.Rd: documentation for the 'hessian' option in 'hansen'

2007-05-22 14:11  kingaa

	* ouch/DESCRIPTION: another version...

2007-05-22 14:07  kingaa

	* ouch/R/hansen.R: Hessian matrix is not computed by default

2007-05-22 13:32  kingaa

	* ouch/man/: anolis.ssd.Rd, bimac.Rd: better documentation
	not all examples are run

2007-05-22 13:32  kingaa

	* ouch/R/: aaa.R, hansen.R: diagnostic output from optim is now included in the hansentree object
	the hessian is also computed and saved

2007-05-22 11:18  kingaa

	* ouch/data/: anolis.ssd.rda, bimac.rda: Initial revision

2007-05-22 10:50  kingaa

	* ouch/: TODO, GPL: Initial revision

2007-05-19 10:23  kingaa

	* ouch/R/: brown.R, hansen.R: bug fix

2007-05-17 12:14  kingaa

	* ouch/: DESCRIPTION, R/methods.R, R/print.R: bug fix

2007-05-17 12:05  kingaa

	* ouch/: DESCRIPTION, NAMESPACE, R/methods.R: use logLik instead of loglik

2007-05-16 16:31  kingaa

	* ouch/R/methods.R: added coef method

2007-05-16 15:03  kingaa

	* ouch/R/ape2ouch.R: bug fix

2007-05-16 14:40  kingaa

	* ouch/R/glssoln.R: small kind changes

2007-05-16 14:39  kingaa

	* ouch/R/hansen.R: all kinds of great improvements

2007-05-16 14:31  kingaa

	* ouch/R/rmvnorm.R: returns the transpose of what it returned before

2007-05-15 13:33  kingaa

	* ouch/man/ape2ouch.Rd: Initial revision

2007-05-15 13:24  kingaa

	* ouch/R/glssoln.R: improved

2007-05-15 13:23  kingaa

	* ouch/R/brown.R: direct computation

2007-05-15 07:13  kingaa

	* ouch/R/ape2ouch.R: Initial revision

2006-11-21 10:42  kingaa

	* ouch/: R/mvouode.R, src/mvouode.c, R/ouchtree.R, man/ouchtree.Rd,
	  R/plot.R, R/print.R, R/methods.R: Initial revision

2006-07-06 10:07  kingaa

	* ouch/R/: brown.R, hansen.R: check for missing data on terminal nodes

2005-11-29 23:19  kingaa

	* ouch/: R/aaa.R, R/zzz.R, man/anolis.ssd.Rd, man/bimac.Rd,
	  man/brown.Rd, man/hansen.Rd: updated author addresses

2005-05-19 18:11  king

	* ouch/R/: brown.R, hansen.R: use explicit names for the nodes and ancestry
	this will make it easier to rearrange, prune, and merge trees

2005-05-19 18:09  king

	* ouch/man/: anolis.ssd.Rd, bimac.Rd, brown.Rd, hansen.Rd: up to date with ouch 1.1

2005-05-19 07:34  king

	* ouch/R/: brown.R, hansen.R: Initial revision

2004-10-09 15:23  king

	* ouch/R/rmvnorm.R: Initial revision

2004-08-30 21:08  king

	* ouch/: DESCRIPTION, man/anolis.ssd.Rd, man/bimac.Rd,
	  man/brown.Rd, man/hansen.Rd: improved documentation

2004-08-28 13:14  king

	* ouch/R/zzz.R: with printed warning

2004-08-28 13:05  king

	* ouch/R/aaa.R: Initial revision

2004-08-28 12:52  king

	* ouch/R/zzz.R: Am. Nat. version

2004-08-20 08:22  king

	* ouch/R/zzz.R: with warning message

2004-07-26 16:29  king

	* ouch/R/zzz.R: Initial revision

2004-07-26 16:22  king

	* ouch/R/glssoln.R: Initial revision

2004-07-08 12:03  king

	* ouch/man/: anolis.ssd.Rd, bimac.Rd, brown.Rd, hansen.Rd: Initial revision

2004-07-08 11:58  king

	* ouch/: DESCRIPTION, NAMESPACE: Initial revision

