2011-08-31  kingaa

	* [r74] DESCRIPTION, NAMESPACE, R/deprecated.R, R/hansen.R,
	  man/ouch-deprecated.Rd, tests/exacttree.R,
	  tests/exacttree.Rout.save: - remove deprecated functions and
	  options, at long last

2011-07-25  kingaa

	* [r73] inst/ChangeLog: - update changelog
	* [r72] DESCRIPTION, inst/ChangeLog, inst/NEWS, man/hansen.Rd: -
	  fix typo in documentation of 'hansen': sqrt.alpha and sigma
	  should have 'nchar*(nchar+1)/2' entries. Thanks to Roland Sookias
	  for bringing this typo to my attention.
	  - put NEWS file into standard format

2010-07-11  kingaa

	* [r69] DESCRIPTION, R/hansen.R, inst/ChangeLog: - an infelicity in
	  the 'simulate' method for 'hansentree' objects was discovered by
	  Philip Bergmann. There was an unwanted (inexplicable) dependence
	  on the data in that the optima were recomputed from the data for
	  each simulation rather than simply being taken from the 'theta'
	  slot. This has been remedied: now the fitted optima are used in
	  the simulations. Thanks to Philip for bringing this to light.

2010-06-23  kingaa

	* [r67] inst/ChangeLog: - update the changelog for version 2.6-2

2010-06-18  kingaa

	* [r66] R/aaa.R: - removed aaa.R: no longer needed
	* [r65] DESCRIPTION, R/brown.R, R/hansen.R, R/ouchtree.R,
	  man/hansen.Rd: - minor cleanup of hansen example
	  - use the Collate field in the DESCRIPTION file
	  - get rid of 'R/aaa.R'
	* [r64] DESCRIPTION, man/hansen.Rd: - add multivariate example to
	  'hansen.Rd'

2010-01-21  kingaa

	* [r60] inst/ChangeLog: - version 2.6-1

2010-01-19  kingaa

	* [r59] man/hansen.Rd: - improve the documentation

2010-01-14  kingaa

	* [r58] R/hansen.R: - pass 'clist' to the optimizers to avoid
	  breaking them
	* [r57] DESCRIPTION, R/aaa.R, R/hansen.R, R/methods.R, inst/NEWS,
	  man/anolis.ssd.Rd, man/bimac.Rd, man/hansen.Rd,
	  man/hansentree-methods.Rd, man/paint.Rd, tests/boot.R,
	  tests/boot.Rout.save, tests/exacttree.R,
	  tests/exacttree.Rout.save, tests/simtree.R,
	  tests/simtree.Rout.save: - In the 'hansen' function, the use of
	  the argument 'alpha' was confusing.
	  This vector parameterizes the "selection" portion of the OU
	  model, which since version 2 has been assumed to be a
	  positive-definite matrix (corresponding to stabilizing
	  selection).
	  In particular, it contains the entries of the lower-triangular
	  matrix square root of this positive definite matrix.
	  To make the name more mnemonic, this argument has been renamed
	  'sqrt.alpha'.
	  This is a superficial change meant to improve intelligibility:
	  the algorithm itself has not changed.
	  To prevent loss of backward compatibility, use of argument
	  'alpha' will continue to work, though it will generate a warning.
	  In some future release, use of 'alpha' as an argument to 'hansen'
	  will no longer generate a warning but will instead be passed
	  through to the control list for 'optim' if method='optim' and
	  will otherwise generate an error.

2009-10-07  kingaa

	* [r56] inst/ChangeLog:
	* [r55] man/hansen.Rd, man/hansentree-methods.Rd: - cosmetology

2009-08-11  kingaa

	* [r45] inst/ChangeLog: version 2.5-7
	* [r44] DESCRIPTION, R/ouchtree.R: now, we use a non-recursive
	  algorithm for constructing the lineages.
	  not sure if this is superior: it does appear to be slightly
	  faster on the examples.
	  also, we now have some additional error checking for
	  self-ancestral nodes.
	* [r43] man/hansen.Rd: minor fix

2009-07-19  kingaa

	* [r42] inst/ChangeLog: version 2.5-6
	* [r41] man/hansentree-methods.Rd: fix codoc mismatch in argument
	  list for plot-hansentree

2009-07-13  kingaa

	* [r40] DESCRIPTION: fixed CITATION typo
	* [r39] inst/CITATION: whoops.

2009-06-26  kingaa

	* [r38] DESCRIPTION: version 0.25-5
	* [r37] man/hansen.Rd, man/hansentree-methods.Rd,
	  man/ouch-package.Rd: minor improvements to documentation

2009-03-29  kingaa

	* [r36] R/hansen.R: pass the hessian option to subplex

2009-03-11  kingaa

	* [r35] DESCRIPTION:
	* [r34] inst/ChangeLog:
	* [r33] man/hansen.Rd, man/hansentree-methods.Rd: fix bug in
	  documentation of alpha, sigma arguments
	  
	  give Details section explaining how the alpha and sigma matrices
	  are parameterized
	* [r32] inst/CITATION: use pomp.r-forge.r-project.org as the URL
	  for the project

2009-01-29  kingaa

	* [r31] inst/ChangeLog:
	* [r30] DESCRIPTION:
	* [r29] man/hansentree-methods.Rd: all arguments are now
	  (nominally) documented.

2009-01-28  kingaa

	* [r28] man/hansentree-methods.Rd:

2009-01-27  kingaa

	* [r27] DESCRIPTION:
	* [r26] man/hansentree-methods.Rd:
	* [r25] man/hansentree-methods.Rd:

2009-01-25  kingaa

	* [r23] DESCRIPTION: minor documentation fixes
	* [r22] man/bimac.Rd, man/browntree-class.Rd,
	  man/ouchtree-class.Rd:

2008-12-16  kingaa

	* [r21] DESCRIPTION, inst/ChangeLog:

2008-12-09  kingaa

	* [r20] inst/ChangeLog:
	* [r19] DESCRIPTION, R/hansen.R: When the Choleski decomposition
	  fails (typically when the vcov matrix has a numerically zero
	  eigenvalue), formerly an error was generated. Under these
	  circumstances, the stationary distribution of the OU process does
	  not exist and the likelihood is therefore zero. This fix traps
	  the error and returns -Inf for the log-likelihood (actually +Inf
	  for the deviance in the return from ou.lik.fn). Optimizers that
	  are robust to Inf can therefore proceed.

2008-12-08  kingaa

	* [r18] inst/CITATION: use r-forge URL

2008-09-11  kingaa

	* [r17] inst/ChangeLog:
	* [r16] DESCRIPTION: fix glitch that occurs when 'data' is not in
	  the same order as the nodes
	  patch contributed by Jim Regetz and Jonathan Davies
	* [r15] R/brown.R, R/hansen.R, tests/exacttree.R,
	  tests/exacttree.Rout.save: fix glitch that occurs when 'data' is
	  not in the same order as the nodes
	  patch contributed by Jim Regetz and Jonathan Davies
	* [r14] R/glssoln.R: cosmetic

2008-07-29  kingaa

	* [r13] inst/NEWS:

2008-07-28  kingaa

	* [r12] inst/ChangeLog:
	* [r11] DESCRIPTION:
	* [r10] tests/snizard.R, tests/snizard.Rout.save,
	  tests/snizard_tree.ape, tests/squamates.csv:

2008-07-25  kingaa

	* [r9] R/paint.R, man/paint.Rd: fix bug in paint when 'tree' is a
	  'hansentree'
	* [r8] DESCRIPTION:
	* [r7] R/aaa.R, R/ape2ouch.R, R/brown.R, R/hansen.R, R/methods.R,
	  R/ouchtree.R, R/paint.R, R/plot.R, R/rmvnorm.R: improve error
	  messages

2008-07-23  kingaa

	* [r6] DESCRIPTION:

2008-07-22  kingaa

	* [r5] inst/ChangeLog:
	* [r4] inst/COPYING, inst/ChangeLog, inst/LICENSE, inst/OCHANGELOG:
	* [r3] R/plot.R, man/ouchtree-class.Rd: fix bug with plot options
	  add 'legend' option to plot-ouchtree
	* [r2] DESCRIPTION, NAMESPACE, R/aaa.R, R/ape2ouch.R, R/brown.R,
	  R/deprecated.R, R/glssoln.R, R/hansen.R, R/methods.R,
	  R/ouchtree.R, R/paint.R, R/plot.R, R/rmvnorm.R, data,
	  data/anolis.ssd.csv, data/bimac.csv, inst, inst/CITATION,
	  inst/COPYING, inst/ChangeLog, inst/GPL, man/anolis.ssd.Rd,
	  man/ape2ouch.Rd, man/bimac.Rd, man/brown.Rd,
	  man/browntree-class.Rd, man/hansen.Rd, man/hansentree-class.Rd,
	  man/hansentree-methods.Rd, man/ouch-deprecated.Rd,
	  man/ouch-package.Rd, man/ouchtree-class.Rd, man/paint.Rd, src,
	  src/covar-matrix.c, src/ouch.h, src/weight-matrix.c, tests,
	  tests/boot.R, tests/boot.Rout.save, tests/exacttree.R,
	  tests/exacttree.Rout.save, tests/simtree.R,
	  tests/simtree.Rout.save, tests/snizard.R,
	  tests/snizard.Rout.save, tests/snizard_tree.ape,
	  tests/squamates.csv: initial transfer to rforge

2007-06-25  stefan7th

	* [r1] ., R, man: Email in Readme changed

