2009-08-11  kingaa

	* [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