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/in.progress/auteur/ChangeLog

http://github.com/eastman/auteur
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 1CHANGES IN AUTEUR VERSION 0.11
 22011-05-11
 3  * moved repository to gitHUB 
 4  * forked auteurExtended (OU, BM, Levy) and auteur (BM only)
 5
 62011-05-04
 7  * updated mcmc.levy to involve appropriate proposal distributions
 8  * changed jumpsize to prop.width in rjmcmc functions to prevent confusion with jumps in mcmc.levy 
 9
102011-04-15
11  * added support for Levy process (jump-Brownian) evolution
12	- mcmc.levy (hidden Markov MCMC algorithm)
13	- updateJvcv (VCV matrix of jumps)
14	- updateLvcv (VCV matrix needed for the multivariate normal model)
15	- adjustjump (table of jumps)
16  * added simulator for the jump-Brownian process
17	- phenogram
18	- levyevolver
19  * added several accessory function from LJ Revell
20	- propose.loc
21	- tree.step
22	- random.node
23	- match.all
24
252011-02-28
26  * updated get.descendants.of.node(), adapting code from GEIGER for optimization
27  * cleaned up compilation warnings for ouweights.cpp and vmat.cpp concerning comparisons between signed and unsigned integers (due to std::vector::size)
28
292011-02-23
30  * added Ornstein-Uhlenbeck as an alternative model of trait evolution
31  * files added are as follows
32	- src: oumat.cpp and ouweights.cpp
33	- R: get.epochs.R, get.times.R, ou.lik.fn.R, oumat.R, ouweights.R, rjmcmc.ou.R, assignroottheta.R, ultrametrize.R, fit.hansen.R
34  * deprecated generate.log() and determine.accepted.proposal()
35  * modified parlogger() to be far more memory efficient and to allow output to be read by Tracer (Drummond 2007)
36  * modified cleanup.files() to deal with new output from parlogger()
37  * modified summarize.run()
38  * modified tracer()
39  * modified pool.rjmcmcsamples()
40  * merged several files by function
41  * revised choose.one() to select edges by branch length
42  * revised calibrate.jumpsize to invoke spline() in jumpsize determination
43
442011-02-08
45  * rewrote vmat() to play with the new API in Rcpp_0.9.0
46  * using STL containers in vmat() rather than those provided by Rcpp
47
482011-01-19
49  * works (only) with Rcpp_0.8.6
50  * updated shifts.plot()
51  * now accommodates measurement error associated with trait values
52
532011-01-18
54  * added a utility for ultrametricizing trees naively (where root to tip lengths are very close but not identical; see ultrametricize())
55  * modified tracer() to allow user-specification of plotting axes in log-likelihood traces
56  * changed package name from rjmcmc.traits to 'auteur' (Accommodating Uncertainty in Trait Evolution Using R)
57
582011-01-16
59  * converted sortedges to a C++ function (see vmat.cpp)
60
612011-01-13
62  * variance-covariance calculation now performed using C++: see vmat.R()
63
642011-01-09 
65  * now storing memory intensive results as (compressed) .rda files
66  * splitormerge(): had treated a global rate as K=1; now assuming that a global rate is not equivalent to a single local rate; now K = 0 for a global-rate model (Drummond and Suchard 2010)
67
682011-01-07  
69  * created package
70