#### /in.progress/auteur/ChangeLog

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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