building geiger from ljh - version 1.3-1 - date 2009-9-02
beginning bitbucket repo of geiger
oops
building initial geiger
add fitDiscrete draft
updating fitContinuous [opt.bm()] to work on cache rather than phy objects
moving likelihood computation of fitContinuous to diversitree
updating in_progress/fitDiscrete
updating in_progress/fitDiscrete.R to allow fit of constrained models
moving new implementation of fitContinuous to package
adding Hessian-based CI support for fitDiscrete [currently called fd()] and fitContinuous
freezing diversitree code into R/diversitree.R for stability and ease of installation
merging geiger_1.3-1.666 with auteur_0.666.0615
adding gbresolve.phylo()
fixing fitContinuous and fitDiscrete to integrate with diversitree:::mcmc slice sampling
adding G Slater implementation of fitContinuousMCMC
allowing rjmcmc.bm() to estimate SE
fixed fitContinuous() with SE estimation -- bug introduced by indexing of swappable SE indicator variable -- had been 0 is now negative value
adding amphibia.rda and _ncbi.rda as well as enhancing gbresolve
primarily updating nodelabel.phylo() to allow for resolution of nearest names -- nodes that are close but not strictly consistent with a given taxonomic table