diversitree: Changes and releases

• 7 May 2012 [0.9-3] Mostly a bug fix release, but includes features:
  • A much faster BM/OU likelihood calculator method="pruning", backend="C", and optimisations for the method="vcv" BM calculator (also note that the "direct" backend is renamed "pruning").
  • GeoSSE tree simuator now included (tree.geosse and via trees))
  • sim.character now faster.
  • BiSSE, MuSSE/multitrait and Mkn/multitrait allow logical trait values, in addition to binary (0=FALSE, 1=TRUE).
  • trait.plot automatically collapses non-monophyletic groups.
  Notable bug fixes:
  • make.musse.multitrait() renamed traits when called with single trait.
  • make.prior.uniform used wrong value for out-of-bounds parameters.
  • BM and OU were mislabelled in sim.character.
• 25 March 2012 [0.9-2] New models and extensions to models:
  • geiger-style vcv based calculations for make.ou, via method="vcv".
  Bug fixes, etc:
  • sim.character was broken in 0.9-1
  • Improved profiles.plot (automatic legends, better colour control).
  • Improved likelihood function printing.
  • This version also has had an enormous behind-the-scenes rewrite (again). Despite the small list of changes, thousands of lines of code have changed, and bugs may still remain.
• 13 March 2012 [0.9-1] New models and extensions to models:
  • Includes BiSSE-ness (by Karen Magnuson-Ford and Sally Otto) and ClaSSE (by Emma Goldberg), extending BiSSE and MuSSE models to non-anagenetic evolution.
  • make.geosse.split (again, contributed by Emma Goldberg) for incorporating topological rate varaition in GeoSSE models.
  • Added make.mkn.multitrait for modelling multiple binary traits (analagous to make.musse.multitrait).
  • Alternate method of calculation for Mk models (make.mkn) with very large numbers of possible states. Select with control=list(method="ode").
  • Non-VCV based Brownian motion likelihood calculations (via the argument control=list(method="direct") to make.bm). This can be substantially faster for very large trees (> 1000 tips).
  • New version of the mkn model that will be substantially faster for many traits (> 30 traits). This mainly affects mkn.multitrait.
  • Ornstein-Uhlenbeck model (for completeness, as this is present in many, many different packages on CRAN already).
  • Function sim.character for simulating traits given a tree.
  • Ancestral state reconstruction under split BiSSE and MuSSE models.
  Notable new features and bug fixes:
  • Updated to work with deSolve 1.10-3
  • mcmc can now return partial results during a long run.
  • make.prior.uniform for specifying uniform priors.
  • make.bd.t did not allow incomplete sampling (reported by Dan Rabosky).
  • Improved the way contrain deals with constraining parameters that are targets of constraints. Also, additional arguments were not being passed to the functions generated by constrain.
  • "Split" functions now allow caching branches (via control=list(caching.branches=TRUE)). This can result in large speedups, particularly for make.quasse.split.
  • Improved consistency of calculation method switching across different likelihood functions (especially bd and bm models).
  • Simulate trees under the musse.multitrait model.
  • The anova function will now refuse to run a likelihood ratio test for non-nested models (it may be overzealous in some cases).
  • Function trait.plot to plot the distribution of multiple traits on a radial phylogeny.
• 18 July 2011 [0.7-7]
  • Works with deSolve 1.10-2.
• 11 July 2011 [0.7-6]
  • New parametrisation of MuSSE available where the multi-state trait is really combinations of binary states. This allows expressing speciation and extinction rates as main effects and interations of the underlying binary traits, and easily restricting trait evolution to a single trait at a time.
  • Some internal streamlining that should speed up most models slightly
  • Faster stochastic character mapping
  • Various bugs fixed (mcmc not passing additional arguments properly, make.bd.split not using unresolved clade information).
• 12 May 2011 [0.7-2]
  • Fixed bug that prevented use on Windows
• 11 May 2011 [0.7-1]
  • New Sundials based solver CVODE available (switch with control=list(backend="CVODES")). In some cases this is 8x faster than the previous version.
  • Bug fixes. In particular, the equilibrium root state treatment (ROOT.EQUI) was incorrect.
  • Works with deSolve 1.10.
• 20 April 2011 [0.6-5] Bug fixes mostly:
  • Better integration control for all ODE-based solvers.
  • Slightly altered root state treatment (exact calculations will change with condition.surv=TRUE)
  • Very basic mixed integer nonlinear optimisation approach for finding ML point for some QuaSSE models that involve a character space variable (poorly documented at present).
  • Assorted minor bug fixes.
• 26 January 2011 [0.6-3]. Bug fixes and some new features/models:
  • Includes Emma Goldberg's GeoSSE model
  • New numerical method-of-lines integrator for QuaSSE, which may be more robust in some situations.
  • Marginal ancestral state reconstructions for MuSSE models.
  • Better support for MuSSE/mkn models with >9 states
  • Works with deSolve 1.9
  • Builds on CRAN for windows!
• 21 October 2010 [0.6-1]. A number of new models.
  • "QuaSSE" (Quantitative Trait Speciation and Extinction): new method is now released. This tests for correlation between a continuous/quantitative character and rates of speciation and/or extinction. Includes support for "split" QuaSSE analyses.
  • Improved support for time dependent models: now, speciation, extinction, and (for BiSSE only) character change rates may be arbitrary functions of time. This is implemented for birth-death models, BiSSE, and MuSSE.
• 23 September 2010 [0.5-3]. A couple of model extensions, documentation improvements, and bug fixes.
  • Now works with deSolve 1.8
  • Time-dependent and "split" MuSSE models are now included. The interface for both is similar to their BiSSE analogues.
  • A new tutorial document.
• 12 August 2010 [0.5-2]. A number of new models and bug fixes.
  • "MuSSE" (Multi-State Speciation and Extinction): the multiple-character extension to BiSSE is now implemented. This allows modelling characters with more than two states, or combinations of characters (similar to the Pagel 1994 method for rates of character evolution). Likelihood calculations and tree simulation are supported.
  • Simple support for Brownian Motion models of continuous trait evolution (single trait only).
  • "Split BiSSE" model: this combines aspects of the MEDUSA model (Alfaro et al. 2009) with the BiSSE model to allow different parts of the tree to have different rates of speciation, extinction, and/or character evolution. For completeness a "Split BD" model is also implemented. None of these assist in searching for positions in the tree where rates shift.
  • "Time-dependent" BiSSE, where different chunks of time have different rates of speciation, extinction, and/or character evolution.
  The new models' documentation is still very preliminary and these are not yet in the tutorial document.
  Other new features:
  • Interrupting a mcmc run will return a truncated set of samples.
  • Constrained functions can be constrained (though this is still limited)
  • subplex is now the default ML search algorithm for BiSSE and MuSSE models.
• 2 March 2010 [0.4-5]. Some important bug fixes (BiSSE likelihood calculations were very slightly incorrect at root and unresolved clade calculations were incorrect when no species within a clade had a known state). Other changes:
  • Added support for sampling and unresolved clades in constant rate birth-death models.
  • Fixes to the Mk2 ancestral state reconstructions
  • Works with deSolve version 1.7
  • Assorted small bug fixes and documentation improvements
• 2 Febrary 2010 [0.4-4]. New features include:
  • Ancestral state reconstruction and stochastic character mapping under Mk2 (?asr.mk2) (slow, but will get faster in future versions)
  • Much faster Mk2 likelihood calculation (speed increase of 20-50x)
  • Ancestral state reconstruction under BiSSE (?asr.marginal.bisse)
  The ancestral state reconstruction code should be regarded as experimental.
• 19 January 2010 [0.4-3]. Mostly a few bug fixes.
• 11 January 2010 [0.4-2]. New features include:
  • Remembering and plotting character histories on simulated trees (see ?tree.bisse
  • Works with deSolve 1.6
  • Support for simulating Yule trees and estimating Yule model parameters
  • Bug fixes and improvements to the MLE code
• 02 December 2009 [0.4-1]. New features include
  • Constant rate birth death model (make.bd) and Mk2/Mk-n (make.mk2, make.mkn) models implemented
  • Now works with the current deSolve package
  • Node states now retained during tree simulation (see ?trees for an example)
  • Simple MCMC plots with profiles.plot
  • Several bugs fixes, documentation improvements, additional examples, and minor features
• 16 October 2009 [0.3-2]:: Minor bugfix
• 15 October 2009 [0.3-1]:
  • New formula-based constraint interface (through function constrain())
  • Subplex available to do ML searches
  • Simple hypothesis testing convenience functions added (anova(), logLik()).
• 5 May 2009 [0.2-1]: Initial public release