simphycoevaltools and associated code and tests. These tools implement fully phylogenetic models of shared or multifurcating divergences under a generalized tree distribution.
Documenting the Pitman-Yor and Uniform distributions over divergence models for
nex2ymltool to take both
Fixing bug related to NAN likelihoods. Under extreme combinations of parameters, NAN likelihoods were being logged, and no error or warning occurred. This release fixes that issue. Any analyses prior to this release that did not report NAN likelihoods were not affected by this bug.
Fixing bug in simcoevolity that prevented the ‘–charsets’ and ‘–max-one-variable-site-per-locus’ options from being used together. There was a sanity check from before the ‘–charsets’ option existed that needed to be skipped when the ‘–charsets’ option was used.
Adding new simulation option to simcoevolity. This new option allows simulating multi-locus datasets (each locus comprised of multiple linked sites) that matches the locus lengths and missing data patterns of the empirical dataset. The information to simulate such datasets is provided in a nexus ‘sets’ block that delineates the locus boundaries with ‘charsets’.
Adding default constructor for MatrixExponentiator to appease Clang. This change does not affect behavior; it simply allows older versions of Clang to compile the code.
Adding more documentation.
Allowing the MCMC operator ‘TimeRootSizeMixer’ to be specified as a ‘global’ operator (rather than only tree-specific), and making this the default behavior. The default behavior before this release was for each tree (population pair) to have it’s own ‘TimeRootSizeMixer’ operator. Having ‘TimeRootSizeMixer’ as a global operator should improve mixing when pairs share divergence times.