Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc. See Dang and Golding
Included automatically built rate matrices. Speeds up model specification as the rate matrix no longer needs to be typed in as long as it is one of the supported matrix types.
Both matrices and dataframes are now accepted for the discrete character data argument.
Finer control of optimization problem boundaries. Expected to be useful when branch lengths are in units other than expected substitutions per site.
Argument matching for some arguments.
A minimum version of 1.0.0 is now required for the stringr dependency.
More tests for arguments in model specification.
More unit tests.
External data example in vignette.
Help file maintainance.
NAMESPACE and DESCRIPTION maintainance.