Package: corHMM 2.10.5

Section 1: Default use of corHMM | 1.1: No hidden rate categories | 1.2: A trait with any number of states and any number of hidden rate categories | 1.3: Estimating "tip fog" | Section 2: How to make and interpret custom models | 2.1: Creating and using custom rate matrices | 2.1.1: One rate category | 2.1.2: Any number of rate categories | 2.2: Biological examples | 2.2.1: Ordered habitat change | 2.2.2: The precursor model | 2.2.3: Ontological relationship of multiple characters | Section 3: Estimating models when node states are fixed | 3.1: Fixing a single node | 3.2: Estimating rates under a parsimony reconstruction | 3.3: Fixing nodes when the model contains hidden states | References