Simulating a practice data set under MiSSE | Setting up a MiSSE model | Using HiSSE and MuHiSSE | Stratigraphic ranges | Plotting simulated data sets | Checking the MiSSE, HiSSE, and MuHiSSE likelihoods | References

Timeline | Rendered equation error in original Beaulieu et al. (2012) | Variance-covariance matrix calculation error in OUwie | Details of the issue | General equations | Expectation of the trait value for species i | Covariance between species i and j | A simple example | FAQ

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

Getting started | Simulating a range-independent process | Setting up the models | Computing Akaike Weights. | Model averaging and plotting. | References

Introduction | HiSSE vs. FiSSE | Reanalysis of Rabosky and Goldberg (2017) with CID-4 in the set | Suggestions | References

Bug fixes and deprecated functions | New Features | Idenfiability tests | Contour plots | Ancestral trait reconstruction | Generalized three-point structured algorithm | Estimating tip fog | References

References

Introduction | Preface | Motivation | The Actual Guide | The dataset | Basic usage | Basic usage - model comparison | Advanced usage | Creating a custom model set | Troubleshooting | FAQs | Why does joint modeling matter? | Why doesn't discrete plus continuous likelihood equal total likelihood (lnLDisc + lnLCont = lnLTot)? | How long is my run going to take? | Why is hOUwie so slow?

Background | Setting up a MiSSE model | Fixing extinction fraction | Other considerations | MiSSE Greedy | References

Getting started | Simulating a practice data set | Setting up a BiSSE model using HiSSE | Setting up a HiSSE model | Setting up a character-independent HiSSE model (i.e., CID-2, CID-4) | Some considerations regarding optimization | References

Background | Simulating a practice data set | Setting up a MuSSE model using MuHiSSE | Setting up a character-dependent MuHiSSE model | Setting up a character-independent MuHiSSE model | Relationship of MuHiSSE to a three-state GeoSSE without cladogenetic changes | Other considerations | References

Getting started | Setting up the transition rate matrix | A common mistake | Changing the output | Setting up the 2-state character-independent (CID-2) model | References