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) | Acounting for tip fog | Some considerations regarding optimization | References

Simulating a practice data set under MiSSE | Setting up a MiSSE model | A cautionary tale about empirical trees and what is considered 'surviving' | Using HiSSE and MuHiSSE | Stratigraphic ranges | Plotting simulated data sets | Checking the MiSSE, HiSSE, and MuHiSSE likelihoods | References

What this vignette is for | 1. Fit a model and get the best joint reconstruction | 2. Sample the joint posterior | 3. A distance between reconstructions | If you want it faster | 4. Consensus clustering | 5. What the axes look like | 6. Where on the tree do they disagree? | 7. Turning axes into numbers | Adapting this to your data | Function reference | Reference

1: Introduction | 2: What's new in AnnotationBustR 2.0+ | 2.1: New Dependencies Provide Up To Date Access, New Features, and Stability | 2.2: Other Minor New Features | 3: Installation | 3.1: Installation From CRAN | 3.2: Installation of Development Version From GitHub | 4: Using AnnotationBustR | 4.1:(Optional Step) Finding the Longest Available | 4.2: Load a Data Frame of Search Terms of Gene Synonyms to Search With: | 4.3:(Optional Step) Merge Search Terms If Neccessary | 4.4 Extract sequences with AnnotationBust | 4.5 Troubleshooting | 5: Final Comments

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

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

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 | References

How much faster is it? | Where the speedup comes from | A steadier optimization problem | Reliability improvements around the likelihood

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?

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

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

Vignette Info | Setup | Import Data | Run All Methods on All 63 Restrictions of GDR using Phylogenetic Linear Models | Output Examples | Results from the first combination of methods | Results of Coefficients using every Method and Restriction | Best Restrictions Explaining Flowering Phenology | Parameter Combinations | Threshold Sets | Best Restriction for Flowering Phenology | Methods Used | Thresholds Applied | Incorporating Additional Dimensions | Additional dimensions of rarity can also be incorporated but must be specified by users | Example: Adding Random Habitat Specificity | Re-run Methods with Habitat Specificity using Linear Models | Best Restrictions with Habitat Specificity | Best Restriction for Flowering Phenology Incorporating Habitat Specificity

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

1: Introduction | 2: Installation | 2.1: Installation From CRAN | 2.2: Installation of Development Version From GitHub | 3: Using dietr | 3.0: Basic Data Necessary to Run dietr for Trophic level Calculations | 3.1: Using dietr to Calculate Trophic Levels From FishBase Diet Data | 3.2: Using dietr to Calculate Trophic Levels from FishBase Food Item Data | 3.3: Using dietr to Calculate Trophic Levels From Your Own Data | 3.4: Using dietr to Calculate Electivity Indices | 3.5: Using dietr to Calculate Composite Diet Indices | 3.5: Using dietr to Calculate the Gastro-somatic Index and Vacuity Index | 4: Final Comments | 5: References

1 Introduction | 2 Installation | 2.1 CRAN | 2.2 Development Version from GitHub | 3 Use | 3.1 Load Data | 3.1.1 Example Files | 3.1.2 Own Files | 3.2 Run Main Analysis | 3.2.1 Taxonomy Based on Tip Labels | 3.2.2 Taxonomy Based on File | 3.2.3 Taxonomy Downloaded from Web | 3.2.4 Other Options | 3.3 Accessing the Results | 3.3.1 First Impression - Summary and Results Tables | 3.3.2 Further Look - Customized Access to Detailed Results | 3.4 Plotting | 3.4.1 Monophyly Plot | 3.4.2 Taxonomy Plot | 3.4.3 Monophyly-Taxonomy Mirror Plot | 3.4.4 Intruder Plot | 3.4.5 Solutions for Large Trees | 4 Final Notes

References

Introduction | Installing NCBI BLAST+ Tools | Pipeline | Setup | Running | Restarting | Changing parameters | Cluster selection | Testing output

I. Installing PHRAPL