Methods
Quick reference pages for the analytical methods used in lab papers — each with a runnable code snippet and a list of the gotchas we’ve actually hit.
| Method | Language | Package | Difficulty |
|---|---|---|---|
| BiSSE | R | diversitree | advanced |
| chromePlus | R | chromePlus | advanced |
| Mk model | R | ape, corHMM | intermediate |
| Simmap | R | phytools | intermediate |
| UCE phylogenetics | Python | phyluce | advanced |
| Ancestral state reconstruction | R | phangorn, ape, phytools | intermediate |
Filter by difficulty
- Intermediate: Mk model, Ancestral state reconstruction, Simmap
- Advanced: BiSSE, chromePlus, UCE phylogenetics
Related
- All topics
- Papers by method
- PCM guide — interactive tutorial site (older, more polished)