Software

The methods are only useful if people can run them. Each package below is open source and installable from its repository; the vignettes are worked examples of what several of them do.

• corHMM

  Correlated hidden Markov models for comparative biology. Fits generalized hidden-rates models to discrete characters, so several traits — including unobserved ones — can be modelled as one system instead of one trait at a time.

• OUwie

  Continuous character evolution under Ornstein–Uhlenbeck models, including the hOUwie approach for jointly modelling discrete and continuous traits.

• dentist

  Quantifies uncertainty by sampling points around a maximum likelihood estimate, rather than trusting the curvature of the likelihood surface at its peak.

• SegmentR

  Deep-learning image segmentation with an R interface, built for biologists working with specimen and morphology images.

• mvh

  Assembles and organizes virtual herbaria from openly available specimen images.

• phyloAMR

  Phylogenetically-informed analysis of antibiotic resistance, applying comparative methods to how resistance emerges and spreads.

• hiSSE

  Hidden state dependent speciation and extinction models for testing trait-associated diversification.