Vignettes

Worked examples in R. Each one runs through a real analysis end to end, so you can see what the method expects as input and what its output actually means.

• corHMM
  Getting started with corHMM

  Fitting generalized hidden Markov models to discrete characters — the general-purpose starting point.

• corHMM
  Correlated and independent models

  Testing whether two discrete traits evolve together or apart, and why the distinction is easy to get wrong.

• corHMM
  Automatic model selection with corHMM dredge

  Searching the space of discrete character models rather than hand-picking one.

• corHMM
  Uncertainty in joint ancestral state reconstruction

  Generating and reading uncertainty around joint ancestral state reconstructions.

• OUwie
  hOUwie starter guide

  Jointly modelling a discrete character and a continuous one in a single framework.