Trait evolution

• Ancestral state reconstruction - Reconstruct ancestral character states

• Character map (synapomorphy/homoplasy mapping) - Map synapomorphies and homoplasies onto a phylogeny

• Concordance-aware ancestral state reconstruction - ASR incorporating gene tree discordance

• Continuous trait evolution model comparison (fitContinuous) - Compare continuous trait evolution models (supports discordance-aware VCV with -g)

• Continuous trait mapping (contMap) - Map continuous traits onto a phylogeny

• Density map - Posterior density of stochastic character maps

• Discrete trait evolution model comparison (fitDiscrete) - Compare ER, SYM, ARD Mk models

• Disparity through time (DTT) - Disparity-through-time analysis with MDI statistic (Harmon et al. 2003)

• Independent contrasts (PIC) - Felsenstein's phylogenetically independent contrasts

• Multi-regime OU models (OUwie) - Multi-regime Ornstein-Uhlenbeck models

• OU shift detection (l1ou) - Detect OU regime shifts on a phylogeny

• Parsimony score - Fitch parsimony score of a tree given an alignment

• Phenogram (traitgram) - Phenogram visualizing trait evolution

• Phylogenetic heatmap - Phylogeny alongside a heatmap of numeric trait values

• Phylogenetic imputation - Impute missing trait values using phylogenetic relationships

• Rate heterogeneity test (multi-rate Brownian motion) - Test for rate heterogeneity in trait evolution

• SIMMAP summary - Per-branch SIMMAP summary with node posteriors (describe.simmap)

• Stochastic character mapping (SIMMAP) - Stochastic character mapping on a phylogeny

• Threshold model - Felsenstein threshold model for trait correlation

• Trait rate map - Per-branch evolutionary rate map for a continuous trait