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Summary of Phylogenetic Comparative Methods - by Diogo B. Provete…

- - - - Makov k-state
        models
        
        Symmetric
        
        All Rates Differ (ARD)
        
        Custom matrix
        
        Equal rates
        
        With intraspecific variation
      - Allow heterogeneity
        in transition rates
        for MultiState traits among clades
        (BayesTraits)
      - Memoryless models
      - With rate heterogeneity
    - - Bayesian (e.g., BayesTraits)
      - Maximum likelihood (using Marvok k-state Models)
      - Stochastic Character Mapping
        (phytools::make.simmap)
      - Squared-change parsimony
      - with hidden states (corHMM)
      - threshold model
      - sMap
    - - Fritz's D
      - Mantel
      - Decomposition of Rao's Quadratic Entropy
        along the nodes of a phylogeny
      - delta statistic
    - - ... more than two levels...
        
        ... ordered
        
        MCMCglmm with family="ordinal" (probit link)
        
        ... unordered
        
        MCMCglmm with family="categorical" (logit link)
      - ... two levels
        
        Phylogenetic logistic regression
        (MCMCglmm or phylolm::phyloglm)
        
        Threshold Model
        (two discrete, or one discrete and one continuous trait)
        
        Correlation of transition rates of binary traits
        Pagel's method
        
        correlation using Mk model
        with hidden states (corHMM)
  - - - Phylogenetic eigenVector Regression
      - PGLS
        
        Phylogenetic ANOVA
        
        equivalent to Phylogenetic Independent Contrasts (PICs)
        when using BM
        
        with intraspecific variation
        in the response trait
        
        RegOU
        
        Robust Phylogenetic Regression
      - Model adequacy issue
        (packages Arbutus, pmc, and sensiPhy)
      - Fitting multiple VCV matrices to a phylogeny
        (phytools::evol.vcv or package ratematrix)
      - Mixed-effects models for complex
        hierarchical/nested designs
        or non-Gaussian phenotypic traits
        
        package MCMCglmm
        
        Bayesian Hierarchical Regression Models
        package brms
      - package SLOUCH
      - Phylogenetic ANCOVA
      - Delayed-response
        phylogenetic correlation
      - Autoregressive method
      - non-linear relationships
      - Phylogenetically weighted regression for non-stationary relationships
      - Allometry
        
        non-stationarity in the relationship between two continuous traits bayou::makeBayouModel bayou 2.0
        
        MGPMs
        
        blouch
      - CTC models
    - - Brownian Motion
        
        Multirate models
        
        geiger::auteur and Variable Rates model in BayesTraits for automatically detecting rate shifts
        
        Pulsed evolution - Lévy Process
        
        Rate shift considering
        fossil data (RRphylo)
        
        MuSSCRat for testing the effect
        of discrete character on the rate of
        a continuous trait
        
        Brownie
        
        MultiRate model with Penalized likelihood
        
        Comparing rates of evolution
        between trees
        
        phytools::evol.rate.mcmc
        
        mk and bm ML multi-rate models
        with fast computation
        
        Trend
        
        package OUwie
      - Ornstein-Uhlenbeck (OU)
        
        Detection of multiple adaptive peaks
        and estimation of OU parameters
        
        Detecting regime shifts
        automatically
        
        package SURFACE
        
        package l1ou
        
        package bayou
        
        phylogeneticEM
        
        package ouch
        
        package OUwie
      - Early Burst
        
        Harmon et al. 2010
        
        Nested EB, Nested Shift, Nested EB rate
      - FPK model
      - Models that incorporate competition conceptually and in model selection approach, and biogeography + competition between lineages
      - Non-Gaussian traits, se here
      - Mixed Gaussian Phylogenetic Models
      - Bounded evolutionary models (BBM) to distinguish between OU and bounded BM
    - - Squared-change Parsimony
        
        Non-weighted
        
        Weighted
      - Bayesian (BayesTraits and bayou)
      - Maximum-Likelihood #
      - with missing data - Rphylopars
      - Under pulsed evolution (RasperGade)
      - Joint estimation of continuous
        and discrete characters hOUwie
    - - Mantel test and correlogram
      - Pagel's Lambda
      - Moran's I (correlogram)
        = Abouheif's C
      - R2 of PVR
      - Blomberg's K without and with intraspecific variation
      - Decomposition of Rao's Quadratic Entropy
        along the nodes of a phylogeny
      - Why the hell am I using quotes in "signal"? Read this
      - delta statistic for categorical traits
    - - w-index
      - theta
      - CI
      - Ct-measures
- - - - Pipelines (e.g., SUPERSMART, phyloGenerator)
      - Supermatrix
      - Supertree
- - - - Phylogenetic Principal Component Analysis
      - Phylogenetic Factor Analysis
      - Phylogenetically Alligned Component Analysis
    - - Phylogenetic Canonical Correlation Analysis
      - Canonical Phylogenetic Ordination
      - Phylogenetic Discriminant Analysis