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Character evolution (including Biogeography) (What kind of trait do I…

- - - - non-linear relationships
      - Mixed-effects models for complex hierarchical/nested designs or non-Gaussian phenotypic traits
        
        package MCMCglmm
        
        Bayesian Hierarchical Regression Models
        
        package brms
      - Autoregressive method
      - Delayed-response phylogenetic correlation
      - Phylogenetic ANCOVA
      - package SLOUCH
      - Model adequacy issue (packages Arbutus, pmc, and sensiPhy)
      - Fitting multiple VCV matrices to a phylogeny(phytools::evol.vcv or package ratematrix)
      - Phylogenetic eigenVector Regression
      - PGLS
        
        equivalent to Phylogenetic Independent Contrasts (PICs) when using BM
        
        Phylogenetic ANOVA
        
        with intraspecific variationin the response trait
    - - Trend
      - Brownian Motion
        
        geiger::auteur and Variable Rates model in BayesTraits for automatically detecting rate shifts
        
        package OUwie
        
        Brownie
        
        Comparing rates of evolution between trees
        
        phytools::evol.rate.mcmc
        
        Detect jumps in evolutionary rates
        
        levolution
        
        Rate shift considering fossil data (RRphylo)
      - Orsntein-Uhlenbeck (OU)
        
        Detection of multiple adaptive peaks and estimation of OU parameters
        
        package ouch
        
        package OUwie
        
        Detecting regime shifts automatically
        
        package SURFACE
        
        package bayou
        
        shifts in allometric relationships
        
        non-stationarity in the relationship between continuous traits bayou::makeBayouModel
        
        package l1ou
        
        Package PhylogeneticEM for detecting shifts in multivariate traits taking into account correlation between them
      - Early Burst
      - FPK model
      - Models that incorporate
        
        competition
        
        biogeography + competition between lineages
        
        Pulsed evolution - Lévy Process
        
        Non-Gaussian traits, se here
    - - Bayesian (BayesTraits and bayou)
      - Maximum-Likelihood #
      - Squared-change Parsimony
        
        Weighted
        
        Non-weighted
      - with missing data - Rphylopars
    - - Moran's I (correlogram)
      - [Abouheif's C]
      - Decomposition of Rao's Quadratic Entropy along the nodes of a phylogeny
      - Blomberg's K
        
        without intraspecific variation
        
        with intraspecific variation
      - Mantel test and correlogram
      - Pagel's Lambda
      - R2 of PVR
      - Why the hell am I using quotes in "signal"? Read this
  - - - two levels
        
        Phylogenetic logistic regression
        
        (MCMCglmm or phylolm::phyloglm)
        
        Correlation of transition rates of binary traits
        
        Pagel's method
        
        Threshold Model
        
        (two discrete, or one discrete and one continuous trait)
        
        correlation using Mk model
        
        with hidden states (corHMM)
      - more than two levels
        
        ordered
        
        MCMCglmm with family="ordinal" (probit link)
        
        unordered
        
        MCMCglmm with family="categorical" (logit link)
    - - Maximum likelihood (using Marvok k-state Models)
      - Stochastic Character Mapping (phytools::make.simmap)
      - Bayesian (e.g., BayesTraits)
      - Squared-change parsimony
      - with hidden states (corHMM)
    - - Symmetric
      - Equal rates
      - All Rates Differ (ARD)
      - Custom matrix
      - Allow heterogeneity in transition rates for MultiState traits among clades (BayesTraits)
      - Comparing rates of evolution #
    - - Decomposition of Rao's Quadratic Entropy along the nodes of a phylogeny
      - Fritz's D
      - Mantel
  - - - RRPP
      - PGLS for multivariate traits
    - - Constrained/Canonical
        
        Canonical Phylogenetic Ordination
        
        Phylogenetic Canonical Correlation Analysis
      - Unconstrained/Factor Analysis
        
        Phylogenetic Principal Component Analysis
        
        Phylogenetic Factor Analysis
    - - Comparing rates between compartments of a multidimensional trait - modularity
    - - Blomberg's K for multiple traits
      - mvSLOUCH
      - for models with evolutionary time lag package mvmorph
      - Detecting shifts in multivariate correlated traits package PhylogeneticEM
      - fitting BM, EB, OU with Penalized LIkelihood