Character evolution (including Biogeography)
What kind of trait do I have?
Continuous
Inference (If the response variable is continuous)
Mixed-effects models for complex hierarchical/nested designs or non-Gaussian phenotypic traits
package MCMCglmm
Bayesian Hierarchical Regression Models
package brms
Phylogenetic ANCOVA
package SLOUCH
Fitting multiple VCV matrices to a phylogeny(phytools::evol.vcv or package ratematrix)
equivalent to Phylogenetic Independent Contrasts (PICs) when using BM
Evolutionary models [remember to include intraspecific variation]
Trend
geiger::auteur and Variable Rates model in BayesTraits for automatically detecting rate shifts
package OUwie
Detect jumps in evolutionary rates
Rate shift considering fossil data (RRphylo)
Detection of multiple adaptive peaks and estimation of OU parameters
package ouch
package OUwie
Detecting regime shifts automatically
package SURFACE
package bayou
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
Models that incorporate
biogeography + competition between lineages
Non-Gaussian traits, se here
Ancestral character estimation (#6b7dda)
Bayesian (BayesTraits and bayou)
Weighted
Non-weighted
with missing data - Rphylopars
Moran's I (correlogram)
[Abouheif's C]
Blomberg's K
Why the hell am I using quotes in "signal"? Read this
Inference(if the response variable is categorical with...)
two levels
Correlation of transition rates of binary traits
(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)
Ancestral character state estimation
Maximum likelihood (using Marvok k-state Models)
Stochastic Character Mapping (phytools::make.simmap)
Bayesian (e.g., BayesTraits)
with hidden states (corHMM)
Symmetric
Equal rates
All Rates Differ (ARD)
Custom matrix
Allow heterogeneity in transition rates for MultiState traits among clades (BayesTraits)
Phylogenetic "signal"
Mantel
Multivariate(e.g., derived from Geometric morphometrics)
Inference
Ordination
Constrained/Canonical
Unconstrained/Factor Analysis
Fitting evolutionary models to multivariate data
for models with evolutionary time lag package mvmorph
Detecting shifts in multivariate correlated traits package PhylogeneticEM
Trait Simulations
[Molecular Evolution]
[Phylogeography / Biogeography]
[Phyloclimatic Modeling]