Comparative 'Phylogenetic' Analyses of Diversification
Argument Names for Vector-Argument Functions
Ancestral State Reconstruction Under BiSSE
Ancestral State Reconstruction Under Mk2/Mkn
Ancestral State Reconstruction
Verbosely Track Function Evaluations
Check Capabilities of the Diversitree Install
Combine Several Likelihood Functions Multiplicatively
Constants Used by Diversitree
Constrain Parameters of a Model
Deprecated and Defunct Functions in Diversitree
tools:::Rd_package_title("diversitree")
Maximimum Likelihood Inference
Extract Character Histories From Simulations
Constant Rate Birth-Death Models
Constant Rate Birth-Death Models: Split Models
Time-varing Birth-Death Models
Binary State Speciation and Extinction Model
Binary State Speciation and Extinction Model: Split Models
Binary State Speciation and Extinction Model: Time Dependant Models
Binary State Speciation and Extinction (Node Enhanced State Shift) Mod...
Brownian Motion and Related Models of Character Evolution
Make a "Clade Tree"
Cladogenetic State change Speciation and Extinction Model
Geographic State Speciation and Extinction Model
Geographic State Speciation and Extinction Model: Split Models
Geographic State Speciation and Extinction Model: Time Dependent Model...
Mk2 and Mk-n Models of character evolution
MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits V...
MuSSE: Multi-State Speciation and Extinction
Multiple State Speciation and Extinction Model: Split Models
Multiple State Speciation and Extinction Model: Time Dependent Models
Phylogenetic Generalised Least Squares
Simple Prior Functions
Quantitative State Speciation and Extinction Model
Quantitative State Speciation and Extinction Model: Split Models
Simple Markov Chain Monte Carlo with Slice Sampling
Plot Character History
Plot Marginal Distributions from MCMC
Protect Function Evaluations
Support Functions for QuaSSE Models
Set Default Arguments of a Function
Simulate a Character Distribution on a Tree
Evolve Birth-Death Trees
Plot a Phylogeny and Traits
Utility Functions
Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.