Package index • StructCoalescent

All functions

BitMigMatC(): Backward-in-time migration matrix conversion

DTA_likelihood(): DTA likelihood

DTA_sampling(): DTA Sampling

DemeDecompC(): Deme Decomposition

Ewing_2004_mcmc(): Ewing et al. (2004) MCMC

FitMigMatC(): Forward-in-time migration matrix conversion

MTT_node_retype(): MultiTypeTree Node Retype

MTT_st_coal_node(): MultiTypeTree Subtree

MTT_transition_kernel(): MultiTypeTree Probability Density

MultiTypeTree_xml(): Generates BEAST2 xml for MultiTypeTree

NodeCountC(): NodeCountC

NodeIndicesC(): Node Indices

StructCoalescent-package StructCoalescent: A short title line describing what the package does

StructCoalescent_mcmc(): StructCoalescent MCMC

Vaughan_2015_MultiTypeTree_mcmc(): MultiTypeTree MCMC

coal_rate_gibbs_update() bit_mig_mat_gibbs_update(): Evolutionary Parameter Gibbs Updates

coalescent_merge(): Coalescent Node Merge Proposal

coalescent_node_pie_charts(): Coalescent Node Pie Charts

coalescent_split(): Coalescent Node Split Proposal

default_priors(): Default StructCoalescent prior parameters

dexp_trunc() pexp_trunc() rexp_trunc(): The Truncated Exponential Distribution

exact_consensus(): Majority Consensus Migration History

fitch(): Fitch Algorithm

local_DTA_likelihood(): Local DTA Likelihood

local_DTA_subtree_proposal(): Local DTA

local_MTT_transition_kernel(): Local MTT Likelihood

master_xml(): Generates xml for structured coalescent simulation using MASTER

migration_birth(): Migration Birth MCMC Move

migration_death(): Migration Death MCMC Move

migration_pair_birth(): Migration Pair Birth MCMC Move

migration_pair_death(): Migration Pair Death MCMC Move

rcpp_hello_world(): Simple function using Rcpp

rstrphylo(): Simulation of Heterochronous Structured Phylogenies

sample_path(): Sample path from the distribution of an endpoint-conditioned CTMC

st_centre_dist(): Subtree Sampling

structured_coalescent_likelihood(): Structured Coalescent likelihood