MultiTypeTree MCMC — Vaughan_2015_MultiTypeTree

Runs an MCMC chain using the NodeRetype move from MultiTypeTree (Vaughan et al., 2014) using Gamma-distributed prior distributions

Usage

Vaughan_2015_MultiTypeTree_mcmc(
  N,
  strphylo,
  coal_rate,
  bit_mig_mat,
  cr_mode,
  cr_var,
  mm_mode,
  mm_var,
  st_depth = 1,
  output_dir,
  run_name = "MultiTypeTree",
  stdout_log = TRUE,
  thin = max(N/5000, 1),
  save_migration_history = TRUE,
  migration_history_thin = thin,
  proposal_rates = c(1000, 1, 1)
)

Arguments

N: Total number of MCMC iterations to complete
strphylo: Initial structured phylogenetic tree
coal_rate: Initial estimate of coalescent rates
bit_mig_mat: Initial estimate of backward-in-time migration rates matrix
cr_mode: Coalescent rates prior mode
cr_var: Coalescent rates prior variance
mm_mode: Backward-in-time migration rates prior mode
mm_var: Backward-in-time migration rates prior variance
output_dir: Directory to output log files to
run_name: Run name to save log files as
stdout_log: (logical) Output logs to stdout()? Default true
thin: Thinning rate for continuous parameter posterior samples
save_migration_history: Logical value indicating whether tree samples are saved (i.e. whether .trees file is created)
migration_history_thin: Thinning rate for tree samples to be saved
proposal_rates: Relative rates of migration history and continuous parameter updates (migration history : coalescent rates : migration rates)