StructCoalescent MCMC — StructCoalescent

Runs an MCMC chain using the StructCoalescent method using radius-based subtrees

Usage

StructCoalescent_mcmc(
  N,
  strphylo,
  coal_rate,
  bit_mig_mat,
  st_radius = NA,
  adaptive = TRUE,
  cr_mode = NA,
  cr_var = NA,
  mm_mode = NA,
  mm_var = NA,
  output_dir = ".",
  run_name = "StructCoalescent",
  stdout_log = TRUE,
  thin = max(N/5000, 1),
  save_migration_history = TRUE,
  migration_history_thin = thin,
  proposal_rates = c(1000, 1, 1),
  adaptation_rate = 0.6,
  target_accept_rate = 0.234
)

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
st_radius: Initial subtree radius
adaptive: (logical) Adaptively update subtree radius within run? (default TRUE)
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)
adaptation_rate: Rate at which adaptive MCMC varies subtree radius (unused if adaptive = FALSE)
target_accept_rate: Target acceptance rate for migration history updates