Run mPTP species delimitation (MCMC)

Calls the mPTP MCMC engine directly via .Call(). Returns ML species assignments plus per-node posterior support values.

Usage

mptp_mcmc(
  tree,
  method = c("multi", "single"),
  mcmc_steps = 1000000L,
  mcmc_sample = 1000L,
  mcmc_burnin = 100000L,
  mcmc_runs = 1L,
  mcmc_credible = 0.95,
  mcmc_startnull = FALSE,
  mcmc_startrandom = FALSE,
  mcmc_startml = FALSE,
  outgroup = NULL,
  outgroup_crop = FALSE,
  pvalue = 0.001,
  minbr = 1e-04,
  seed = as.integer(Sys.time()),
  quiet = FALSE
)

Arguments

tree

A path to a Newick tree file (character) or a phylo object from ape. See mptp for details.

method

Coalescent rate model: "multi" (default) or "single".

mcmc_steps

Integer. Total MCMC steps per run (default 1,000,000).

mcmc_sample

Integer. Sampling frequency (default 1,000).

mcmc_burnin

Integer. Steps discarded as burn-in (default 100,000).

mcmc_runs

Integer. Number of independent runs (default 1).

mcmc_credible

Numeric. Credible interval (default 0.95).

mcmc_startnull

Logical. Start from the null (one-species) model.

mcmc_startrandom

Logical. Start from a random delimitation.

mcmc_startml

Logical. Start from the ML delimitation.

outgroup

Character. Outgroup taxon name for rooting (optional).

outgroup_crop

Logical. Remove outgroup after rooting (default FALSE).

pvalue

Numeric. LRT significance threshold (default 0.001).

minbr

Numeric. Minimum branch length threshold (default 0.0001).

seed

Integer. Random seed (default: current time).

quiet

Logical. Suppress C-level progress messages (default FALSE).

Value

An object of classes c("mptp_mcmc", "mptp_ml"), a list with all fields of "mptp_ml" plus:

support

Data frame with columns node_label and support (0–1); posterior probability of each inner node being a coalescent root.

mcmc_steps

Integer.

mcmc_sample

Integer.

mcmc_burnin

Integer.

mcmc_runs

Integer.

seed

Integer. Actual seed used.

See also

mptp, mptp_tbl

Examples

if (FALSE) { # \dontrun{
result <- mptp_mcmc(
  "tree.nwk",
  mcmc_steps    = 5000000L,
  mcmc_burnin   = 500000L,
  mcmc_runs     = 3L,
  seed          = 42L,
  outgroup      = "Outgroup1",
  outgroup_crop = TRUE
)
print(result)
head(result$support)
} # }