Run mPTP species delimitation (Maximum Likelihood)

Calls the mPTP C engine directly via .Call() — no external process, no file parsing. Results are returned as a structured R object.

Usage

mptp(
  tree,
  method = c("multi", "single"),
  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 an read.tree phylo object. Rooted and unrooted trees are both accepted.

method

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

outgroup

Character. Name of the outgroup taxon used for rooting an unrooted tree (optional; if omitted, the longest tip branch is used).

outgroup_crop

Logical. If TRUE, removes the outgroup after rooting (default FALSE).

pvalue

Numeric. Significance threshold for the likelihood ratio test (default 0.001).

minbr

Numeric. Minimum branch length; edges shorter than this are excluded from the analysis (default 0.0001).

seed

Integer. Random seed (default: current time).

quiet

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

Value

An object of class "mptp_ml", a list with:

n_species

Integer. Number of delimited species.

method

Character. "multi" or "single".

null_logl

Numeric. Null-model log-likelihood.

best_logl

Numeric. Best log-likelihood under mPTP.

pvalue

Numeric. LRT p-value.

lrt_passed

Logical. Whether the LRT rejected the null.

edge_count

Integer. Edges longer than minbr.

total_edges

Integer. Total edges in the tree.

assignments

Data frame with columns labels and mptp (integer index; ptp when method = "single").

See also

mptp_mcmc, mptp_tbl

Examples

if (FALSE) { # \dontrun{
result <- mptp("tree.nwk", outgroup = "Outgroup1",
                       outgroup_crop = TRUE)
print(result)
head(result$assignments)

library(ape)
phy <- read.tree("tree.nwk")
result <- mptp(phy)
} # }