Phylogenetic Logistic Regression

Phylogenetic logistic regression for binary traits (Ives & Garland 2010)

Command identity

Canonical command:

phylo_logistic

Handler:

phylo_logistic

Aliases:

phylo_logreg, plogreg

Standalone executables:

pk_phylo_logistic, pk_phylo_logreg, pk_plogreg

Categories:

Phylogenetic comparative methods

Runtime interface

Synopsis

phykit phylo_logistic --tree <tree> --trait-data <trait_data> --response <response> --predictor <predictor> [--method <method>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
-t, --tree	true	str	required	any
-d, --trait-data	true	str	required	any
--response	true	str	required	any
--predictor	true	str	required	any
--method	false	str	logistic_MPLE	logistic_MPLE, logistic_IG10
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Fit a Phylogenetic Logistic Regression for binary (0/1) response data while accounting for phylogenetic non-independence among species (Ives & Garland 2010).

Uses Maximum Penalized Likelihood Estimation (logistic_MPLE) with Firth's bias-correction penalty and jointly estimates the phylogenetic signal parameter alpha via the OU-transformed variance-covariance matrix.

The multi-trait input file should be tab-delimited with a header row: taxon<tab>trait1<tab>trait2<tab>...

Output includes coefficient estimates, standard errors, z-values, p-values, alpha, log-likelihood, penalized log-likelihood, and AIC.

phykit phylo_logistic -t <tree> -d <trait_data> --response <column> --predictor <column> [--method logistic_MPLE|logistic_IG10] [--json]

Options:
-t/--tree: a tree file in Newick format
-d/--trait-data: tab-delimited multi-trait file with header row
--response: binary response column name (must contain only 0 and 1)
--predictor: predictor column name(s), comma-separated for multiple
--method: estimation method: logistic_MPLE or logistic_IG10 (default: logistic_MPLE)
--json: optional argument to print results as JSON

R validation: Validated against phylolm in R (see tests/r_validation/validate_phylo_logistic.R).