Phylogenetic imputation

Impute missing trait values using phylogenetic relationships

Command identity

Canonical command:: phylo_impute
Handler:: phylo_impute
Aliases:: impute, phylo_imp
Standalone executables:: pk_phylo_impute, pk_impute, pk_phylo_imp
Categories:: Trait evolution

Runtime interface

Synopsis

phykit phylo_impute --tree <tree> --trait-data <trait_data> --output <output> [--gene-trees <gene_trees>] [--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
`-o, --output`	true	str	required	any
`-g, --gene-trees`	false	str	none	any
`--json`	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Impute missing continuous trait values using phylogenetic relationships and between-trait correlations under Brownian motion. Missing values (NA, ?, or empty) in a multi-trait TSV are predicted from:

Phylogenetic neighbors: closely related species with observed values contribute more to the imputation via the phylogenetic VCV
Trait correlations: if a taxon has observed values for other traits, between-trait covariance improves the prediction

Reports imputed values with standard errors and 95% confidence intervals. The output TSV is a drop-in replacement for the input with all missing values filled in.

phykit phylo_impute -t <tree> -d <trait_data> -o <output> [--json]
phykit phylo_impute -t <tree> -d <trait_data> -o <output> -g <gene_trees>

Options:
-t/--tree: tree file in Newick format (required)
-d/--trait-data: multi-trait TSV with header; missing values as NA, ?, or empty (required)
-o/--output: output TSV file with imputed values (required)
-g/--gene-trees: gene trees for discordance-aware VCV
--json: optional argument to print results as JSON

R validation: Validated against Rphylopars in R (see tests/r_validation/validate_phylo_impute.R).