paco_links {paco}

Contribution of individual links

Description

Uses a jackknife procedure to perform bias correction on procrustes residuals (i.e. interactions) that are indicative of the degree to which individual interactions are more supportive of a hypothesis of phylogenetic congruence than others. Interactions are iteratively removed, the global fit of the two phylogenies is reassessed and bias in observed residuals calculated and corrected.

Usage

paco_links(D, .parallel = FALSE, proc.warnings = TRUE)

Arguments

D

A list of class paco as returned by paco::PACo.

.parallel

If TRUE, calculate the jackknife contribution in parallel using the backend provided by foreach.

proc.warnings

As in PACo. If TRUE, any warnings produced by internal calls of paco::PACo will be available for the user to view. If FALSE, warnings are internally suppressed.

Value

The input list of class paco with the added object jackknife which contains the bias-corrected residual for each link.

Examples

data(gopherlice)
require(ape)
gdist <- cophenetic(gophertree)
ldist <- cophenetic(licetree)
D <- prepare_paco_data(gdist, ldist, gl_links)
D <- add_pcoord(D)
D <- PACo(D, nperm=10, seed=42, method="r0")
D <- paco_links(D)