paco_links: Contribution of individual links
In paco: Procrustes Application to Cophylogenetic Analysis

Description Usage Arguments Value Examples

View source: R/paco_links.r

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.

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

`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.

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

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)