Description Usage Arguments Value Examples
Uses a jackknife procedure to estimate 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 the difference between global fit with and without an interaction estimates the strength of support of said interaction to a hypothesis of phylogenetic congruence.
1 | paco_links(D, .parallel = FALSE, proc.warnings = TRUE)
|
D |
A list of class |
.parallel |
If TRUE, calculate the jackknife contribution in parallel using the backend provided by foreach. |
proc.warnings |
As in PACo. If |
The input list of class paco
with the added object jackknife which containing the mean and upper CI values for each link.
1 2 3 4 5 6 7 8 | 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)
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