Description Usage Arguments Value Examples
Takes the Procrustes object from vegan::procrustes
of the global superimpostion and pulls out either the residual matrix of superimposition or the residual of each individual interaction (link between host and parasite).
1 | residuals_paco(object, type = "interaction")
|
object |
An obejct of class |
type |
Character string. Whether the whole residual matrix ( |
If type=interaction
, a named vector of the Procrustes residuals is returned where names are the interactions. If type=matrix
, a matrix of residuals from Procrustes superimposition is returned.
1 2 3 4 5 6 7 8 | data(gopherlice)
library(ape)
gdist <- cophenetic(gophertree)
ldist <- cophenetic(licetree)
D <- prepare_paco_data(gdist, ldist, gl_links)
D <- add_pcoord(D, correction='cailliez')
D <- PACo(D, nperm=100, seed=42, method='r0')
residuals_paco(D$proc)
|
There were 50 or more warnings (use warnings() to see the first 50)
Ound-Gset Ocav-Gpan Oche-Gche Ohet-Gcos Ohis-Gcha GburB-Ggeo GburA-Gokl
0.04740129 0.04976048 0.04016673 0.03812147 0.04378583 0.02700916 0.02529977
Gbre-Gewi Gpers-Gtex Ccas-Gexp Tbot-Gact Cmer-Gpero Ttal-Gtho Ztri-Gtri
0.05593318 0.05003108 0.04876865 0.11335455 0.05684718 0.08996408 0.05191354
Pbul-Gnad Tbot-Tmin Ttal-Tbar
0.02482918 0.10680919 0.12299913
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