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Phylogenetic Association with Co-diversification (PACo) analysis

Source: R/paco_wf.R
paco_wf.Rd

Performs PACo (Phylogenetic Association with Co-diversification) analysis to test host-symbiont co-evolution. Uses principal coordinates to reduce phylogenetic distance matrices and computes a goodness-of-fit statistic.

Usage

paco_wf(
  i_host_subtree,
  i_symbiont_subtree,
  i_host_to_symbiont_mat,
  permutations,
  seed
)

Arguments

i_host_subtree

A phylo object for the host subtree

i_symbiont_subtree

A phylo object for the symbiont subtree

i_host_to_symbiont_mat

A binary matrix with hosts as rows and symbionts as columns, where 1 indicates an association

permutations

Number of randomizations for significance testing; at least 99 recommended

seed

Random seed for reproducibility; if NA, no seed is set

Value

A PACo object containing:

  • gof: Goodness-of-fit statistics including ss (squared sum) and p-value from permutation test

  • Additional fields from paco::PACo()

References

Balbuena JA, Míguez-Argüello R, Blasco-Costa I, Llopis-Beltrán A (2013). PACo: A novel procedure to estimate the packedness of a given association matrix. Journal of Biogeography 40: 948-960.

Examples

# \donttest{
h_tree <- ape::rtree(5)
s_tree <- ape::rtree(15)
links <- data.frame(Host = rep(h_tree$tip.label, 3),
                    Symbiont = s_tree$tip.label)
hs_mat <- host_symbiont_links(links)   # binary host-by-symbiont matrix
result <- paco_wf(h_tree, s_tree, hs_mat, permutations = 99, seed = 123)
# }