parafit_stat: Calculate the ParafitGlobal statistic on 2 trees and their...
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Details Value Functions References See Also Examples

View source: R/calculate_cophylo_summary_stat.R

Calculate the ParafitGlobal Statistic to be used in the hypothesis test described in Legendre et al. (2002). The null hypothesis of this test being that the evolution of the two trees together with their associations at the present have been independent.

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parafit_stat(host_tr, symb_tr, assoc_mat)

parafit_test(host_tr, symb_tr, assoc_mat, D, reps = 99)

`host_tr`	The host tree of class "phy"
`symb_tr`	The symbiont tree of class "phy
`assoc_mat`	Association matrix between the extant tips of 'host_tr' and 'symb_tr'
`D`	the statistic calculated using 'parafit_stat'
`reps`	Number of permutations to perform on the association matrix for the hypothesis test

'parafit_stat' drops any non-extant tips from the tree. Then the phylogenetic distance matrix is obtained for both host and symbiont tree. Next the principal coordinates are found for the host and symbiont distance matrices before these PCoA vectors are used in the following matrix multiplication following Legendre et al. (2002): D = H t(A) A. The trace is then found of this to get our ParaFitGlobal Statistic.

The test function 'parafit_test' performs a row-wise permutation of the association matrix as described in Legendre et al. 2002. This is performed a number of times set by the user (default is 999) and a p-value is output.

The value from this is input into the test function. Note that this gives only the raw statistic unlike 'ape::parafit'. That is the only reason it is implemented here in treeducken (similar to 'treeducken::cherries').

A p-value for the hypothesis test described above

parafit_test: Perform ParaFit Hypothesis Test

Legendre, P., Y. Desdevises and E. Bazin. 2002. A statistical test for host-parasite coevolution. Systematic Biology, 51(2), 217–234.

parafit_test

tr_pair <- sim_cophyBD(hbr=0.1,
                          hdr=0.05,
                          sdr=0.1,
                          host_exp_rate=0.4,
                          sbr = 0.05,
                          cosp_rate = 1.0,
                          numbsim = 1,
                          time_to_sim = 1)
# maybe we are interested in only cophylogenetic object 1
ht <- tr_pair[[1]]$host_tree
st <- tr_pair[[1]]$symb_tree
A <- tr_pair[[1]]$association_mat
pfs <- parafit_stat(host_tr = ht, symb_tr = st, assoc_mat = A)

parafit_test(ht, st, A, pfs, reps = 19)