paraF | R Documentation |
For any trimmed matrix produced with
trimHS_maxC()
or
trimHS_maxI()
, it prunes the host (H) and
symbiont (S) phylogenies to conform with the trimmed matrix and runs
ape::parafit()
(Legendre et al. 2002) to
calculate the ParaFitGlobal Statistic.
paraF(ths, treeH, treeS, ei.correct = "none", strat = "sequential", cl = 1)
ths |
Trimmed matrix. |
treeH |
Host phylogeny. An object of class |
treeS |
Symbiont phylogeny. An object of class |
ei.correct |
Specifies how to correct potential negative eigenvalues
from the conversion of phylogenetic distances into Principal
Coordinates: |
strat |
Flag indicating whether execution is to be |
cl |
Number of cluster to be used for parallel computing.
|
A number object with the ParaFitGlobal Statistic of host-symbiont test for the N trimmed matrix.
Legendre P., Desdevises Y., Bazin E. (2002). A Statistical Test for Host–Parasite Coevolution. Systematic Biology. 51:217–234.
Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I. (2020). Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot. Systematic Biology. 69:1212–1230.
data(amph_trem)
N = 10 #for the example, we recommend 1e+4 value
n = 8
TAM <- trimHS_maxC(N, am_matrix, n, check.unique = TRUE)
PF <- paraF(TAM, amphipod, trematode, ei.correct = "sqrt.D",
strat = "parallel", cl = 8)
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