paco_ss | 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
Procruste Approach to Cophylogeny (PACo) to produce the squared sum of
residuals of the Procrustes superimposition of the host and symbiont
configurations in Euclidean space.
paco_ss(
ths,
treeH,
treeS,
symmetric = FALSE,
proc.warns = FALSE,
ei.correct = "none",
strat = "sequential",
cl = 1
)
ths |
Trimmed matrix. |
treeH |
Host phylogeny. An object of class |
treeS |
Symbiont phylogeny. An object of class |
symmetric |
Specifies the type of Procrustes superimposition. Default
is |
proc.warns |
Switches on/off trivial warnings returned when treeH and
treeS differ in size (number of tips). Default is |
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 sum of squared residuals.
Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I. (2022). User’s Guide Random Tanglegram Partitions V.1.0.0. Zenodo.
Balbuena J.A., Miguez-Lozano R., Blasco-Costa I. (2013). PACo: A Novel Procrustes Application to Cophylogenetic Analysis. PLOS ONE. 8:e61048.
Balbuena J.A., Perez-Escobar Ó.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)
PACO <- paco_ss(TAM, amphipod, trematode, symmetric = TRUE,
ei.correct = "sqrt.D", strat = "parallel", cl = 8)
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