optim.phylo.wls: Phylogeny inference using the weighted least squares method

In TKF: Pairwise Distance Estimation with TKF91 and TKF92 Model

Description

This function performs phylogeny inference using weighted least-squares.

Usage

optim.phylo.wls(Dist, Var=NULL, stree=NULL, set.neg.to.zero=TRUE,
                fixed=FALSE, tol=1e-10, collapse=TRUE)

Arguments

Dist	a distance matrix.
Var	a covariance matrix of the distance. When it is NULL, ordinary least squares tree will be built.
stree	an optional starting tree for the optimization.
set.neg.to.zero	a logical value indicating whether to set negative branch lengths to zero (default "TRUE").
fixed	a logical value indicating whether to estimate the topology - if "TRUE" only the branch lengths will be computed.
tol	a tolerance value used to assess whether the optimization has converged.
collapse	a logical indicating whether to collapse branches with zero length.

Details

This function extends the function optim.phylo.ls in package phytools to support weighted least squares tree reconstruction. For more details, please check the help page of optim.phylo.ls.

Value

An objec of class "phylo" that (may be) the least-squares tree with branch lengths; also returns the sum of squares in 'attr(tree,"Q-score")'.

Author(s)

Ge Tan

Examples

  Dist <- matrix(c(0.00000, 27.78202, 29.54125, 29.06183, 40.63082, 41.20910,
                   27.78202, 0.00000, 14.82329, 24.26988, 47.40101, 43.76202,
                   29.54125, 14.82329, 0.00000, 26.82772, 48.17819, 41.27872,
                   29.06183, 24.26988, 26.82772, 0.00000, 44.66941, 44.39078,
                   40.63082, 47.40101, 48.17819, 44.66941, 0.00000, 45.63394,
                   41.20910, 43.76202, 41.27872, 44.39078, 45.63394, 0.00000),
                   ncol=6, dimnames=list(c("YARLI", "KLULA", "CANGA", "DEBHA",
                   "CRYNE", "ASPFU"), c("YARLI", "KLULA", "CANGA", "DEBHA",
                   "CRYNE", "ASPFU")))
  Var <- matrix(c(0.000000, 6.261368, 6.816608, 6.660132, 11.361800, 12.037978,
                  6.261368, 0.000000, 2.877505, 5.054447, 14.315551, 12.734813,
                  6.816608, 2.877505, 0.000000, 5.699967, 12.638321, 11.598558,
                  6.660132, 5.054447, 5.699967, 0.000000, 12.189609, 13.185733,
                  11.36180, 14.31555, 12.63832, 12.18961, 0.00000, 15.19872,
                  12.03798, 12.73481, 11.59856, 13.18573, 15.19872, 0.00000),
                  ncol=6, dimnames=list(c("YARLI", "KLULA", "CANGA", "DEBHA",
                   "CRYNE", "ASPFU"), c("YARLI", "KLULA", "CANGA", "DEBHA",
                   "CRYNE", "ASPFU")))
  tree <- optim.phylo.wls(Dist, Var)
  plot(tree, type="unrooted")

TKF documentation built on May 2, 2019, 7:59 a.m.