vnminin / phylolsnodist

Phylogenetic least squares without distances paper

phyloLSnoDist

This package performs phylogenetic inference under the least squares framework but without the use of traditional evolutionary distances, as described in ``Phylogenetic least squares estimation without genetic distances''.

Installation

First, two packages need to be installed:

• robustDist
• phyloLSnoDist

Installation of robustDist can be accomplished with the following:

install.packages("robustDist", repos=c("http://R-Forge.R-project.org",
                                       "http://cran.at.r-project.org"),dependencies=TRUE)

You may also need to include the option INSTALL_opts = c('--no-lock').

Then, the easiest way to install phyloLSnoDist will be to use install_github from the devtools package:

install.packages("remotes") # if not installed already
remotes::install_github("vnminin/phyloLSnoDist")

Simple Example

First we must load the phyloLSnoDist package, which should also load its dependencies:

library(phyloLSnoDist)

Using the rtree function from the ape package, we generate a 4-taxon tree which we will use for demonstration:

set.seed(100)
my_tree <- rtree(4)
plot(my_tree, type='u')

With this tree, let us generate some DNA nucleotide sequence data, and convert it to phyDat format for usage by the phylo.ls.nodist function:

my_DNA <- simSeq(my_tree, 2000)
my_DNA_pD <- as.phyDat(my_DNA)

Then, we run our phylo.ls.nodist function to run phylogenetic inference with our new loss function. Since there are only three unrooted topologies, we do an exhaustive search by setting search.all = TRUE:

nodist_tree <- phylo.ls.nodist(my_DNA_pD, search.all = TRUE)
plot(nodist_tree, type='u')

Extended Vignette

A longer vignette, showing the above code with its intended output, along with replication of select simulation experiments from the manuscript, is available in the vignette directory. The output pdf is vignette.pdf along with associated R Markdown file, vignette.Rmd.

Other Notes

The analysis directory of this repository contains scratchwork, older versions of code, and unpublished simulation experiments. All final code for the manuscript is in the manuscript directory.