Re-write of internally used function phyloDesign

I have totally re-written the internally used function, phyloDesign, which computes a design matrix for least-squares phylogeny estimation in the phytools function optim.phylo.ls, which does unweighted least-squares phylogeny estimation from a distance matrix.

Here's a simple demo using a DNA dataset from Jackman et al. (1999; Syst. Biol.).

library(devtools)
install_github("liamrevell/phytools",quiet=TRUE)

packageVersion("phytools")

## [1] '0.5.3'

library(phytools)
## load data
dna<-read.nexus.data(file="http://www.phytools.org/UMB2015/data/Jackman-etal.nex")
dna<-as.DNAbin(dna)
dna

## 55 DNA sequences in binary format stored in a list.
## 
## All sequences of same length: 1456 
## 
## Labels: Diplolaemus_darwinii Polychrus_acutirostris Anolis_acutus Anolis_cristatellus Anolis_krugi Anolis_stratulus ...
## 
## Base composition:
##     a     c     g     t 
## 0.339 0.261 0.118 0.281

## compute distance matrix
D<-dist.dna(dna)
## estimate tree, using NJ as a starting tree:
ls.fit<-optim.phylo.ls(D,phangorn::NJ(D))

## 1 set(s) of nearest neighbor interchanges. best Q so far = 0.187309346 
## 2 set(s) of nearest neighbor interchanges. best Q so far = 0.185881266 
## 3 set(s) of nearest neighbor interchanges. best Q so far = 0.1847435677 
## 4 set(s) of nearest neighbor interchanges. best Q so far = 0.1839579959 
## 5 set(s) of nearest neighbor interchanges. best Q so far = 0.1835163321 
## 6 set(s) of nearest neighbor interchanges. best Q so far = 0.1830769343 
## 7 set(s) of nearest neighbor interchanges. best Q so far = 0.1827496093 
## 8 set(s) of nearest neighbor interchanges. best Q so far = 0.18261176 
## 9 set(s) of nearest neighbor interchanges. best Q so far = 0.1823425143 
## 10 set(s) of nearest neighbor interchanges. best Q so far = 0.1821113405 
## 11 set(s) of nearest neighbor interchanges. best Q so far = 0.1819861917 
## 12 set(s) of nearest neighbor interchanges. best Q so far = 0.1819386781 
## 13 set(s) of nearest neighbor interchanges. best Q so far = 0.1819014877 
## 14 set(s) of nearest neighbor interchanges. best Q so far = 0.1814029139 
## 15 set(s) of nearest neighbor interchanges. best Q so far = 0.1813641191 
## 16 set(s) of nearest neighbor interchanges. best Q so far = 0.180996378 
## best Q score of 0.180996378 found after 16 nearest neighbor interchange(s).

plotTree(root(ls.fit,outgroup="Diplolaemus_darwinii",resolve.root=TRUE),
    fsize=0.8,ftype="i")

It's hard to summarize where the speed-up in phyloDesign (which is many-fold for reasonable sized trees) comes from. The original version was written with loops & logical statements. The new version with apply family functions and set comparisons. Basically, I'm a bit better at R programming nowadays than I was five years ago when I wrote the earlier version of this function. (But still not all that good….)

That's it!