tests/testthat/newick_notes.md

In richfitz/forest: New Phylogenetics Data Structures in R

The Newick format

There are a bunch of newick readers out there, and little description of the format.

The closest thing to a "formal" description is the page here: http://evolution.genetics.washington.edu/phylip/newicktree.html

Neither ape's read.tree() nor phylip's treeread() will read unifurcations, but phytools' read.nexus will.

• The tree ends with a semicolon.

• The bottommost node in this tree is an interior node, not a tip. Interior nodes are represented by a pair of matched parentheses. Between them are representations of the nodes that are immediately descended from that node, separated by commas.

• Tips are represented by their names. A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets.

• An underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in.

• Any name may also be empty: a tree like "(,(,,),);" is allowed.

• Trees can be multifurcating at any level.

• Branch lengths can be incorporated into a tree by putting a real number, with or without decimal point, after a node and preceded by a colon. This represents the length of the branch immediately below that node. Thus the above tree might have lengths represented as: "(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);"

Test suite:

I would like to be able to parse a wide range of trees, as a test. Could start with the Harmon trees, but do others too. This could be kept separate from the rest of the tests, and grabbing files from dryad etc.

On my computer, I have a file with comments for testing: nescent/ksi/proteaceae/

Performance

The tree parser in the current tests is very slow; it takes about .4s to read a 200 taxon tree, wheras ape takes 0.02s (so 20x slower). Writing is even worse; ape takes 0.015s but we take 1.1s.

Here it is clear that it is the translation overhead killing us; This will be a problem is we want really super fast access and a few careful Rcpp::Function calls might be better than the big heavyweight things that I currently have.

Rprof()
for (i in 1:5)
  tr <- read.newick(str)
Rprof(NULL)
summaryRprof()

richfitz/forest documentation built on May 27, 2019, 8:17 a.m.