TODO.txt

In RLink:
==========

* Expose directory methods in Mesquite to R (for example, list all
  algorithms (i.e., classes) that will operate on a tree and a
  character, ideally with a short description).

* Expose directory methods for inquiring about installed packages.

In Mesquite:
============

* Register location of headless Mesquite in preferences directory.

In R:
=====

* Try to obtain Mesquite location in a more automated fashion.
** More or less done. Refinement pending to Mesquite writing its home
   into a file that can distinguish between headless and awt.

* Ancestral state reconstruction.
** Should be done, but needs testing.

* Method to convert state matrix from Java to R


To build RMesquite in R
=======================
To build, cd into workspace directory.  Then:  sudo R CMD INSTALL RMesquite



#run this script, e.g. using source("~/example.txt")

mer <- getMatrixInWindow()
rmer <- as.matrix(mer)

library(RMesquite)
startMesquite()
data(bird.families)
birds <- mesquiteTree(tree = bird.families)

birds2 <- editTree(birds)
tree.returned <- as.phylo(birds2)

plot(tree.returned)
tree.tosend <- as.phylo(birds)
plot(tree.tosend)
========

library(RMesquite)
startMesquite()
tree <- getTreeInWindow()
tp <- as.phylo(tree)
matrix <- getMatrixInWindow()
m <- as.matrix(matrix)
a <- ancestralStatesCategorical(tp, m, method="ML", charIndex=1)