Merge pull request #36 from nexml/master

example character data
implement character classes
updated documentation from one
tinkering with documentation
cannot build documentation on strata
build the documentation on one
update makefile to handle dependencies
documentation working now on strata
implementing characters nodes. Need to add handling for empty elements still
Added ability to read in <characters> data into S4 representation.
Still needs to support conversion to/from R matrices for character traits.
Basic tests provided but could be flushed out more as well.
Try nexml.read('comp_analysis.xml') as a test case.  Progress on #12
nexml can contain multiple otus nodes!
extended this in most places, still a few tests to check (one ape test failing..)
also work on characters, not quite complete. More details to come in next commit
which should hopefully fix the remaining issues to be clean enough to push to
origin/master.  gotta run now though, so better commit than no commit
basic character matrix extraction implemented.
Provides the S4 definitions for character matrices (serializing and parsing the XML) for issue #12.
Provides basic test cases in test_characters.R.  Provides basic extraction of character matrix as discussed in #38.
Conversion of discrete states to their symbol values not yet implemented.  Still need to add support for multiple
states nodes corresponding to multiple characters, and dereferencing these appropriately
handle character column classes based on xsi:type, provide option of single data frame with all taxa. #38
added new df merging scheme
begin mapping out function to serialize character matrices into nexml
Merge branch 'master' of github.com:ropensci/RNeXML
changes to get_characters using base fxns
Merge branch 'master' of github.com:ropensci/RNeXML
updated get_characters fxn, should be more rrobust, added test for get_characters
working on serializing char matrix data