clean up and add @export and @exportMethod where appropriate

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@923 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
major re-organization of the docs with transition to roxygen

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@924 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
converted readNCL unit tests to testthat

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@925 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
removing nData-methods, content transferred to phylo4d-accessors.R

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@926 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
dealing with formatData not being exported

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@927 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
dealing with modified output of rootNode

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@928 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
adding change to rootNode to NEWS

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@929 edb9625f-4e0d-4859-8d74-9fd3b1da38cb