added/formated documentation for nodeId and edgeId

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@899 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
updated/added documentation for edgeLength methods

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@900 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
updated roxygen formatting

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@901 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
updated roxygen formatting for phylobase.options

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@902 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
cleaned up added doc for prune/subset/extractTree, extractTree in its own file, prune incorporated with subset

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@903 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
renaming subset subset-methods

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@904 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
cleaning up doc, making hasSingle hasPoly and hasRetic methods

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@905 edb9625f-4e0d-4859-8d74-9fd3b1da38cb