rncl: An Interface to the Nexus Class Library

An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.

Install the latest version of this package by entering the following in R:
install.packages("rncl")
AuthorFrancois Michonneau [aut, cre], Ben Bolker [aut], Mark Holder [aut], Paul Lewis [aut], Brian O'Meara [aut]
Date of publication2016-12-16 11:20:37
MaintainerFrancois Michonneau <francois.michonneau@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version0.8.2
https://github.com/fmichonneau/rncl

View on CRAN

Files

inst
inst/newick_good
inst/newick_good/singleton_with_edge_length.tre
inst/newick_good/missing_edge_lengths.tre
inst/newick_good/simpleTree.tre
inst/newick_good/test_sing.tre
inst/newick_good/tree1.tre
inst/newick_good/singleton_tree.tre
inst/newick_good/tree2.tre
inst/newick_good/Gudrun.tre
inst/nexusfiles
inst/nexusfiles/badnex.nex
inst/nexusfiles/test_subset_alltaxa.nex
inst/nexusfiles/MultiLineTrees.nex
inst/nexusfiles/multiLines.rds
inst/nexusfiles/test_subset_taxa.nex
inst/nexusfiles/co1.nex
inst/nexusfiles/treeWithDiscreteData.nex
inst/nexusfiles/treeWithUnderscoreLabels.nex
inst/nexusfiles/test_underscores.nex
inst/nexusfiles/newick.tre
inst/nexusfiles/test_empty.nex
inst/newick_bad
inst/newick_bad/bad_newick.tre
inst/newick_bad/Gudrun.nex
tests
tests/testthat
tests/testthat/test.badnex.R tests/testthat/test.rncl.R tests/test-all.R
src
src/Makevars
src/nxspublicblocks.cpp
src/nxsdistancedatum.cpp
src/nxsdatablock.cpp
src/nxsexception.cpp
src/nxssetreader.cpp
src/nxsemptyblock.cpp
src/nxsassumptionsblock.cpp
src/collapse_singles.cpp
src/nxsunalignedblock.cpp
src/nxsdistancesblock.cpp
src/nxscxxdiscretematrix.cpp
src/nxsreader.cpp
src/nxstaxablock.cpp
src/nxsmultiformat.cpp
src/nxstaxaassociationblock.cpp
src/nxscharactersblock.cpp
src/GetNCL.cpp
src/nxstreesblock.cpp
src/nxsblock.cpp
src/nxstoken.cpp
src/Makevars.win
src/RcppExports.cpp
src/nxsstring.cpp
src/ncl
src/ncl/nxsunalignedblock.h
src/ncl/nxsdistancesblock.h
src/ncl/nxscxxdiscretematrix.h
src/ncl/nxstoken.h
src/ncl/nxsexception.h
src/ncl/nxsdefs.h
src/ncl/nxsdiscretedatum.h
src/ncl/ncl.h
src/ncl/nxspublicblocks.h
src/ncl/nxscharactersblock.h
src/ncl/nxsreader.h
src/ncl/nxsdatablock.h
src/ncl/nxsdistancedatum.h
src/ncl/nxsmultiformat.h
src/ncl/nxsdiscretematrix.h
src/ncl/nxsemptyblock.h
src/ncl/nxsstring.h
src/ncl/nxsutilcopy.h
src/ncl/nxstaxaassociationblock.h
src/ncl/nxssetreader.h
src/ncl/nxstreesblock.h
src/ncl/nxsindent.h
src/ncl/nxstaxablock.h
src/ncl/nxsassumptionsblock.h
src/ncl/nxsallocatematrix.h
src/ncl/nxsblock.h
src/ncl/nxscdiscretematrix.h
NAMESPACE
NEWS.md
R
R/rncl.R R/RcppExports.R R/collapse_singles.R R/rncl-package.R
README.md
MD5
DESCRIPTION
man
man/read_nexus_phylo.Rd man/rncl.Rd
cleanup
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.