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()'.

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 in this package

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

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