rncl: An Interface to the Nexus Class Library
Version 0.8.2

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
URL https://github.com/fmichonneau/rncl
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rncl")

Getting started

README.md

Popular man pages

read_nexus_phylo: Read phylogenetic trees from files
rncl: rncl: An R interface to the NEXUS Class Library
See all...

All man pages Function index File listing

Man pages

read_nexus_phylo: Read phylogenetic trees from files
rncl: rncl: An R interface to the NEXUS Class Library

Functions

RNCL Source code
build_phylo Source code
build_raw_phylo Source code
collapse_single_cpp Source code
collapse_singles Source code
get_edge_length Source code
get_edge_matrix Source code
has_node_labels Source code
internal_make_phylo Source code
make_phylo Man page Source code
n_singletons Source code
read_newick_phylo Man page Source code
read_nexus_phylo Man page Source code
rncl Man page Source code
rncl-package Man page

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
rncl documentation built on May 19, 2017, 4:40 p.m.

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