Package: treeio 1.37.0.001

Guangchuang Yu

treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

Authors:Guangchuang Yu [aut, cre], Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb], Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb]

treeio_1.37.0.001.tar.gz
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treeio_1.37.0.001.tgz(r-4.6-any)treeio_1.37.0.001.tgz(r-4.5-any)
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treeio_1.37.0.001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treeio/json (API)

# Install 'treeio' in R:

install.packages('treeio', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #179

Bug tracker:https://github.com/yulab-smu/treeio/issues

On BioConductor:treeio-1.37.0(bioc 3.24)treeio-1.36.1(bioc 3.23)

software annotation clustering dataimport datarepresentation alignment multiplesequencealignment phylogenetics exporter parser phylogenetic-trees

12.17 score 104 stars 131 packages 2.8k scripts 76 exports 31 dependencies

Last updated from:e397d39824 (on devel). Checks:10 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	168
pkgdown docs	OK	210
source / vignettes	OK	220
linux-release-x86_64	OK	180
macos-release-arm64	OK	94
macos-oldrel-arm64	OK	125
windows-devel	OK	116
windows-release	OK	122
windows-oldrel	OK	110
wasm-release	OK	161

Exports:.data %<>%%>%ancestor as_tibble as.phylo as.treedata child drop.tip find.hclust full_join get.data get.fields get.placements get.tree get.treetext getNodeNum inner_join is.ggtree is.rooted isTip label_branch_paml mask merge_tree MRCA Nnode Nnode2 nodeid nodelab Ntip offspring parent raxml2nwk read.astral read.beast read.beast.newick read.codeml read.codeml_mlc read.fasta read.hyphy read.hyphy.seq read.iqtree read.jplace read.jtree read.mcmctree read.mega read.mega_tabular read.mrbayes read.newick read.nextstrain.json read.nexus read.nhx read.paml_rst read.phylip read.phylip.seq read.phylip.tree read.phyloxml read.r8s read.raxml read.tree read.treeqza read.treetime rename_taxa rescale_tree root rootnode rtree spt tibble treedata write.beast write.beast.newick write.jplace write.jtree write.nexus write.tree

Dependencies:ape cli cpp11 digest dplyr fs generics glue jsonlite lattice lazyeval lifecycle magrittr nlme pillar pkgconfig purrr R6 rappdirs Rcpp rlang stringi stringr tibble tidyr tidyselect tidytree utf8 vctrs withr yulab.utils

treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Rendered fromtreeio.Rmdusingknitr::rmarkdown

Last update: 2023-11-29
Started: 2016-12-06

Help page	Topics
as.treedata	as.treedata.phylo
find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.	find.hclust
get.placements	get.placements get.placements.jplace
get.tree	get.tree
get.treetext method	get.treetext
getNodeNum	getNodeNum Nnode2
is.ggtree	is.ggtree
Class "jplace" This class stores phylogenetic placements	jplace-class
label_branch_paml	label_branch_paml
mask	mask
merge_tree	merge_tree
print	print.treedataList
raxml2nwk	raxml2nwk
read.astral	read.astral
read.beast	read.beast read.beast.newick read.mega read.mrbayes
read.codeml	read.codeml
read.codeml_mlc	read.codeml_mlc
read.fasta	read.fasta
read.hyphy	read.hyphy
read.hyphy.seq	read.hyphy.seq
read.iqtree	read.iqtree
read.jplace	read.jplace
read.jtree	read.jtree
read.mcmctree	read.mcmctree
read.mega_tabular	read.mega_tabular
read.newick	read.newick
read.nextstrain.json	read.nextstrain.json
read.nhx	read.nhx
read.paml_rst	read.paml_rst
read.phylip	read.phylip
read.phylip.seq	read.phylip.seq
read.phylip.tree	read.phylip.tree
read.phyloxml	read.phyloxml
read.r8s	read.r8s
read.raxml	read.raxml
read.treeqza	read.treeqza
read.timetree	read.timetree read.treetime
rename_taxa	rename_taxa
rescale_tree	rescale_tree
spt method	spt
write.beast	write.beast
write.beast.newick	write.beast.newick
write.jplace	write.jplace
write.jtree	write.jtree

Package: treeio 1.37.0.001

treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

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