Package: tidytree 0.4.6.002

Guangchuang Yu

tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Authors:Guangchuang Yu [aut, cre, cph], Bradley Jones [ctb], Zebulun Arendsee [ctb]

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tidytree.pdf |tidytree.html
tidytree/json (API)
NEWS

# Install 'tidytree' in R:
install.packages('tidytree', repos = c('https://yulab-smu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

phylogenetic-treetidyversetree-data

13.56 score 52 stars 127 packages 496 scripts 24k downloads 10 mentions 52 exports 29 dependencies

Last updated 4 months agofrom:1115d91fe1. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:.data%<>%%>%ancestorarrangeas_tibbleas.phyloas.treedataas.ultrametricchilddrop.tipfilterfull_joinget_tree_dataget.dataget.fieldsget.treetextgetNodeNumgroupCladegroupOTUis.rootedisTipkeep.tipleft_joinMRCAmutateNnodenode.labelnode.label<-nodeidnodelabNtipoffspringparentpullread.treerenamerootrootnodertreeselectshowsiblingsummarisesummarizetibbletip.labeltip.label<-transmutetree_subsettreedataunnest

Dependencies:apeclicpp11digestdplyrfansifsgenericsgluelatticelazyevallifecyclemagrittrnlmepillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithryulab.utils

tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation

Rendered fromtidytree.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2021-05-22
Started: 2017-12-07

Readme and manuals

Help Manual

Help pageTopics
ancestorancestor ancestor.tbl_tree
as.treedataas.treedata as.treedata.tbl_tree
as.ultrametricas.ultrametric
childchild child.tbl_tree
drop.tip methoddrop.tip drop.tip,phylo drop.tip,phylo-method drop.tip,treedata drop.tip,treedata-method keep.tip keep.tip,phylo-method keep.tip,treedata-method
get_tree_dataget_tree_data
get.data methodget.data get.data,treedata-method
get.fields methodget.fields get.fields,treedata get.fields,treedata-method
get.treetext methodget.treetext get.treetext,treedata-method
getNodeNumgetNodeNum
groupCladegroupClade
groupOTUgroupOTU
isTipisTip isTip.phylo isTip.tbl_tree isTip.treedata
MRCAMRCA
NnodeNnode.treedata
extract the node label of phylo, treedata or tbl_treenode.label
nodeidnodeid
nodelabnodelab
offspringoffspring offspring.tbl_tree
parentparent parent.tbl_tree
rootroot.treedata
rootnoderootnode
show methodshow
siblingsibling
the tip or internal node label assign of tbl_tree phylo and treedatanode.label<- node.label<-.phylo node.label<-.tbl_tree node.label<-.treedata td-label-assign tip.label<- tip.label<-.phylo tip.label<-.tbl_tree tip.label<-.treedata
extract the tip label of phylo treedata or tbl_treetip.label
Subset tree objects by related nodestree_subset tree_subset.phylo tree_subset.treedata
treedatatreedata
Class "treedata" This class stores phylogenetic tree with associated datashow,treedata-method treedata-class