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:
tidytree_0.4.6.002.tar.gz
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tidytree.pdf |tidytree.html✨
tidytree/json (API)
NEWS
| # Install 'tidytree' in R: |
| install.packages('tidytree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/tidytree/issues
phylogenetic-treetidyversetree-data
Last updated 5 months agofrom:1115d91fe1. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 27 2024 |
| R-4.5-win | OK | Nov 27 2024 |
| R-4.5-linux | OK | Nov 27 2024 |
| R-4.4-win | OK | Nov 27 2024 |
| R-4.4-mac | OK | Nov 27 2024 |
| R-4.3-win | OK | Nov 27 2024 |
| R-4.3-mac | OK | Nov 27 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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ancestor | ancestor ancestor.tbl_tree |
| as.treedata | as.treedata as.treedata.tbl_tree |
| as.ultrametric | as.ultrametric |
| child | child child.tbl_tree |
| drop.tip method | drop.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_data | get_tree_data |
| get.data method | get.data get.data,treedata-method |
| get.fields method | get.fields get.fields,treedata get.fields,treedata-method |
| get.treetext method | get.treetext get.treetext,treedata-method |
| getNodeNum | getNodeNum |
| groupClade | groupClade |
| groupOTU | groupOTU |
| isTip | isTip isTip.phylo isTip.tbl_tree isTip.treedata |
| MRCA | MRCA |
| Nnode | Nnode.treedata |
| extract the node label of phylo, treedata or tbl_tree | node.label |
| nodeid | nodeid |
| nodelab | nodelab |
| offspring | offspring offspring.tbl_tree |
| parent | parent parent.tbl_tree |
| root | root.treedata |
| rootnode | rootnode |
| show method | show |
| sibling | sibling |
| the tip or internal node label assign of tbl_tree phylo and treedata | node.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_tree | tip.label |
| Subset tree objects by related nodes | tree_subset tree_subset.phylo tree_subset.treedata |
| treedata | treedata |
| Class "treedata" This class stores phylogenetic tree with associated data | show,treedata-method treedata-class |
