Package tidytree. June 13, 2018
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1 Package tidytree June 13, 2018 Title A Tidy Tool for Phylogenetic Tree Data Manipulation Version 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. Depends R (>= 3.4.0) Imports ape, dplyr, lazyeval, magrittr, methods, tibble Suggests ggtree, knitr, prettydoc, testthat, treeio VignetteBuilder knitr ByteCompile true License Artistic-2.0 URL BugReports Encoding UTF-8 LazyData true RoxygenNote NeedsCompilation no Author Guangchuang Yu [aut, cre, cph] (< Bradley Jones [ctb], Zebulun Arendsee [ctb] Maintainer Guangchuang Yu <guangchuangyu@gmail.com> Repository CRAN Date/Publication :59:50 UTC R topics documented: ancestor as.treedata
2 2 ancestor child get get.fields get_tree_data groupclade groupotu MRCA offspring parent rootnode show sibling treedata treedata-class Index 13 ancestor ancestor access ancestor data ancestor(,.node,...) ## S3 method for class 'tbl_tree' ancestor(,.node,...).node node number ancestor data
3 as.treedata 3 Examples library(ape) tree <- rtree(4) x <- as_data_frame(tree) ancestor(x, 3) as.treedata as.treedata convert a tree object to treedata object as.treedata(tree,...) ## S3 method for class 'tbl_tree' as.treedata(tree,...) tree tree object treedata object Examples library(ape) set.seed(2017) tree <- rtree(4) d <- tibble(label = paste0('t', 1:4), trait = rnorm(4)) x <- as_data_frame(tree) full_join(x, d, by = 'label') %>% as.treedata
4 4 get child child access child data child(,.node,...) ## S3 method for class 'tbl_tree' child(,.node,...).node node number child data Examples library(ape) tree <- rtree(4) x <- as_data_frame(tree) child(x, 4) get get method get method
5 get.fields 5 get(object,...) ## S4 method for signature 'treedata' get(object) object treedata object... additional parameter associated data of phylogeny get.fields get.fields method get.fields method get.fields(object,...) ## S4 method for signature 'treedata' get.fields(object) object treedata object... additional parameter available annotation variables
6 6 groupclade get_tree_data get_tree_data get associated data stored in treedata object get_tree_data(tree_object) tree_object a treedata object tbl_df groupclade groupclade grouping clades groupclade(,.node,...) tree object (phylo, treedata, tbl_tree, ggtree etc.).node selected nodes... additional parameter updated tree with group information or group index Guangchuang Yu
7 groupotu 7 groupotu groupotu grouping OTUs groupotu(,.node,...) tree object (phylo, treedata, tbl_tree, ggtree etc.).node selected nodes... additional parameter updated tree with group information or group index MRCA MRCA access most recent common ancestor data MRCA(,...) MRCA data
8 8 parent offspring offspring access offspring data offspring(,.node,...) ## S3 method for class 'tbl_tree' offspring(,.node,...).node node number offspring data Examples library(ape) tree <- rtree(4) x <- as_data_frame(tree) offspring(x, 4) parent parent access parent data
9 rootnode 9 parent(,.node,...) ## S3 method for class 'tbl_tree' parent(,.node,...).node node number parent data Examples library(ape) tree <- rtree(4) x <- as_data_frame(tree) parent(x, 2) rootnode rootnode access root node data rootnode(,...) root node data
10 10 sibling show show method show method for treedata instance show(object) object treedata object print info Guangchuang Yu sibling sibling access sibling data sibling(,...) sibling
11 treedata 11 treedata treedata treedata object contructor treedata(...)... parameters treedata object treedata-class Class "treedata" This class stores phylogenetic tree with associated data Class "treedata" This class stores phylogenetic tree with associated data Slots file tree file treetext newick tree string phylo phylo object for tree structure data associated data extrainfo extra information, reserve for merge_tree tip_seq tip sequences anc_seq ancestral sequences seq_type sequence type, one of NT or AA tipseq_file tip sequence file ancseq_file ancestral sequence file info extra information, e.g. metadata, software version etc.
12 12 treedata-class
13 Index Topic classes treedata-class, 11 ancestor, 2 as.treedata, 3 child, 4 get, 4 get,treedata-method (get), 4 get.fields, 5 get.fields,treedata-method (get.fields), 5 get_tree_data, 6 groupclade, 6 groupotu, 7 MRCA, 7 offspring, 8 parent, 8 rootnode, 9 show, 10 show,treedata-method (treedata-class), 11 sibling, 10 treedata, 11 treedata-class, 11 13
Package treeio. April 1, 2018
Package treeio April 1, 2018 Title Base Classes and Functions for Phylogenetic Tree Input and Output Version 1.3.13 Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports
Package treeio. January 1, 2019
Package treeio January 1, 2019 Title Base Classes and Functions for Phylogenetic Tree Input and Output Version 1.7.2 Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports
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