treeman v1.1.4
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Phylogenetic Tree Manipulation Class and Methods
S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
Readme
treeman
An R package for manipulating phylogentic trees using an intuitive S4 class structure.
The treeman R package provides a list based class for encoding phylogenetic trees in R, making manipulating phylogenetic trees easier to code and more efficient to run. treeman is aimed to be fast, simple and intuitive.
Installation
With CRAN:
install.packages('treeman')
Installing the development copy via GitHub
library(devtools)
install_github('dombennett/treeman')
Quick guide
# working with the TreeMan class
library(treeman)
?TreeMan # check the documentation
tree <- randTree(10) # generate a random tree of 10 tips
summary(tree) # check key stats
tree["tips"] # extract key stats
For more details check out the wiki.
Licence
GPL-2
Status
Version 1.1 released.
Reference
Bennett, D.J., Sutton, M.D. & Turvey, S.T., 2017. treeman: an R package for efficient and intuitive manipulation of phylogenetic trees. BMC Research Notes, 10(1), p.30. Available online
Author
D.J. Bennett (but I welcome pull requests!)
Functions in treeman
| Name | Description | |
| TreeMan-to-phylo | Convert TreeMan to phylo | |
| addTip | Add tip to a tree | |
| Node-class | Node-class | |
| TreeMen-to-multiPhylo | Convert TreeMen to multiPhylo | |
| birds | Phylogenetic tree of Aves | |
| TreeMen-class | TreeMen-class | |
| TreeMan-class | TreeMan-class | |
| addClade | Add clade to tree | |
| blncdTree | Generate a balanced tree | |
| addNdmtrx | Add node matrix to a tree | |
| cTrees | cTrees | |
| getLvng | Get extant tips from a tree | |
| calcPhyDv | Calculate phylogenetic diversity | |
| getDcsd | Get extinct tips from a tree | |
| getNdSlt | Get a node slot | |
| getCnnctdNds | Get all nodes connected by given tips | |
| calcOvrlp | Calculate phylogenetic overlap | |
| calcDstBLD | Calculate the BLD between two trees | |
| getNdPrids | Get pre-nodes to root | |
| getNdAge | Get age | |
| calcDstMtrx | Calculate the distance matrix | |
| getNdsSlt | Get a node slot for multiple nodes | |
| getNdPtids | Get post-nodes to tips | |
| getNdsSstr | Get sister id | |
| calcDstTrp | Calculate the triplet distance between two trees | |
| calcPrtFrPrp | Calculate evolutionary distinctness for part of tree | |
| getPath | Get path between nodes | |
| calcNdsBlnc | Calculate the balances of all nodes | |
| calcNdBlnc | Calculate the balance of a node | |
| getOtgrp | Get outgroup | |
| checkNdlst | Check if ndlst is correct | |
| getNdsAge | Get ages for multiple nodes | |
| getNdsFrmTxnyms | Get IDs for nodes represented txnyms | |
| getNdsKids | Get children IDs for multiple nodes | |
| calcFrPrp | Calculate evolutionary distinctness | |
| getNdSstr | Get sister id | |
| multiPhylo-to-TreeMen | Convert multiPhylo to TreeMen | |
| getUnqNds | Get unique nodes represented by tips | |
| writeTrmn | Write a .trmn tree | |
| checkTreeMen | Check if trees are correct | |
| saveTreeMan | Save a TreeMan object in serialization format | |
| phylo-class | phylo class | |
| calcDstRF | Calculate the Robinson-Foulds distance between two trees | |
| fastCheckTreeMan | Check if tree is correct, fast! | |
| searchTxnyms | Get node labels based on online taxonomic database | |
| getNdKids | Get children IDs | |
| isUltrmtrc | Is tree ultrametric? | |
| list-to-TreeMen | Convert list to a TreeMen | |
| getNdPD | Get phylogenetic diversity of node | |
| getNdPrdst | Get pre-distance | |
| loadTreeMan | Load a TreeMan object in serialization format | |
| getBiprts | Get the sets of labels for each bipartition in tree | |
| phylo-to-TreeMan | Convert phylo to TreeMan | |
| rmNdmtrx | Remove node matrix | |
| pinTips | Pin tips to a tree | |
| getAge | Get age of tree | |
| getNdLng | Get lineage | |
| setAge | Set the age of a tree | |
| getNdsPtids | Get post-nodes to tips for multiple nodes | |
| getSpnAge | Get age range | |
| getNdsPrids | Get pre-nodes for multiple nodes | |
| getPrnt | Get parent | |
| getSubtree | Get subtree | |
| getNdsPrdst | Get pre-distances | |
| getSpnsAge | Get age ranges for multiple nodes | |
| getNdsPD | Get phylogenetic diversities of nodes | |
| setNdID | Set the ID of a node | |
| getNdsLng | Get lineage for multiple nodes | |
| readTrmn | Read a .trmn tree | |
| plants | Phylogenetic tree of European Flora | |
| pstMnp | Update prinds and tinds | |
| rmClade | Remove a clade from a tree | |
| mammals | Phylogenetic tree of Mammalia | |
| setNdsSpn | Set the branch lengths of specific nodes | |
| setPD | Set the phylogenetic diversity | |
| rmNodes | Remove nodes from a tree | |
| treeman-package | Phylogenetic Tree Manipulation | |
| updateSlts | Update tree slots after manipulation | |
| twoer | Generate a tree of two tips | |
| setNdsID | Set the IDs of multiple nodes | |
| setNdsOther | Set a user defined slot for multiple nodes | |
| writeTree | Write a Newick tree | |
| multiPhylo-class | multiPhylo class | |
| unblncdTree | Generate an unbalanced tree | |
| setNdSpn | Set the branch length of a specific node | |
| ultrTree | Make tree ultrametric | |
| setNdOther | Set a user defined slot | |
| rmOtherSlt | Remove a user-defined slot | |
| randTree | Generate a random tree | |
| rmTips | Remove tips from a tree | |
| readTree | Read a Newick tree | |
| setTxnyms | Set the txnym slots in a tree | |
| taxaResolve | Resolve taxonmic names online | |
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Details
| Type | Package |
| License | GPL-2 |
| RoxygenNote | 7.0.2 |
| Collate | 'calc-methods.R' 'check_methods.R' 'cnvrt-methods.R' 'gen-methods.R' 'get-nd-methods.R' 'get-nds-methods.R' 'get-spcl-methods.R' 'manip-methods.R' 'ndlst-methods.R' 'ndmtrx-methods.R' 'node-declaration.R' 'read-write-methods.R' 'server-methods.R' 'set-methods.R' 'treeman-declaration.R' 'treemen-declaration.R' 'update-methods.R' 'viz-methods.R' 'zzz.R' |
| NeedsCompilation | yes |
| Packaged | 2020-05-26 17:31:36 UTC; domben |
| Repository | CRAN |
| Date/Publication | 2020-05-26 22:40:02 UTC |
| imports | ape , bigmemory , plyr , RJSONIO , stringr |
| depends | methods , R (>= 3.2.4) |
| suggests | testthat |
| Contributors | D.J. Bennett |
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