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phylobase

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About this package

phylobase provides classes and methods to easily associate, manipulate, explore, and plot phylogenetic trees and data about the species they include. The goal of this package is to provide a base set of tools likely to be shared by all packages designed for phylogenetic analysis. This standardization will benefit both end-users by allowing them to move results across packages and keep data associated with the phylogenetic trees; and developers by focusing on method development instead of having to rewrite the base functions.

  • Authors: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O’Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
  • Maintainer: Francois Michonneau
  • Licence: GPL (>= 2)
  • Issues, bug reports, feature requests, discussion: https://github.com/fmichonneau/phylobase/issues

Installation

Stable version

The stable version (the minor and patch version numbers are even, e.g., 0.6.8) can be downloaded from CRAN.

install.packages("phylobase")

Development version

The development version (the patch version number is odd, e.g., 0.6.9) is available on GitHub (https://github.com/fmichonneau/phylobase), and can be installed using the devtools package.

pak::install_github("fmichonneau/phylobase")
library(phylobase)

Getting started

phylobase comes with example data sets geospiza and geospiza_raw.

  • geospiza is a phylo4d object (the phylobase class that holds together a phylogenetic tree and associated data, the phylo4 class is for phylogenetic trees only).
  • geospiza_raw is a list that contains the tree geospiza_raw$tree (as an ape::phylo object) and the data geospiza_raw$data (as a data.frame) that were used to build the geospiza object.

Now we’ll take the data from and merge it with the tree. However, since is included in the tree but not in the data set, we will initially run into some trouble:

data(geospiza_raw)
g1 <- as(geospiza_raw$tree, "phylo4")
geodata <- geospiza_raw$data
g2 <- phylo4d(g1, geodata)
#> Error in formatData(phy = x, dt = tip.data, type = "tip", ...): The following nodes are not found in the dataset:  olivacea

To deal with G. olivacea missing from the data, we have a few choices. The easiest is to use missing.data="warn" to allow R to create the new object with a warning (you can also use missing.data="OK" to proceed without warnings):

g2 <- phylo4d(g1, geodata, missing.data="warn")
#> Warning in formatData(phy = x, dt = tip.data, type = "tip", ...): The following
#> nodes are not found in the dataset: olivacea
head(g2)
#>           label node ancestor edge.length node.type    wingL  tarsusL  culmenL
#> 1    fuliginosa    1       24     0.05500       tip 4.132957 2.806514 2.094971
#> 2        fortis    2       24     0.05500       tip 4.244008 2.894717 2.407025
#> 3  magnirostris    3       23     0.11000       tip 4.404200 3.038950 2.724667
#> 4   conirostris    4       22     0.18333       tip 4.349867 2.984200 2.654400
#> 5      scandens    5       21     0.19250       tip 4.261222 2.929033 2.621789
#> 6    difficilis    6       20     0.22800       tip 4.224067 2.898917 2.277183
#> 7       pallida    7       25     0.08667       tip 4.265425 3.089450 2.430250
#> 8      parvulus    8       27     0.02000       tip 4.131600 2.973060 1.974420
#> 9    psittacula    9       27     0.02000       tip 4.235020 3.049120 2.259640
#> 10       pauper   10       26     0.03500       tip 4.232500 3.035900 2.187000
#> 11   Platyspiza   11       18     0.46550       tip 4.419686 3.270543 2.331471
#> 12        fusca   12       17     0.53409       tip 3.975393 2.936536 2.051843
#> 13 Pinaroloxias   13       16     0.58333       tip 4.188600 2.980200 2.311100
#> 14     olivacea   14       15     0.88077       tip       NA       NA       NA
#> 15         <NA>   15        0          NA      root       NA       NA       NA
#> 16         <NA>   16       15     0.29744  internal       NA       NA       NA
#> 17         <NA>   17       16     0.04924  internal       NA       NA       NA
#> 18         <NA>   18       17     0.06859  internal       NA       NA       NA
#> 19         <NA>   19       18     0.13404  internal       NA       NA       NA
#> 20         <NA>   20       19     0.10346  internal       NA       NA       NA
#>       beakD   gonysW
#> 1  1.941157 1.845379
#> 2  2.362658 2.221867
#> 3  2.823767 2.675983
#> 4  2.513800 2.360167
#> 5  2.144700 2.036944
#> 6  2.011100 1.929983
#> 7  2.016350 1.949125
#> 8  1.873540 1.813340
#> 9  2.230040 2.073940
#> 10 2.073400 1.962100
#> 11 2.347471 2.282443
#> 12 1.191264 1.401186
#> 13 1.547500 1.630100
#> 14       NA       NA
#> 15       NA       NA
#> 16       NA       NA
#> 17       NA       NA
#> 18       NA       NA
#> 19       NA       NA
#> 20       NA       NA

Importing data

From NEXUS files

phylobase has a robust parser for NEXUS files (it uses the NEXUS Class Library from Paul Lewis and Mark Holder, NCL). It can be used to import simultaneously tree and species data.

myrmeFile <- system.file("nexusfiles/treeWithDiscreteData.nex", package="phylobase")
myrme <- readNexus(file=myrmeFile)
head(myrme)
#>                      label node ancestor edge.length node.type        time
#> 1   Myrmecocystussemirufus    1       27    1.724765       tip     diurnal
#> 2   Myrmecocystusplacodops    2       27    1.724765       tip     diurnal
#> 3      Myrmecocystusmendax    3       26    4.650818       tip     diurnal
#> 4    Myrmecocystuskathjuli    4       28    1.083870       tip     diurnal
#> 5    Myrmecocystuswheeleri    5       28    1.083870       tip     diurnal
#> 6     Myrmecocystusmimicus    6       30    2.708942       tip     diurnal
#> 7     Myrmecocystusdepilis    7       30    2.708942       tip     diurnal
#> 8    Myrmecocystusromainei    8       32    2.193845       tip     diurnal
#> 9  Myrmecocystusnequazcatl    9       32    2.193845       tip     diurnal
#> 10       Myrmecocystusyuma   10       31    4.451425       tip crepuscular
#> 11   Myrmecocystuskennedyi   11       23    6.044804       tip     diurnal
#> 12 Myrmecocystuscreightoni   12       22   10.569191       tip crepuscular
#> 13  Myrmecocystussnellingi   13       33    2.770378       tip crepuscular
#> 14 Myrmecocystustenuinodis   14       33    2.770378       tip crepuscular
#> 15  Myrmecocystustestaceus   15       20   12.300701       tip crepuscular
#> 16  Myrmecocystusmexicanus   16       34    5.724923       tip   nocturnal
#> 17   Myrmecocystuscfnavajo   17       35    2.869547       tip   nocturnal
#> 18     Myrmecocystusnavajo   18       35    2.869547       tip   nocturnal
#> 19                    <NA>   19        0          NA      root        <NA>
#> 20                    <NA>   20       19    1.699299  internal        <NA>
#>         subgenus
#> 1   Endiodioctes
#> 2   Endiodioctes
#> 3   Endiodioctes
#> 4   Endiodioctes
#> 5   Endiodioctes
#> 6   Endiodioctes
#> 7   Endiodioctes
#> 8   Endiodioctes
#> 9   Endiodioctes
#> 10  Eremnocystus
#> 11  Endiodioctes
#> 12  Eremnocystus
#> 13  Eremnocystus
#> 14  Eremnocystus
#> 15 Myrmecocystus
#> 16 Myrmecocystus
#> 17 Myrmecocystus
#> 18 Myrmecocystus
#> 19          <NA>
#> 20          <NA>

From NeXML

library(RNeXML)
#> Loading required package: ape
#> 
#> Attaching package: 'ape'
#> The following object is masked from 'package:phylobase':
#> 
#>     edges
nxmlFile <- system.file("nexmlfiles/comp_analysis.xml", package="phylobase")
nxml <- nexml_read(nxmlFile)
nxmlEx <- phylo4(nxml)

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Install

install.packages('phylobase')

Monthly Downloads

3,618

Version

0.8.12

License

GPL (>= 2)

Issues

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Stars

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Last Published

January 30th, 2024

Functions in phylobase (0.8.12)

ancestor

Tree traversal and utility functions
geospiza

Data from Darwin's finches
getNode

Node and Edge look-up functions
owls4

'Owls' data from ape
nTips

nTips, nNodes, nEdges
pdata-class

Class "pdata"
nodeId

nodeId methods
checkPhylo4

Validity checking for phylo4 objects
print

print a phylogeny
phylo4d-class

phylo4d class
phylo4d-methods

Combine a phylogenetic tree with data
Import Nexus and Newick files

Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file
treePlot-methods

Phylogeny plotting
hasEdgeLength

edgeLength methods
extractTree

Get tree from tree+data object
formatData

Format data for use in phylo4d objects
phylobase.options

Set or return options of phylobase
edges

Edges accessors
MRCA

MRCA
hasSingle

Test trees for polytomies, inline nodes (singletons), or reticulation
phylo4-labels

Labels for phylo4/phylo4d objects
addData

Adding data to a phylo4 or a phylo4d object
phylo4-methods

Create a phylogenetic tree
multiPhylo-class

multiPhylo4 and extended classes
hasTipData

Tests for presence of data associated with trees stored as phylo4d objects
phylobubbles

Bubble plots for phylo4d objects
pdata

Constructor for pdata (phylogenetic data) class
phyloXXYY

Calculate node x and y coordinates
phylobase-package

Utilities and Tools for Phylogenetics
phylo4-class

The phylo4 class
reorder-methods

reordering trees within phylobase objects
isRooted

Methods to test, access (and modify) the root of a phylo4 object.
phylomat-class

matrix classes for phylobase
tdata

Retrieving or updating tip and node data in phylo4d objects
tip.data.plot

Plotting trees and associated data
plotOneTree

Plot a phylo4 object
subset-methods

Methods for creating subsets of phylogenies
setAs

Converting between phylo4/phylo4d and other phylogenetic tree formats
shortestPath

shortestPath-methods
summary-methods

Summary for phylo4/phylo4d objects