phylobase

[[codecov.io][(https://app.codecov.io/github/fmichonneau/phylobase?branch=master)](https://app.codecov.io/github/fmichonneau/phylobase?branch=master)

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)