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