Function for extract a named vector from an object of class treedata.table

This function extracts a named vector for any trait from an object of class treedata.table.

# S3 method for treedata.table
[[(x, ..., exact = TRUE)

Arguments

x	An object of class `treedata.table`
...	Column name in class `character`
exact	whether exact search should be conducted

Value

A new object of class vector with names set to labels corresponding to tip labels in the provided treedata.table object.

Examples

data(anolis)
# With a phylo object
td <- as.treedata.table(anolis$phy, anolis$dat)
#> Tip labels detected in column: X
#> Phylo object detected 
#> All tips from original tree/dataset were preserved
td[["SVL"]]
#>            ahli         allogus     rubribarbus           imias          sagrei 
#>        4.039125        4.040138        4.078469        4.099687        4.067162 
#>         bremeri quadriocellifer      ophiolepis         mestrei           jubar 
#>        4.113371        3.901619        3.637962        3.987147        3.952605 
#>      homolechis        confusus           guafe         garmani        opalinus 
#>        4.032806        3.938442        3.877457        4.769473        3.838376 
#>         grahami     valencienni      lineatopus      reconditus       evermanni 
#>        4.154274        4.321524        4.128612        4.482607        4.165605 
#>       stratulus           krugi      pulchellus       gundlachi       poncensis 
#>        3.869881        3.886500        3.799022        4.188105        3.820378 
#>           cooki    cristatellus    brevirostris        caudalis          marron 
#>        4.091535        4.189820        3.874155        3.911743        3.831810 
#>        websteri       distichus        barbouri         alumina    semilineatus 
#>        3.916546        3.928796        3.663932        3.588941        3.696631 
#>         olssoni      etheridgei         fowleri       insolitus       whitemani 
#>        3.793899        3.657991        4.288780        3.800471        4.097479 
#>       haetianus        breslini         armouri         cybotes         shrevei 
#>        4.316542        4.051111        4.121684        4.210982        3.983003 
#>   longitibialis         strahmi        marcanoi        baleatus       barahonae 
#>        4.242103        4.274271        4.079485        5.053056        5.076958 
#>        ricordii   eugenegrahami     christophei         cuvieri        barbatus 
#>        5.013963        4.128504        3.884652        4.875012        5.003946 
#>          porcus  chamaeleonides       guamuhaya   altitudinalis        oporinus 
#>        5.038034        5.042349        5.036953        3.842994        3.845670 
#>        isolepis        allisoni        porcatus     argillaceus       centralis 
#>        3.657088        4.375390        4.258991        3.757869        3.697941 
#>         pumilis        loysiana         guazuma        placidus        sheplani 
#>        3.466860        3.701240        3.763884        3.773967        3.682924 
#>         alayoni     angusticeps        paternus       alutaceus    inexpectatus 
#>        3.815705        3.788595        3.802961        3.554891        3.537439 
#>       clivicola    cupeyalensis    cyanopleurus         alfaroi      macilentus 
#>        3.758726        3.462014        3.630161        3.526655        3.715765 
#>       vanidicus     argenteolus          lucius        bartschi    vermiculatus 
#>        3.626206        3.971307        4.198915        4.280547        4.802849 
#>        baracoae          noblei      smallwoodi    luteogularis       equestris 
#>        5.042780        5.083473        5.035096        5.101085        5.113994 
#>       monticola   bahorucoensis dolichocephalus      hendersoni     darlingtoni 
#>        3.770613        3.827445        3.908550        3.859835        4.302036 
#>        aliniger      singularis    chlorocyanus     coelestinus        occultus 
#>        4.036557        4.057997        4.275448        4.297965        3.663049 

# With a multiPhylo object
treesFM <- list(anolis$phy, anolis$phy)
class(treesFM) <- "multiPhylo"
td <- as.treedata.table(treesFM, anolis$dat)
#> Tip labels detected in column: X
#> Multiphylo object detected 
#> All tips from original tree/dataset were preserved
td[["SVL"]]
#>            ahli         allogus     rubribarbus           imias          sagrei 
#>        4.039125        4.040138        4.078469        4.099687        4.067162 
#>         bremeri quadriocellifer      ophiolepis         mestrei           jubar 
#>        4.113371        3.901619        3.637962        3.987147        3.952605 
#>      homolechis        confusus           guafe         garmani        opalinus 
#>        4.032806        3.938442        3.877457        4.769473        3.838376 
#>         grahami     valencienni      lineatopus      reconditus       evermanni 
#>        4.154274        4.321524        4.128612        4.482607        4.165605 
#>       stratulus           krugi      pulchellus       gundlachi       poncensis 
#>        3.869881        3.886500        3.799022        4.188105        3.820378 
#>           cooki    cristatellus    brevirostris        caudalis          marron 
#>        4.091535        4.189820        3.874155        3.911743        3.831810 
#>        websteri       distichus        barbouri         alumina    semilineatus 
#>        3.916546        3.928796        3.663932        3.588941        3.696631 
#>         olssoni      etheridgei         fowleri       insolitus       whitemani 
#>        3.793899        3.657991        4.288780        3.800471        4.097479 
#>       haetianus        breslini         armouri         cybotes         shrevei 
#>        4.316542        4.051111        4.121684        4.210982        3.983003 
#>   longitibialis         strahmi        marcanoi        baleatus       barahonae 
#>        4.242103        4.274271        4.079485        5.053056        5.076958 
#>        ricordii   eugenegrahami     christophei         cuvieri        barbatus 
#>        5.013963        4.128504        3.884652        4.875012        5.003946 
#>          porcus  chamaeleonides       guamuhaya   altitudinalis        oporinus 
#>        5.038034        5.042349        5.036953        3.842994        3.845670 
#>        isolepis        allisoni        porcatus     argillaceus       centralis 
#>        3.657088        4.375390        4.258991        3.757869        3.697941 
#>         pumilis        loysiana         guazuma        placidus        sheplani 
#>        3.466860        3.701240        3.763884        3.773967        3.682924 
#>         alayoni     angusticeps        paternus       alutaceus    inexpectatus 
#>        3.815705        3.788595        3.802961        3.554891        3.537439 
#>       clivicola    cupeyalensis    cyanopleurus         alfaroi      macilentus 
#>        3.758726        3.462014        3.630161        3.526655        3.715765 
#>       vanidicus     argenteolus          lucius        bartschi    vermiculatus 
#>        3.626206        3.971307        4.198915        4.280547        4.802849 
#>        baracoae          noblei      smallwoodi    luteogularis       equestris 
#>        5.042780        5.083473        5.035096        5.101085        5.113994 
#>       monticola   bahorucoensis dolichocephalus      hendersoni     darlingtoni 
#>        3.770613        3.827445        3.908550        3.859835        4.302036 
#>        aliniger      singularis    chlorocyanus     coelestinus        occultus 
#>        4.036557        4.057997        4.275448        4.297965        3.663049

Function for extract a named vector from an object of class `treedata.table`

Arguments

Value

See also

Examples