Function for extract a named vector from an object of class treedata.table
Source: R/treedata.table.R
sub-sub-.treedata.table.RdThis function extracts a named vector for any trait from an object of class
treedata.table.
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