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Returns the character matrix or phylogeny from a treedata.table object

Usage

pulltreedata.table(tdObject, type = c("dat", "phy"))

Arguments

tdObject

A treedata.table object

type

Whether the output of the function is a tree ('type="phylo"') or a data.table ('type="dat"')

Value

A data.table or phylo object from the original treedata.table object

Examples

data(anolis)
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
pulltreedata.table(td, type = "phy")
#> 
#> Phylogenetic tree with 100 tips and 99 internal nodes.
#> 
#> Tip labels:
#>   ahli, allogus, rubribarbus, imias, sagrei, bremeri, ...
#> 
#> Rooted; includes branch lengths.
pulltreedata.table(td, type = "dat")
#>            tip.label      SVL   PCI_limbs   PCII_head PCIII_padwidth_vs_tail
#>               <char>    <num>       <num>       <num>                  <num>
#>   1:            ahli 4.039125 -3.24828599  0.37225191             -1.0422187
#>   2:         allogus 4.040138 -2.84557021  0.60011341             -1.0253056
#>   3:     rubribarbus 4.078469 -2.23834859  1.11997785             -1.1929572
#>   4:           imias 4.099687 -3.04891725  2.33203488              0.1616442
#>   5:          sagrei 4.067162 -1.74105547  2.02282431              0.1693635
#>   6:         bremeri 4.113371 -1.81361138  2.60675012              0.6399320
#>   7: quadriocellifer 3.901619 -2.26789400  0.99092075              0.3553405
#>   8:      ophiolepis 3.637962  0.79151174  1.45857603             -1.3152005
#>   9:         mestrei 3.987147 -2.60261906  1.27568612              0.4640379
#>  10:           jubar 3.952605 -2.22414593  0.94489985              0.6600716
#>  11:      homolechis 4.032806 -2.74499346  0.87926009              0.8679694
#>  12:        confusus 3.938442 -2.49591732  0.16823269              0.1551290
#>  13:           guafe 3.877457 -2.61408710  0.65608676              0.6071245
#>  14:         garmani 4.769473 -0.77352640  0.93712494              0.2594994
#>  15:        opalinus 3.838376 -1.77943710 -0.32453812              1.5569939
#>  16:         grahami 4.154274 -2.30565354 -1.91393689              1.6852579
#>  17:     valencienni 4.321524  2.94241389 -0.88460072              1.8543308
#>  18:      lineatopus 4.128612 -2.43081291 -3.12552390             -1.7564495
#>  19:      reconditus 4.482607 -2.72704156 -0.21040657             -2.3534242
#>  20:       evermanni 4.165605 -2.52899245  0.12548098              1.8824633
#>  21:       stratulus 3.869881 -1.62264165 -0.52957490              2.2166952
#>  22:           krugi 3.886500 -1.68879533 -0.83128181             -1.2588892
#>  23:      pulchellus 3.799022  0.16238151 -2.33846103             -1.5906715
#>  24:       gundlachi 4.188105 -2.64936274 -0.56251604             -2.2852265
#>  25:       poncensis 3.820378  0.52782664  1.24062035             -1.6249761
#>  26:           cooki 4.091535 -2.22079009  0.05979850             -0.1092647
#>  27:    cristatellus 4.189820 -3.33026331 -0.62225189              1.2175309
#>  28:    brevirostris 3.874155 -3.28900081  1.38425488              2.4070756
#>  29:        caudalis 3.911743 -1.78270839  1.90870776              1.7530966
#>  30:          marron 3.831810 -2.84709341 -0.12032028              1.6898101
#>  31:        websteri 3.916546 -2.50870054  0.97482786              2.9024438
#>  32:       distichus 3.928796 -3.84343343  0.83890749              2.4922170
#>  33:        barbouri 3.663932 -0.87536237  1.34009434             -2.6138245
#>  34:         alumina 3.588941  0.72166993  1.52514444             -2.6721669
#>  35:    semilineatus 3.696631  0.18403236 -0.13872022             -2.8957227
#>  36:         olssoni 3.793899  0.81682668  3.87442813             -2.4337310
#>  37:      etheridgei 3.657991 -3.81065955 -0.75340900             -2.0659201
#>  38:         fowleri 4.288780 -1.03667003  1.50383762             -1.7589251
#>  39:       insolitus 3.800471  5.03062671  0.24137669              0.9139707
#>  40:       whitemani 4.097479 -2.54584901 -3.25974024             -1.9200701
#>  41:       haetianus 4.316542 -3.40402925 -3.78444664             -1.7798344
#>  42:        breslini 4.051111 -2.97497529 -3.34153375             -1.8978249
#>  43:         armouri 4.121684 -3.16993598 -4.08620441             -0.8883209
#>  44:         cybotes 4.210982 -3.11637922 -2.99620854             -0.8299057
#>  45:         shrevei 3.983003 -2.25952607 -3.55788235             -1.3884348
#>  46:   longitibialis 4.242103 -3.52243048 -1.61670439             -1.6182845
#>  47:         strahmi 4.274271 -3.87340303 -1.01635836             -0.9366696
#>  48:        marcanoi 4.079485 -2.84448243 -2.78644148             -0.8020303
#>  49:        baleatus 5.053056  0.73766495  1.79646028             -0.5409516
#>  50:       barahonae 5.076958  0.90731040  2.33222342             -0.6158464
#>  51:        ricordii 5.013963  0.58940470  1.34670464             -0.8626956
#>  52:   eugenegrahami 4.128504 -4.21209140  4.83351955              1.0228151
#>  53:     christophei 3.884652 -2.70596332  1.70527559             -0.1725921
#>  54:         cuvieri 4.875012 -1.18955124 -0.71983364             -1.0167340
#>  55:        barbatus 5.003946  2.25020229 -3.30818172              1.3476390
#>  56:          porcus 5.038034  3.50614537 -2.98667964              0.7500647
#>  57:  chamaeleonides 5.042349  2.95597428 -3.69231889              1.3297304
#>  58:       guamuhaya 5.036953  3.10947396 -4.07973423             -0.1820287
#>  59:   altitudinalis 3.842994  2.86751469 -6.12805047              2.3331196
#>  60:        oporinus 3.845670  3.05888289 -2.91565342              2.2875989
#>  61:        isolepis 3.657088  3.05697642 -4.34018373              2.4409248
#>  62:        allisoni 4.375390  2.03597967 -3.74252815              0.5203703
#>  63:        porcatus 4.258991  1.93193251 -3.82953305              0.9781194
#>  64:     argillaceus 3.757869 -0.11307851 -1.48944374              2.3710815
#>  65:       centralis 3.697941  0.73073876 -0.41683597              1.7586477
#>  66:         pumilis 3.466860  0.55404946 -0.42584152              2.1572563
#>  67:        loysiana 3.701240  0.31536951 -1.08038145              2.7442074
#>  68:         guazuma 3.763884  8.16566506 -0.60605865              1.7597408
#>  69:        placidus 3.773967  7.38332866  0.53958973              2.7042981
#>  70:        sheplani 3.682924 10.27389091  2.27784409              1.6981742
#>  71:         alayoni 3.815705  3.40888624 -1.78335850              2.2084510
#>  72:     angusticeps 3.788595  4.58711071 -1.97673831              1.1594671
#>  73:        paternus 3.802961  2.90637723 -0.95846093              0.9491115
#>  74:       alutaceus 3.554891  1.17338999 -0.61493813             -1.6539883
#>  75:    inexpectatus 3.537439  2.50607244 -0.52340367             -2.8057449
#>  76:       clivicola 3.758726 -1.05114421 -0.58903393             -1.2178042
#>  77:    cupeyalensis 3.462014  2.72419698  0.48960424             -2.4795271
#>  78:    cyanopleurus 3.630161  0.43328510  0.98930100             -2.8189997
#>  79:         alfaroi 3.526655  2.58175921  0.77876335             -2.4463337
#>  80:      macilentus 3.715765  3.15177391  3.26626613             -3.7238293
#>  81:       vanidicus 3.626206  4.04436760  1.08716320             -2.4921192
#>  82:     argenteolus 3.971307 -2.92797328  2.61964493              0.9791727
#>  83:          lucius 4.198915 -4.38139803  1.25981123              2.1899604
#>  84:        bartschi 4.280547 -3.25502168  0.80565652              1.1234288
#>  85:    vermiculatus 4.802849  0.22783467  1.41411087             -1.8467441
#>  86:        baracoae 5.042780  0.76817392  0.06987127              0.1805891
#>  87:          noblei 5.083473 -0.09337994 -0.96088851              0.8905492
#>  88:      smallwoodi 5.035096 -0.13770527 -1.15140405              0.4296432
#>  89:    luteogularis 5.101085  0.39614254  0.73584435              1.0058546
#>  90:       equestris 5.113994  1.05461517  0.70720387              0.7108046
#>  91:       monticola 3.770613 -3.25118016  0.15599344             -2.2390082
#>  92:   bahorucoensis 3.827445 -0.04747332 -2.55694724             -3.0896949
#>  93: dolichocephalus 3.908550  2.60131528 -2.59530770             -4.1439327
#>  94:      hendersoni 3.859835  1.28963045 -2.06309845             -3.4656535
#>  95:     darlingtoni 4.302036  4.06703170 -1.49378979             -0.2002259
#>  96:        aliniger 4.036557  0.12323898 -1.67467041              2.3871336
#>  97:      singularis 4.057997  0.36326789 -0.95422871              1.6562154
#>  98:    chlorocyanus 4.275448  0.43906343  1.35403450              1.9531470
#>  99:     coelestinus 4.297965 -0.02721683  0.36875369              1.6364316
#> 100:        occultus 3.663049  7.92078444 -0.19013968              2.4922819
#>            tip.label      SVL   PCI_limbs   PCII_head PCIII_padwidth_vs_tail
#>      PCIV_lamella_num  awesomeness    hostility    attitude ecomorph
#>                 <num>        <num>        <num>       <num>   <char>
#>   1:      -2.41474228 -0.241651698 -0.173476906  0.64437708       TG
#>   2:      -2.46331106  0.624468879 -0.500096224  0.71289104       TG
#>   3:      -2.08743282 -0.427757376  0.480044450 -0.96742634       TG
#>   4:      -2.11260585  0.169425977 -0.410812337  0.19635800       TG
#>   5:      -1.37576941 -0.630433775  0.719312962 -1.22282764       TG
#>   6:      -1.62629939 -1.754300558  1.412718374  0.18323450       TG
#>   7:      -2.10505922 -0.257638879  0.462708058 -0.27127944       TG
#>   8:      -2.23775137  0.354418772  0.053661422 -0.09389530       GB
#>   9:      -1.19666399 -0.228920131  0.820920959 -0.73929564       TG
#>  10:      -1.65749549  2.145582200 -0.993730897  1.05775273       TG
#>  11:      -1.56665822 -0.085375433  0.092602997 -0.08130904       TG
#>  12:      -1.39796407  0.496114209 -0.544543392  1.36010631       TG
#>  13:      -1.48220834 -0.139145550 -0.310434629 -0.50480610       TG
#>  14:       0.10511495  0.167791307  0.676756002 -0.69460080       CG
#>  15:       0.93665013  1.483021624 -0.908266532  0.72613483       TC
#>  16:       1.01441926  0.410642801 -0.117462571  0.70229589       TC
#>  17:       0.12882327 -0.088370075  0.465286788 -0.56754896       TW
#>  18:      -1.43952303  0.800931449  0.170290172  0.33555714       TG
#>  19:      -0.79929053  0.260965443 -0.271697917  0.01367143        U
#>  20:       1.92392086  1.871367582 -2.029729624  1.02877511       TC
#>  21:       0.94622231 -0.314853533  0.515229477 -0.40828716       TC
#>  22:       0.24029913  0.972494741 -0.371866585  1.46109470       GB
#>  23:       0.68180888  0.978157532 -0.810754596  1.39277529       GB
#>  24:      -2.48420519 -0.426336538  0.613014449 -0.69318262       TG
#>  25:      -0.94924727 -0.289982852  0.510241609 -0.18543914       GB
#>  26:      -0.50826932  1.277956446 -1.082760383  1.37721870       TG
#>  27:      -1.21819703  0.830658098 -0.007447027  0.39061232       TG
#>  28:      -0.82666991 -1.538338585  1.633533660 -1.24247895        T
#>  29:      -1.44378878 -0.601304152  0.216500950  0.85182003        T
#>  30:      -1.57063776 -2.149486418  2.413050748 -2.14378229        T
#>  31:      -1.53259879  0.025584758  0.124044450  0.11758642        T
#>  32:      -1.03972507  1.973200862 -1.608003643  0.91461500        T
#>  33:      -4.30147185  1.788945648 -0.913725183  0.64025272        U
#>  34:       1.23487950 -1.253724344  1.308419442 -0.96110895       GB
#>  35:       0.92280509 -0.612226281  0.807322377 -0.82943161       GB
#>  36:       0.62906887 -1.391771586  1.210221860 -0.29186894       GB
#>  37:      -0.74890866  0.848149691 -0.960258609  0.18291181        U
#>  38:      -1.71914111  1.456935239 -1.448418148  0.07531334        U
#>  39:      -0.42075245  0.066715596 -0.290651288  0.07286240       TW
#>  40:      -2.41993928 -1.457775289  1.096071557 -0.87393333       TG
#>  41:      -2.20379012  0.721747833 -0.969190196  0.74101761       TG
#>  42:      -2.16718706 -1.944082859  2.147925602 -2.07465046       TG
#>  43:      -2.02129909 -0.158605136 -0.369246555 -0.26866597       TG
#>  44:      -2.09049464  0.905454434 -0.262630999  0.68467864       TG
#>  45:      -2.19082487  0.257277082  0.029600473  0.39422885       TG
#>  46:      -2.67106616  2.537213358 -1.420542767  1.71562944       TG
#>  47:      -1.57843390  0.340077411 -0.690011247  2.11135720       TG
#>  48:      -1.04842823  1.182343323 -0.167193617  0.58279004       TG
#>  49:      -0.16220546  2.727286255 -2.487661729  2.78477616       CG
#>  50:      -0.19473780  1.831370900 -1.331616706  1.70626854       CG
#>  51:       0.03516802 -0.456651495  0.663302028 -0.64625837       CG
#>  52:       1.66539278  2.155800992 -2.494661307  1.11438687        U
#>  53:       0.64693336 -0.266699615  0.220410336  1.46547483        U
#>  54:      -0.02153073 -0.115917120  0.281153377 -0.97876663       CG
#>  55:      -1.64780456  2.156287540 -2.094147109  1.97196598        U
#>  56:      -1.19909229  0.158971414 -0.350187677  0.45987065        U
#>  57:      -1.51973745 -1.193993760  1.858148718 -1.43308743        U
#>  58:      -0.10748930 -0.137962568  0.119982369  0.04203987        U
#>  59:       0.68195498  1.164592168 -0.865462260  0.63326685       TC
#>  60:      -0.08659903  0.573048475 -0.985921965  0.88025286       TC
#>  61:      -0.07418779 -0.194644197  0.001671326  0.16264659       TC
#>  62:       2.05565172 -0.132309870  0.464556617 -0.54956842       TC
#>  63:       2.88538479 -0.074646660  0.148259194 -0.57178426       TC
#>  64:       0.33264142  0.007554828 -0.259421287 -0.62559912        U
#>  65:      -1.13869021 -0.620236225  0.330225203 -0.71777358        U
#>  66:      -1.12208954  0.459254083 -0.162682657 -0.47694819        U
#>  67:      -0.52657687  2.153959487 -1.198967281  1.51422456        T
#>  68:       1.55102509 -0.015197500 -0.020516523  0.08678021       TW
#>  69:      -0.31778878  0.078986096  0.504242392 -0.40436325       TW
#>  70:      -0.25962432 -0.431283305  0.321955192 -0.80553288       TW
#>  71:       0.94969689 -0.259032167  0.127344278  0.29597325       TW
#>  72:       0.38835687  1.713217290 -1.884387903  0.92471752       TW
#>  73:       1.80146660 -0.299550789  0.846263466 -0.96311064       TW
#>  74:       1.41160228  0.325807029 -0.523648505  0.50405157       GB
#>  75:       1.68036114  0.244666550 -0.307162858  0.06937286       GB
#>  76:      -0.55865998  0.340444764 -0.599034616  1.78969146       GB
#>  77:      -0.03297035  1.327984163 -0.994951781  0.04668455       GB
#>  78:       0.87176931  0.413447859  0.073949884 -0.50654925       GB
#>  79:       0.70036608 -0.462062012  0.178370302 -0.01958915       GB
#>  80:       1.21810218  0.868463721 -0.287882420  0.69946303       GB
#>  81:       0.18942396 -1.287008036  1.023037680 -0.67591746       GB
#>  82:       2.94194227  0.490363636 -0.505416684 -0.20254651        U
#>  83:       1.75435972  0.126135253  0.545903248 -0.58505782        U
#>  84:       1.74943703 -1.189744988  1.025075387  0.25994625        U
#>  85:       0.71173422  0.159291276 -0.024230945 -0.31575501        U
#>  86:       2.66309134  1.821981086 -1.522244645  2.17591511       CG
#>  87:       2.09456880 -0.974406590  1.602507741 -0.42228829       CG
#>  88:       2.44067497 -0.018317012 -0.366531140  1.59163441       CG
#>  89:       1.98043577  0.194610912  0.713343825 -0.56222110       CG
#>  90:       1.66043194  1.080566180 -1.266611407  0.66730260       CG
#>  91:       0.13156827  0.628989307  0.146877669 -0.44097752        U
#>  92:       1.56271877  2.553879072 -2.337986521  2.47075117       GB
#>  93:       3.67023402  0.739483022 -0.989799476  1.09191365       GB
#>  94:       2.58336718  0.385454354 -0.713316425 -0.39597920       GB
#>  95:       0.31138087  1.718720076 -1.690079016  1.02145675       TW
#>  96:       0.58486431  0.006869282  0.144815367  0.29376432       TC
#>  97:       1.00756926  1.592083294 -1.701052660  1.45313446       TC
#>  98:       1.80512493 -1.065610146  0.920097708 -0.93721735       TC
#>  99:       1.02571762  0.290926638 -0.620965953  1.28033350       TC
#> 100:      -0.09577977 -1.191686980  1.215301402  0.03244860       TW
#>      PCIV_lamella_num  awesomeness    hostility    attitude ecomorph
#>           island
#>           <char>
#>   1:        Cuba
#>   2:        Cuba
#>   3:        Cuba
#>   4:        Cuba
#>   5:        Cuba
#>   6:        Cuba
#>   7:        Cuba
#>   8:        Cuba
#>   9:        Cuba
#>  10:        Cuba
#>  11:        Cuba
#>  12:        Cuba
#>  13:        Cuba
#>  14: Puerto Rico
#>  15:     Jamaica
#>  16: Puerto Rico
#>  17:     Jamaica
#>  18:     Jamaica
#>  19:     Jamaica
#>  20: Puerto Rico
#>  21: Puerto Rico
#>  22: Puerto Rico
#>  23: Puerto Rico
#>  24: Puerto Rico
#>  25: Puerto Rico
#>  26: Puerto Rico
#>  27: Puerto Rico
#>  28:  Hispaniola
#>  29:  Hispaniola
#>  30:  Hispaniola
#>  31:  Hispaniola
#>  32:  Hispaniola
#>  33:  Hispaniola
#>  34:  Hispaniola
#>  35:  Hispaniola
#>  36:  Hispaniola
#>  37:  Hispaniola
#>  38:  Hispaniola
#>  39:  Hispaniola
#>  40:  Hispaniola
#>  41:  Hispaniola
#>  42:  Hispaniola
#>  43:  Hispaniola
#>  44:  Hispaniola
#>  45:  Hispaniola
#>  46:  Hispaniola
#>  47:  Hispaniola
#>  48:  Hispaniola
#>  49:  Hispaniola
#>  50:  Hispaniola
#>  51:  Hispaniola
#>  52:  Hispaniola
#>  53:  Hispaniola
#>  54: Puerto Rico
#>  55:        Cuba
#>  56:        Cuba
#>  57:        Cuba
#>  58:        Cuba
#>  59:        Cuba
#>  60:        Cuba
#>  61:        Cuba
#>  62:        Cuba
#>  63:        Cuba
#>  64:        Cuba
#>  65:        Cuba
#>  66:        Cuba
#>  67:        Cuba
#>  68:        Cuba
#>  69:  Hispaniola
#>  70:  Hispaniola
#>  71:        Cuba
#>  72:        Cuba
#>  73:        Cuba
#>  74:        Cuba
#>  75:        Cuba
#>  76:        Cuba
#>  77:        Cuba
#>  78:        Cuba
#>  79:        Cuba
#>  80:        Cuba
#>  81:        Cuba
#>  82:        Cuba
#>  83:        Cuba
#>  84:        Cuba
#>  85:        Cuba
#>  86:        Cuba
#>  87:        Cuba
#>  88:        Cuba
#>  89:        Cuba
#>  90:        Cuba
#>  91:  Hispaniola
#>  92:  Hispaniola
#>  93:  Hispaniola
#>  94:  Hispaniola
#>  95:  Hispaniola
#>  96:  Hispaniola
#>  97:  Hispaniola
#>  98:  Hispaniola
#>  99:  Hispaniola
#> 100: Puerto Rico
#>           island