Returns the character matrix or phylogeny from a treedata.table object
Source:R/pulltreedata.table.R
pulltreedata.table.RdReturns 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"')
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