R/pulltreedata.table.R
pulltreedata.table.RdReturns the character matrix or phylogeny from a treedata.table object
pulltreedata.table(tdObject, type = c("dat", "phy"))
| tdObject | A treedata.table object |
|---|---|
| type | Whether the output of the function is a tree ('type="phylo"') or a data.table ('type="dat"') |
A data.table or phylo object from the original treedata.table
object
#>#>#>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 #> 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 #> 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 #> 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