This function standardizes continuous traits. It can be useful before
computing functional space. You will have to choose which standardized
method to use based on your data. For this function to work, there must be
no NA in your sp_tr data frame.
tr.cont.scale(sp_tr, std_method = "scale_center")a data frame of traits values (columns) for each species (rows). Note that species names must be specified in the row names and traits must be continuous.
a character string referring to the standardization
method. Possible values:
range (standardize by the range),
center (use the center transformation: \(x' = x - mean(x)\)),
scale (use the scale transformation: \(x' = \frac{x}{sd(x)}\)), or
scale_center (use the scale-center transformation:
\(x' = \frac{x - mean(x)}{sd(x)}\)).
Default is scale_center.
A data frame of standardized trait values (columns) for each species (rows).
load(system.file('extdata', 'sp_tr_cestes_df', package = 'mFD'))
mFD::tr.cont.scale(sp_tr = sp_tr, std_method = 'scale_center')
#> logM OgSf OgSh OgPo
#> Achirus_lineatus -0.58299801 -0.681449298 -0.263909738 2.554334103
#> Anchoa_mitchilli -1.97956543 1.130469237 1.743827528 0.317005423
#> Archosargus_probatocephalus -0.12376213 -0.595576382 -0.613948846 -0.988102973
#> Archosargus_rhomboidalis 0.49201000 -0.818845965 -0.806198305 -0.751637341
#> Ariopsis_felis 0.28738128 0.185867157 -1.051044313 -0.419675971
#> Bagre_marinus -0.59902883 0.829914029 -1.040162268 0.230604519
#> Bairdiella_chrysoura -0.12847708 -0.003053259 -0.006368011 0.148751031
#> Bairdiella_ronchus 0.76641994 -0.432417841 -0.610321498 -0.428770803
#> Cathorops_melanopus -0.12093316 -0.149037217 -0.840658113 -0.756184757
#> Cetengraulis_edentulus -0.35385156 0.297501948 2.073916221 -0.788016669
#> Chaetodipterus_faber 1.08420739 -0.896131589 -0.588557409 -0.383296643
#> Chilomycterus_schoepfii 2.20636488 -0.878957006 -1.509903869 -0.064977522
#> Chloroscombrus_chrysurus -1.57313696 -0.209148258 1.268644905 1.335626611
#> Citharichthys_spilopterus -0.64334933 -0.767322215 -0.996634089 2.554334103
#> Conodon_nobilis 0.14498987 -0.217735550 0.019023426 0.385216663
#> Cynoscion_arenarius -0.43023371 0.580882572 0.323720681 1.008212657
#> Cynoscion_nebulosus 0.95407485 1.061770904 -0.289301176 1.012760074
#> Cynoscion_nothus -0.40288702 0.340438406 0.359994164 0.962738497
#> Dasyatis_sabina 2.64674097 -0.853195131 -1.132659649 -1.993081913
#> Diapterus_auratus -0.55282234 -0.801671381 0.525038510 0.030518214
#> Diapterus_rhombeus -0.54716441 -0.878957006 -0.097051718 -0.110451682
#> Dorosoma_petenense 0.06012082 0.177279865 0.934928864 0.812673769
#> Eucinostomus_argenteus -1.68912467 -0.664274715 0.554057296 0.139656199
#> Eucinostomus_gula -0.88664062 -0.810258673 0.347298445 0.180582943
#> Eucinostomus_melanopterus -1.00262833 -0.586989090 0.675573463 0.048707878
#> Gobionellus_oceanicus -0.01626133 1.722992359 0.330975378 0.212414855
#> Menticirrhus_americanus 0.34301766 -0.372306800 -0.329202007 -0.969913309
#> Menticirrhus_saxatilis 0.23740284 -0.475354299 -0.621203543 -0.856227909
#> Micropogonias_undulatus 0.10727029 -0.372306800 -0.282046480 -0.919891733
#> Opsanus_beta 1.17944933 2.263991733 -0.898695686 0.762652193
#> Orthopristis_chrysoptera -0.15676676 0.091406949 0.129657549 -0.601572612
#> Peprilus_paru -0.44626453 -0.810258673 0.156862661 0.203320023
#> Polydactylus_octonemus 0.41751383 0.220216323 -0.287487502 -0.992650389
#> Prionotus_carolinus -0.73387632 1.765928818 -0.532333510 -1.074503878
#> Prionotus_scitulus -0.06718276 1.207754861 -0.523265140 -1.169999614
#> Selene_setapinnis -1.03563296 -0.501116174 2.284302420 -0.292348323
#> Selene_vomer -1.25912147 -0.561227216 3.007958400 -0.165020675
#> Sphoeroides_nephelus 0.63911636 -0.535465341 -0.545029229 -0.178662923
#> Sphoeroides_pachygaster 0.55519030 -0.501116174 -0.289301176 -0.242326747
#> Sphoeroides_testudineus 1.45951721 -0.896131589 -1.067367380 0.003233718
#> Stellifer_lanceolatus -0.71973148 -0.020227843 -0.240331975 0.230604519
#> Symphurus_plagiusa -0.49718597 -0.836020548 -0.564979645 2.554334103
#> Synodus_foetens 0.66834903 3.758180477 1.009289504 0.144203615
#> Trichiurus_lepturus -0.25578066 1.250691320 1.560646441 0.307910591
#> Urobatis_jamaicensis 2.55527099 -0.758734923 -1.277753580 -1.993081913
#> EySz GrLg GtLg EyPo
#> Achirus_lineatus -1.753090654 -0.8300723 0.30349122 2.179709071
#> Anchoa_mitchilli 1.127439829 2.1200914 -0.72954982 -0.905437898
#> Archosargus_probatocephalus -0.584825969 -0.5590599 1.06741279 -0.401135028
#> Archosargus_rhomboidalis -0.477809356 -0.5822895 1.89460104 -0.438216121
#> Ariopsis_felis -0.754268938 0.1610588 0.58299775 -0.438216121
#> Bagre_marinus 0.084027859 0.2694638 0.65476294 -0.690367556
#> Bairdiella_chrysoura 0.797471941 0.7805158 -0.41132786 -0.504962089
#> Bairdiella_ronchus 0.547766512 0.4243280 -0.31878853 -0.282475529
#> Cathorops_melanopus 0.182126420 0.6024219 0.50462261 -0.504962089
#> Cetengraulis_edentulus 1.296882799 4.0558944 3.15238044 -1.224335301
#> Chaetodipterus_faber -0.968302163 -0.6674649 3.74255470 -0.638454026
#> Chilomycterus_schoepfii -0.442137152 -0.8300723 1.94275926 0.355319277
#> Chloroscombrus_chrysurus -0.388628846 0.4630441 -0.80981352 -0.237978217
#> Citharichthys_spilopterus 0.877734400 -0.7139241 -0.46137463 2.179709071
#> Conodon_nobilis 0.547766512 0.5017601 -0.22813776 0.318238184
#> Cynoscion_arenarius 0.868816349 1.0437850 -0.46326319 -0.252810654
#> Cynoscion_nebulosus 0.164290318 0.7882590 -0.45382040 0.206994903
#> Cynoscion_nothus 0.485340155 0.9895825 -0.53125127 -0.193480905
#> Dasyatis_sabina 1.609014585 -0.8300723 -1.06476881 2.179709071
#> Diapterus_auratus 0.529930410 -0.6752081 -0.43682339 -1.202086645
#> Diapterus_rhombeus 0.717209482 -0.6752081 -0.13087705 -1.172421770
#> Dorosoma_petenense 1.207702288 0.5637058 0.31954396 -0.720032431
#> Eucinostomus_argenteus 1.145275931 -0.6752081 -0.21869498 -0.957351429
#> Eucinostomus_gula 0.645865074 -0.6984377 -0.24607906 -0.979600085
#> Eucinostomus_melanopterus 0.904488553 -0.7061809 -0.43682339 -1.305913706
#> Gobionellus_oceanicus -0.647252326 -0.8223291 0.09574987 0.993114083
#> Menticirrhus_americanus -0.245940030 -0.4506549 -0.48498161 -0.008075438
#> Menticirrhus_saxatilis -0.406464948 -0.4506549 -0.45382040 0.118000279
#> Micropogonias_undulatus 0.075109808 -0.2648179 -0.44343334 -0.401135028
#> Opsanus_beta -0.433219101 -0.5590599 -0.19508801 1.193351987
#> Orthopristis_chrysoptera -1.110990980 -0.3732228 -0.29990296 0.162497591
#> Peprilus_paru -0.852367500 -0.4429117 -0.17336959 -1.291081269
#> Polydactylus_octonemus 1.065013472 2.1123482 -0.63701050 -0.920270335
#> Prionotus_carolinus -0.549153765 0.5404762 -0.46609603 0.548140963
#> Prionotus_scitulus -0.834531398 0.5095034 -0.36694675 0.518476088
#> Selene_setapinnis -1.735254552 -0.1796425 -0.86174886 -0.912854117
#> Selene_vomer -1.690664297 -0.2880475 -0.58129805 -0.564291839
#> Sphoeroides_nephelus -1.530139378 -0.8300723 0.01265334 0.740962648
#> Sphoeroides_pachygaster -1.075318775 -0.8300723 0.08725136 0.370151714
#> Sphoeroides_testudineus -1.494467174 -0.7216674 0.96448639 0.963449208
#> Stellifer_lanceolatus 0.003765399 1.2760813 -0.37355670 -0.245394436
#> Symphurus_plagiusa -1.191253439 -0.8300723 -0.39621940 2.179709071
#> Synodus_foetens 0.717209482 -0.6364920 -0.81170208 0.140248935
#> Trichiurus_lepturus 1.412817462 -0.2493314 -1.06193597 -0.134151156
#> Urobatis_jamaicensis 2.153015698 -0.8300723 -0.77676376 2.179709071
#> BdSh BdSf PfPo PfSh
#> Achirus_lineatus -1.17042446 0.17755278 -2.42187116 -2.042954308
#> Anchoa_mitchilli 0.50227657 3.46001748 1.08394608 -0.420805564
#> Archosargus_probatocephalus 0.39550842 -0.71122088 0.59866478 0.796405014
#> Archosargus_rhomboidalis 0.40135145 -0.86207612 0.47167528 2.071121604
#> Ariopsis_felis -0.70404418 -0.74938907 1.23361228 0.041638612
#> Bagre_marinus -0.70670010 0.03033261 0.58052343 0.157848677
#> Bairdiella_chrysoura -0.05015565 -0.60398643 0.37643316 0.223740982
#> Bairdiella_ronchus -0.16860987 -0.90569692 0.21769628 0.029658193
#> Cathorops_melanopus -0.60683735 -0.35498440 1.10208744 -0.377676056
#> Cetengraulis_edentulus 0.24093364 -0.26229021 1.38781381 0.209963500
#> Chaetodipterus_faber 0.91766311 -0.42405066 0.51702868 -0.912002747
#> Chilomycterus_schoepfii -0.81559299 -1.13652361 -0.75286632 -1.648798520
#> Chloroscombrus_chrysurus 1.34420453 0.61921332 -0.20409027 1.412198555
#> Citharichthys_spilopterus -1.17945460 0.55559966 -2.42187116 -2.042954308
#> Conodon_nobilis -0.17232816 -0.20412916 0.39003918 0.420818876
#> Cynoscion_arenarius -0.02040930 -0.33317400 0.22223162 0.652639985
#> Cynoscion_nebulosus -0.23713271 -1.21467753 0.26758502 0.050024905
#> Cynoscion_nothus -0.07671489 -0.44404352 0.29026171 0.044633717
#> Dasyatis_sabina -1.19698370 -1.13470608 -2.42187116 0.006296376
#> Diapterus_auratus 0.66588150 0.48835094 0.62587682 1.497858551
#> Diapterus_rhombeus 0.62285553 0.45200028 0.59866478 1.353494501
#> Dorosoma_petenense 0.56389401 0.95000433 1.21093558 0.262677344
#> Eucinostomus_argenteus 0.32804795 0.94455173 0.52609935 0.861698298
#> Eucinostomus_gula 0.37585458 0.16119499 0.46260460 1.491868342
#> Eucinostomus_melanopterus 0.07148567 1.04269852 0.42632189 0.921001372
#> Gobionellus_oceanicus -0.43792058 -0.40042273 -0.81182573 -0.463935073
#> Menticirrhus_americanus -0.28387698 -0.25320255 0.26304968 -0.262065012
#> Menticirrhus_saxatilis -0.28812646 -0.36952466 0.29479705 0.242310632
#> Micropogonias_undulatus -0.10061821 -0.20594669 0.24037298 0.759265715
#> Opsanus_beta -0.80390693 -0.78755727 -0.94788590 -1.370852797
#> Orthopristis_chrysoptera 0.12407297 -1.17469181 0.34468578 -0.719717020
#> Peprilus_paru 1.54233647 0.39747428 -0.04988873 0.115917210
#> Polydactylus_octonemus 0.07892226 -0.25683762 0.73472496 0.952150462
#> Prionotus_carolinus -0.68067205 1.32078108 0.25851434 -0.626868773
#> Prionotus_scitulus -0.70510655 0.51379640 0.36736248 -0.033838028
#> Selene_setapinnis 3.46097608 1.76244161 -0.31293841 0.425611044
#> Selene_vomer 3.45141475 2.50036003 -0.21769628 0.573569219
#> Sphoeroides_nephelus -0.70085707 0.27933464 0.06803009 -1.310351681
#> Sphoeroides_pachygaster -0.60311906 1.25898495 -0.10884814 -1.449324542
#> Sphoeroides_testudineus -0.63233423 -0.79846247 -0.35829180 -1.449324542
#> Stellifer_lanceolatus -0.23182086 0.19572812 0.20862561 0.707749913
#> Symphurus_plagiusa -1.14492759 -0.20776422 -2.42187116 -2.042954308
#> Synodus_foetens -0.67057953 -0.80209753 -0.25397900 -0.034437049
#> Trichiurus_lepturus 0.48687221 -1.23103533 0.75740166 0.390867828
#> Urobatis_jamaicensis -1.18529764 -1.28192626 -2.42187116 0.535830899
#> CpHt CfSh FsRt FsSf
#> Achirus_lineatus -0.91103742 -0.9176609 -1.07107750 -0.635307836
#> Anchoa_mitchilli 0.04457675 1.1875436 -0.48969182 0.628536554
#> Archosargus_probatocephalus 0.10795933 0.5445614 0.68922913 -0.335794028
#> Archosargus_rhomboidalis 0.33223612 0.8062507 0.15167809 -0.337525322
#> Ariopsis_felis 0.81004321 2.0364599 -0.17016041 -0.211140883
#> Bagre_marinus 1.23700493 1.5040886 -0.35011312 -0.185171478
#> Bairdiella_chrysoura -0.32457449 -0.4680231 -0.42740050 -0.185171478
#> Bairdiella_ronchus -0.27651518 -0.4176636 -0.22091630 -0.228453820
#> Cathorops_melanopus 0.76198389 1.6686561 -0.31550683 -0.439671650
#> Cetengraulis_edentulus 0.19850586 1.2046298 -0.56467212 -0.289914746
#> Chaetodipterus_faber 0.17203841 0.6066114 -0.29589660 -0.892404948
#> Chilomycterus_schoepfii 0.02228838 -0.6065115 2.12885081 -0.856913428
#> Chloroscombrus_chrysurus 2.48167149 1.0013935 -0.04673131 -0.057921392
#> Citharichthys_spilopterus -1.00158395 -0.9176609 -1.07107750 -0.817959320
#> Conodon_nobilis -0.48477220 -0.4896057 -0.02481399 -0.344450497
#> Cynoscion_arenarius -0.37124078 -0.6397847 -0.64311305 -0.437940356
#> Cynoscion_nebulosus -0.34477333 -0.5462601 -0.52545166 -0.282989571
#> Cynoscion_nothus -0.42487219 -0.6226985 -0.59235715 -0.503729516
#> Dasyatis_sabina -1.69182713 -1.6074054 -1.07107750 3.418516327
#> Diapterus_auratus 0.39910125 0.8718978 -0.38933358 -0.224991233
#> Diapterus_rhombeus 0.32318147 0.7891644 -0.16323915 -0.199021827
#> Dorosoma_petenense 0.23193842 0.3943824 -0.58658944 -0.049264924
#> Eucinostomus_argenteus 0.06547211 0.3835911 -0.18977064 -0.110725849
#> Eucinostomus_gula 0.28139076 0.8107470 -0.29935723 -0.270004868
#> Eucinostomus_melanopterus 0.32736054 0.6911434 -0.33857769 -0.269139222
#> Gobionellus_oceanicus -1.03501651 -1.3376227 -0.20130607 2.180641343
#> Menticirrhus_americanus -0.59203502 -0.6964391 0.39392212 0.009599062
#> Menticirrhus_saxatilis -0.56835362 -0.7018348 -0.03058171 -0.083025150
#> Micropogonias_undulatus -0.31412682 -0.7773739 -0.44816428 -0.161799013
#> Opsanus_beta -0.72158621 -0.7710790 1.98927210 -0.432746475
#> Orthopristis_chrysoptera 0.37193729 1.1021124 0.30971348 -0.021564225
#> Peprilus_paru 1.16178166 0.7684811 0.46890242 -0.340122263
#> Polydactylus_octonemus -0.07034769 0.7352079 -0.47469577 0.538509282
#> Prionotus_carolinus -0.11004886 -0.6757558 3.58462209 2.076763721
#> Prionotus_scitulus -0.13651631 -0.7476978 3.17511432 1.829188725
#> Selene_setapinnis 2.76166923 1.0076884 0.19205209 -0.052727511
#> Selene_vomer 2.84594716 1.5724336 -0.02596753 -0.268273575
#> Sphoeroides_nephelus 0.10308374 -0.4626274 0.58887089 -0.381673311
#> Sphoeroides_pachygaster -0.22427679 -0.5525550 0.81150469 -0.489879166
#> Sphoeroides_testudineus -0.35731055 -0.6595688 0.31086702 -0.344450497
#> Stellifer_lanceolatus -0.46805592 -0.7917623 -0.14939664 -0.488147873
#> Symphurus_plagiusa -1.69182713 -1.6074054 -1.07107750 -1.637726880
#> Synodus_foetens 0.46318034 0.5427629 -0.40432964 -0.176515009
#> Trichiurus_lepturus -1.69182713 -1.6074054 -1.07107750 -0.866435543
#> Urobatis_jamaicensis -1.69182713 -1.6074054 -1.07107750 3.228939669