Soil Ordi
Jonathan Spiess
January 29, 2021
Microbes!
Ordination for both years and determining which variables are significant
Mic_canb1920 <- capscale(MicBiomass1920 ~ 1, metaMDSdist = "true", dist="canb")## Square root transformation
## Wisconsin double standardizationsummary(Mic_canb1920)##
## Call:
## capscale(formula = MicBiomass1920 ~ 1, distance = "canb", metaMDSdist = "true")
##
## Partitioning of squared Canberra distance:
## Inertia Proportion
## Total 0.7544 1
## Unconstrained 0.7544 1
##
## Eigenvalues, and their contribution to the squared Canberra distance
##
## Importance of components:
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6 MDS7
## Eigenvalue 0.2743 0.2090 0.06902 0.04532 0.02121 0.02048 0.01531
## Proportion Explained 0.3635 0.2770 0.09149 0.06007 0.02811 0.02714 0.02029
## Cumulative Proportion 0.3635 0.6405 0.73200 0.79207 0.82018 0.84732 0.86761
## MDS8 MDS9 MDS10 MDS11 MDS12 MDS13
## Eigenvalue 0.01074 0.01005 0.008573 0.007235 0.006870 0.005993
## Proportion Explained 0.01424 0.01332 0.011363 0.009590 0.009106 0.007943
## Cumulative Proportion 0.88185 0.89517 0.906531 0.916121 0.925226 0.933170
## MDS14 MDS15 MDS16 MDS17 MDS18 MDS19
## Eigenvalue 0.005048 0.004499 0.004294 0.003464 0.003224 0.002804
## Proportion Explained 0.006692 0.005964 0.005692 0.004591 0.004274 0.003717
## Cumulative Proportion 0.939861 0.945825 0.951517 0.956108 0.960382 0.964099
## MDS20 MDS21 MDS22 MDS23 MDS24 MDS25
## Eigenvalue 0.002535 0.002206 0.001952 0.001778 0.001563 0.001453
## Proportion Explained 0.003360 0.002924 0.002587 0.002357 0.002071 0.001926
## Cumulative Proportion 0.967459 0.970382 0.972969 0.975326 0.977397 0.979324
## MDS26 MDS27 MDS28 MDS29 MDS30 MDS31
## Eigenvalue 0.001251 0.001236 0.001147 0.001051 0.0009334 0.0009141
## Proportion Explained 0.001659 0.001639 0.001520 0.001393 0.0012372 0.0012116
## Cumulative Proportion 0.980983 0.982621 0.984141 0.985534 0.9867710 0.9879826
## MDS32 MDS33 MDS34 MDS35 MDS36
## Eigenvalue 0.0008877 0.0008231 0.0007321 0.0006480 0.0006173
## Proportion Explained 0.0011766 0.0010911 0.0009704 0.0008589 0.0008182
## Cumulative Proportion 0.9891593 0.9902503 0.9912207 0.9920797 0.9928979
## MDS37 MDS38 MDS39 MDS40 MDS41
## Eigenvalue 0.0005797 0.0004756 0.0004417 0.0004201 0.0003747
## Proportion Explained 0.0007683 0.0006304 0.0005855 0.0005568 0.0004967
## Cumulative Proportion 0.9936662 0.9942966 0.9948820 0.9954388 0.9959355
## MDS42 MDS43 MDS44 MDS45 MDS46
## Eigenvalue 0.0003414 0.0003045 0.0002623 0.0002475 0.0002177
## Proportion Explained 0.0004525 0.0004036 0.0003477 0.0003280 0.0002885
## Cumulative Proportion 0.9963881 0.9967917 0.9971394 0.9974674 0.9977560
## MDS47 MDS48 MDS49 MDS50 MDS51
## Eigenvalue 0.0002081 0.0001984 0.0001875 0.0001587 0.0001401
## Proportion Explained 0.0002758 0.0002630 0.0002486 0.0002103 0.0001857
## Cumulative Proportion 0.9980318 0.9982948 0.9985433 0.9987537 0.9989394
## MDS52 MDS53 MDS54 MDS55 MDS56
## Eigenvalue 0.0001269 0.0001163 0.0001088 8.587e-05 7.007e-05
## Proportion Explained 0.0001681 0.0001542 0.0001442 1.138e-04 9.288e-05
## Cumulative Proportion 0.9991075 0.9992617 0.9994059 9.995e-01 9.996e-01
## MDS57 MDS58 MDS59 MDS60 MDS61
## Eigenvalue 6.505e-05 6.207e-05 5.590e-05 4.397e-05 3.442e-05
## Proportion Explained 8.623e-05 8.228e-05 7.409e-05 5.827e-05 4.562e-05
## Cumulative Proportion 9.997e-01 9.998e-01 9.999e-01 9.999e-01 1.000e+00
## MDS62 MDS63 MDS64 MDS65
## Eigenvalue 1.66e-05 1.066e-05 2.167e-06 1.444e-06
## Proportion Explained 2.20e-05 1.413e-05 2.872e-06 1.913e-06
## Cumulative Proportion 1.00e+00 1.000e+00 1.000e+00 1.000e+00
##
## Scaling 2 for species and site scores
## * Species are scaled proportional to eigenvalues
## * Sites are unscaled: weighted dispersion equal on all dimensions
## * General scaling constant of scores: 3.305679
##
##
## Species scores
##
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6
## AM_bio 0.6646 1.0218 -0.21336 0.66898 -0.10368 0.275024
## GNB_bio -0.7598 0.1485 0.10985 -0.07613 0.11218 0.170861
## Euk_bio -0.1947 -1.3553 -0.81879 0.21488 0.28606 -0.004307
## Fungi_bio 1.6666 -0.6082 0.66533 -0.31465 -0.03091 -0.054508
## GPB_bio -0.6111 0.2164 0.16546 -0.43640 0.20715 0.102452
## Actino_bio -0.7655 0.5769 0.09152 -0.05668 -0.47080 -0.489522
##
##
## Site scores (weighted sums of species scores)
##
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6
## 1 -0.0369695 0.0898106 0.159371 -0.240620 0.230416 -0.0088546
## 2 -0.0415938 0.1665197 0.035890 0.083024 -0.007866 -0.0372538
## 3 0.0429115 -0.0685428 0.102400 -0.230483 -0.163611 -0.3609278
## 4 0.0171653 0.3704033 0.280396 0.248266 0.229522 -0.0463457
## 5 -0.0875452 0.2850594 0.199050 -0.089846 0.334613 -0.2586987
## 6 -0.0224025 0.1193976 0.028197 0.082363 -0.013818 -0.0222232
## 7 -0.0535266 0.1569063 -0.159602 0.189053 -0.120392 0.4818769
## 8 -0.1752163 0.4814127 0.034216 0.201637 -0.119190 -0.1879646
## 9 0.0378010 0.0691875 0.023044 0.189865 -0.012296 0.1421983
## 10 0.0277758 0.1122485 0.078592 0.162870 0.007408 0.0595762
## 11 -0.0685055 0.4081563 0.174238 0.235961 0.134233 -0.2675216
## 12 -0.0287512 0.3596117 0.244232 0.128102 0.193638 -0.1797085
## 13 -0.0001362 0.3479710 0.295664 0.296408 0.109208 -0.3838932
## 14 0.0701848 -0.0798545 0.010214 0.043799 -0.126054 -0.1714915
## 15 0.1654910 0.0706679 0.404347 -0.054689 -0.006747 -0.0374245
## 16 -0.0821962 0.1031634 -0.155514 0.136981 -0.293783 -0.0662975
## 17 -0.0993079 0.3715960 0.290845 0.090461 0.192747 -0.7122963
## 18 -0.0228820 0.3383599 0.284998 0.153574 0.160592 -0.3230694
## 19 -0.0212759 0.3043892 0.319297 0.030081 0.178477 -0.3916757
## 20 -0.0708053 0.1579740 0.022220 0.145787 -0.181146 -0.2744591
## 21 -0.0826722 0.2811880 0.061740 0.150815 0.075306 -0.0416495
## 22 -0.0438347 0.1017774 -0.076215 0.140105 -0.145126 -0.0422079
## 23 0.1313663 -0.1597233 0.123620 -0.237604 -0.208475 -0.0782520
## 24 0.0224743 0.0653969 0.133804 -0.024289 0.017561 -0.0754633
## 25 -0.1260624 0.1081242 -0.145263 -0.039460 -0.242002 -0.0335298
## 26 -0.1221876 0.0672145 -0.264543 0.151881 -0.384667 -0.1217718
## 27 -0.0034029 0.0272841 -0.113615 0.195715 -0.100519 0.0386109
## 28 -0.0363236 0.0237630 0.050633 -0.231641 0.313580 0.1980481
## 29 -0.1971177 0.3387670 -0.094110 0.003025 -0.224668 0.3316268
## 30 -0.0106056 0.2810355 0.135803 0.275631 0.123221 -0.0801860
## 31 -0.0697218 0.1403912 -0.054739 0.031740 -0.011904 0.2097442
## 32 0.2173953 -0.2919884 0.158754 -0.483904 -0.252715 0.0099341
## 33 -0.1840084 0.3411048 0.024825 -0.083736 0.118009 -0.0006608
## 34 -0.1327856 0.1853348 -0.096265 -0.052516 -0.129398 0.2061365
## 35 -0.1796489 0.6252502 -0.033938 0.240549 0.078026 0.1349357
## 36 0.0678834 0.4074939 0.397529 0.030307 1.578129 1.7883198
## 37 -0.0272433 0.2238673 0.058004 0.145324 0.226484 0.3398711
## 38 -0.1120643 0.1766490 0.145408 -0.213456 0.124971 -0.3117690
## 39 -0.0158210 0.0619281 0.072937 -0.089099 0.146554 0.0869379
## 40 0.0442654 0.0611840 0.349700 -0.393693 0.299145 -0.0106249
## 41 -0.0100378 0.0269611 -0.122380 0.164635 0.053623 0.2408506
## 42 -0.2148870 0.4136105 -0.030486 -0.048324 -0.005105 0.2423781
## 43 -0.1758430 0.1965843 -0.185418 -0.006013 -0.343703 0.3500882
## 44 -0.0036532 0.2000404 0.153000 0.061432 0.229966 0.1534896
## 45 0.2967771 -0.1644282 0.402482 -0.367809 -0.021197 0.1147585
## 46 0.0704777 -0.0337656 0.196705 -0.266463 -0.020352 0.0034796
## 47 0.0177605 0.1030791 0.166423 -0.025467 0.065283 -0.1067402
## 48 -0.0376236 0.0834242 0.046247 -0.075560 0.073489 0.0010504
## 49 0.0560165 -0.4613462 -0.885086 0.248492 0.469673 -0.4156487
## 50 0.1765038 -0.1122586 0.268328 -0.322452 -0.080488 0.0724719
## 51 -0.1244960 0.3996142 0.164008 -0.002090 0.364786 -0.2448825
## 52 -0.0908969 0.1521270 -0.100537 0.020780 -0.080086 0.2742298
## 53 -0.0960831 0.1167090 -0.028188 -0.124227 0.026670 0.0219751
## 54 -0.1919248 0.0570076 -0.146573 -0.432118 -0.089726 0.0001802
## 55 -0.3044117 0.2976446 0.193407 -0.686034 0.235240 -0.4599998
## 56 0.0474773 0.0651427 0.423049 -0.514417 0.108942 -0.2082910
## 57 0.0299612 0.0813303 0.004006 0.177469 0.017715 0.2251339
## 58 -0.0336579 0.2060566 0.055154 0.206360 -0.045030 -0.1078547
## 59 -0.0787545 0.1332751 0.050994 -0.110966 0.052902 -0.1187780
## 60 -0.1864401 0.1411550 -0.325167 0.057464 -0.519731 0.3624802
## 61 0.0739921 -0.0311320 0.126289 -0.113153 -0.108515 -0.0980437
## 62 0.1410024 -0.2410576 0.063071 -0.216665 -0.167916 -0.0934422
## 63 0.0777890 -0.0176181 0.129000 -0.050512 -0.138004 -0.1185235
## 64 0.0994478 0.0242973 0.132254 0.119563 -0.043858 0.1497852
## 65 0.0643299 -0.0642323 -0.055120 0.184426 0.023472 -0.0151178
## 66 -0.0092051 0.0670281 -0.088168 0.158563 -0.106411 0.1355065
## 67 -0.2850408 0.1880609 -0.387193 -0.070342 -0.690426 0.5046652
## 68 -0.0579377 0.2391763 -0.073181 0.232836 -0.135322 0.2051160
## 69 -0.1878391 0.5828510 0.008905 0.247395 -0.123688 -0.1782674
## 70 -0.1678681 0.0968798 -0.165457 -0.128130 -0.363085 -0.1108555
## 71 -0.2456023 0.3856167 -0.092696 -0.052809 -0.341695 0.3392652
## 72 -0.1899450 0.2106870 -0.031342 -0.278190 0.041796 0.1130399
## 73 -0.0167956 -0.0216881 -0.049715 -0.027106 0.125300 0.0367797
## 74 -0.1208773 0.0616460 -0.138313 -0.175135 -0.085748 0.1198483
## 75 -0.1329178 0.0663664 -0.137698 -0.192735 -0.114668 0.0360049
## 76 -0.0779172 -0.0075192 -0.207972 0.041148 -0.076076 -0.1168925
## 77 -0.0234955 -0.0507494 -0.199949 0.109640 0.068800 -0.0733935
## 78 -0.0823419 0.2521419 0.053535 0.065861 0.047441 -0.0159525
## 79 -0.1599519 0.2582800 0.112949 -0.252867 0.255234 -0.1901197
## 80 -0.0927125 0.0632832 -0.244032 0.100594 -0.228855 0.2094364
## 81 0.0506308 0.0005301 0.076297 0.017077 -0.072224 -0.0679052
## 82 -0.1173783 -0.0083510 -0.346233 0.101159 -0.114395 0.0796842
## 83 -0.0048453 -0.0550522 -0.074351 -0.037610 0.097187 -0.0771011
## 84 0.0958965 -0.0336566 0.163452 -0.123818 -0.119180 -0.0583634
## 85 0.0137630 -0.0116691 -0.085975 0.136295 0.083477 0.1272264
## 86 -0.1604282 0.0439402 -0.340753 0.020780 -0.217861 0.2386118
## 87 0.0256169 -0.0119567 0.012945 -0.008553 0.159876 0.1899611
## 88 -0.0804838 -0.1248322 -0.247173 -0.195774 0.284034 -0.1454606
## 89 -0.1743566 0.0293915 -0.293307 -0.099616 -0.275501 -0.1175233
## 90 -0.0841795 -0.1417481 -0.407763 0.135100 0.144363 -0.1077420
## 91 -0.0196269 -0.0786772 -0.132890 -0.004605 0.173126 -0.1026514
## 92 -0.1431810 0.0567292 -0.151933 -0.241225 -0.135298 0.0712646
## 93 -0.0731830 0.5205331 0.290833 0.188510 0.247151 -0.4511986
## 94 -0.1737221 0.1933237 -0.268593 -0.011074 -0.504646 0.5791919
## 95 0.0118298 -0.0653754 0.140546 -0.425809 0.337145 0.2282682
## 96 -0.0171058 0.0392013 0.081498 -0.149058 0.029258 -0.1466819
## 97 -0.1079569 0.0891216 0.014843 -0.244793 0.043308 -0.1382041
## 98 -0.1650371 0.1662110 -0.173501 -0.052776 -0.289277 0.2480800
## 99 -0.0157936 0.0444069 0.053157 -0.084152 0.043493 -0.0283796
## 100 -0.0077842 -0.0464531 -0.184835 0.177558 0.265746 0.1594556
## 101 -0.1184725 0.1105946 -0.019968 -0.151537 -0.126392 -0.1962782
## 102 0.1174430 0.1260784 0.345983 0.039093 0.042943 0.0247443
## 103 0.0786477 -0.0636228 -0.138484 0.358526 0.123554 0.2072779
## 104 0.1837509 -0.0906820 0.088260 0.200957 -0.240935 0.2257522
## 105 0.0205130 0.0078073 -0.141319 0.288021 -0.083597 0.0470732
## 106 0.1193319 0.0409166 0.170376 0.163564 -0.064505 0.1852934
## 107 -0.0072875 0.0591531 -0.064856 0.159746 -0.123806 -0.0187103
## 108 0.1383392 -0.1118516 0.014343 0.179563 -0.023146 0.1692668
## 109 -0.0294118 0.0507433 -0.100030 0.188841 -0.248563 -0.2546828
## 110 0.0753599 -0.0157249 0.143872 -0.076351 -0.070888 -0.0063224
## 111 0.0556300 -0.3662133 -0.552847 0.717751 0.540925 -0.2414568
## 112 0.0505884 0.0050129 0.001729 0.160885 -0.043977 0.0608147
## 113 -0.1110734 0.0716866 0.019020 -0.309212 0.098169 -0.0825266
## 114 0.1472380 0.1243950 0.390215 0.095984 -0.180516 -0.2834516
## 115 0.3390116 -0.3313343 0.060937 0.095764 -0.291209 0.1995407
## 116 0.0033996 0.3442454 0.408581 0.042193 0.138691 -0.5040828
## 117 0.2977925 -0.2406464 0.111099 0.100179 -0.435314 0.1419631
## 118 0.2583989 -0.1761897 0.193999 -0.038924 -0.424751 -0.0188989
## 119 0.0036480 -0.0059008 -0.163583 0.265487 -0.074874 -0.0668394
## 120 0.1638550 -0.1774561 0.043469 0.016486 -0.342421 -0.2130748
## 121 0.2164610 -0.3080631 0.012308 -0.047750 -0.101816 -0.1093401
## 122 -0.0376760 -0.0316693 -0.368529 0.373399 -0.092023 0.0781392
## 123 -0.0516755 0.0672989 -0.061124 0.041239 -0.035010 -0.0203942
## 124 0.0973788 -0.1190751 0.225855 -0.467152 -0.031765 0.0785396
## 125 0.1015139 -0.0360056 0.062719 0.124220 -0.184562 -0.0235664
## 126 -0.0431487 0.0160895 -0.074166 0.006558 -0.079885 -0.1602111
## 127 0.0355152 -0.0406034 0.037473 -0.047072 0.007972 0.0012054
## 128 0.1352563 -0.0859134 0.138624 -0.056752 -0.333203 -0.2139817
## 129 0.0080129 -0.0671919 -0.195518 0.246555 -0.047842 -0.3818668
## 130 -0.0462775 -0.0130945 -0.268257 0.223985 -0.025198 0.0913916
## 131 0.1064450 -0.0719289 -0.055131 0.277592 0.068117 0.2393232
## 132 0.0526998 0.0088007 -0.226776 0.441323 -0.204395 0.0966602
## 133 -0.0058747 0.0538428 -0.100777 0.208875 -0.187435 -0.0506990
## 134 0.1006534 -0.0928052 0.066754 -0.024593 0.005490 0.1299835
## 135 0.0087195 -0.0498425 -0.162362 0.204742 0.165111 0.0671940
## 136 0.0779910 -0.1511209 -0.026509 -0.004634 0.174716 -0.0079948
## 137 -0.0472067 0.1289741 -0.012359 0.053606 0.077858 0.1937100
## 138 0.1077768 -0.1890819 0.037035 -0.161773 0.121868 0.0525498
## 139 0.1396829 -0.2811025 0.254158 -0.799933 0.196080 0.4083472
## 140 0.1262475 -0.1718980 0.149507 -0.338551 -0.099884 0.1121893
## 141 0.1457429 -0.1816305 0.002633 0.060560 -0.148189 -0.1652580
## 142 0.2323346 -0.2220650 0.098889 -0.015921 -0.204387 0.1636098
## 143 0.2574455 0.0307718 0.435438 0.158317 -0.178042 -0.0310569
## 144 0.1717695 -0.2916056 0.004736 -0.118463 0.122156 -0.0790450
## 145 -0.0454181 -0.0403074 -0.286383 0.196226 0.053106 0.1046071
## 146 0.2094575 -0.1985623 0.077346 0.035534 -0.187540 0.0878895
## 147 -2.4806251 -1.5452716 1.324485 0.675561 -0.102321 0.1740712
## 148 -0.8140361 -0.2283070 -1.208012 -1.025618 0.556796 -0.0973440
## 149 -0.6425831 -0.1009854 -0.815376 -1.054856 -0.038027 -0.0473606
## 150 -0.1312111 -0.0487865 -0.285966 -0.159539 0.112724 0.2769862
## 151 -0.1873665 0.0483872 0.114848 -0.606005 0.116562 -0.3104123
## 152 -0.0901014 0.0931132 0.055095 -0.236160 0.072156 -0.1648053
## 153 -0.1286832 0.2405144 -0.047126 0.136396 -0.235476 -0.0708682
## 154 0.2979912 -0.1450718 0.344372 -0.122328 -0.121971 0.2429415
## 155 -0.1816288 0.1587987 -0.130609 -0.111075 -0.353680 -0.0186008
## 156 -0.0305277 0.0517350 -0.108211 0.140192 -0.164976 -0.0644491
## 157 0.1130492 -0.0863018 0.052803 0.046591 -0.023099 0.1120213
## 158 0.2331963 -0.1927522 0.171275 -0.151234 -0.101246 0.3549779
## 159 0.1647483 -0.3738445 -0.145842 0.197142 0.362204 -0.3796364
## 160 0.0293534 -0.0865461 -0.087099 0.104484 0.144081 -0.0746790
## 161 -0.0027210 0.0401847 0.051333 -0.032932 0.069764 0.0276342
## 162 0.2192492 -0.3170568 -0.049459 0.141259 0.147440 0.0022589
## 163 0.0152373 -0.0196939 -0.263548 0.387746 -0.070957 0.1216589
## 164 0.1155037 -0.1857347 -0.089695 0.194044 0.273906 0.0534545
## 165 0.1735026 -0.3727286 -0.217327 0.467559 0.604890 -0.1545983
## 166 0.0657676 -0.1700767 -0.068825 0.024760 0.233386 -0.0998303
## 167 0.1831538 -0.3141016 -0.012452 -0.074567 0.170935 -0.0795802
## 168 -0.0056990 -0.0043989 0.032565 -0.117756 0.161031 0.1119145
## 169 0.2511048 -0.0625907 0.424136 -0.173908 -0.006462 0.0994863
## 170 0.2695713 -0.2799831 0.150789 -0.200583 -0.293728 0.0852982
## 171 -0.0500562 -0.0171289 -0.080997 -0.027102 -0.076623 -0.3445012
## 172 0.1318109 -0.0267083 0.185137 -0.005074 -0.078625 0.0992112
## 173 0.0793332 -0.0821383 0.107601 -0.190722 -0.110021 -0.0900964
## 174 0.3254310 -0.5004660 0.013660 -0.243108 0.053216 0.0941435
## 175 -0.0122773 -0.1400395 -0.176745 0.001564 0.197554 -0.4404845
## 176 0.3563139 -0.5241940 -0.023153 -0.166597 -0.008037 -0.0897090
## 177 0.4090748 -0.5175434 -0.008373 -0.040574 0.005659 0.1219615
## 178 0.2005064 -0.2485664 -0.062120 0.267474 0.015307 0.0033965
## 179 0.4061864 -0.4150800 0.125098 -0.180161 -0.382221 0.1252590
## 180 0.2275629 -0.3204350 -0.069455 0.179002 -0.050556 -0.2089569
## 181 0.3186656 -0.5196143 -0.045944 0.081864 0.377195 0.0707353
## 182 0.0579922 -0.3889797 -0.301933 0.185312 0.749468 -0.6010588
## 183 0.1840996 -0.2586578 -0.058020 0.189539 0.246110 0.1222459
## 184 0.1687889 -0.0834250 0.149628 0.043926 -0.251373 0.0283205
## 185 0.0709839 0.0343081 0.157689 0.015441 -0.076677 -0.0963303
## 186 0.0253658 -0.1176629 -0.235408 0.271876 0.299393 0.0255144
## 187 0.1544682 -0.2507190 -0.004434 -0.032108 0.037951 -0.1202162
## 188 0.0202790 -0.0010358 0.081103 -0.117924 0.018692 -0.0118456
## 189 0.2080184 -0.1757132 0.102574 0.024775 -0.251978 0.0808570
## 190 -0.0279274 -0.1053434 -0.292646 0.209589 0.169112 -0.0924646
## 191 0.1931428 -0.2352415 0.065651 -0.072713 -0.082989 0.0636132
## 192 -0.0196906 -0.0277170 -0.085017 0.016412 0.026943 -0.0987995scores(Mic_canb1920, display = "species", choices = c(1:3))## MDS1 MDS2 MDS3
## AM_bio 0.6645547 1.0217934 -0.21336481
## GNB_bio -0.7597643 0.1485117 0.10984641
## Euk_bio -0.1947162 -1.3553374 -0.81879407
## Fungi_bio 1.6665622 -0.6082357 0.66532649
## GPB_bio -0.6111313 0.2164050 0.16546118
## Actino_bio -0.7655052 0.5768630 0.09152479
## attr(,"const")
## [1] 3.305679scores(Mic_canb1920, display = "site", choices = c(1:3))## MDS1 MDS2 MDS3
## 1 -0.0369694848 0.0898106053 0.159370722
## 2 -0.0415937901 0.1665196730 0.035889849
## 3 0.0429115223 -0.0685427997 0.102400243
## 4 0.0171653405 0.3704032622 0.280396386
## 5 -0.0875451826 0.2850593795 0.199050455
## 6 -0.0224025480 0.1193976055 0.028196965
## 7 -0.0535266441 0.1569062634 -0.159601764
## 8 -0.1752163124 0.4814126554 0.034216232
## 9 0.0378009934 0.0691875109 0.023043912
## 10 0.0277757799 0.1122484994 0.078591852
## 11 -0.0685054907 0.4081563253 0.174237593
## 12 -0.0287512045 0.3596116652 0.244232385
## 13 -0.0001362237 0.3479709545 0.295663967
## 14 0.0701847850 -0.0798545197 0.010214239
## 15 0.1654910441 0.0706679436 0.404347445
## 16 -0.0821961805 0.1031633642 -0.155514175
## 17 -0.0993079367 0.3715960048 0.290845121
## 18 -0.0228819631 0.3383599328 0.284997535
## 19 -0.0212758768 0.3043892397 0.319296854
## 20 -0.0708052641 0.1579739975 0.022220058
## 21 -0.0826722140 0.2811879764 0.061739917
## 22 -0.0438347222 0.1017773956 -0.076214764
## 23 0.1313663456 -0.1597232789 0.123620435
## 24 0.0224743332 0.0653968991 0.133803946
## 25 -0.1260623701 0.1081242254 -0.145262560
## 26 -0.1221876023 0.0672145451 -0.264543081
## 27 -0.0034028862 0.0272841072 -0.113614925
## 28 -0.0363236073 0.0237629893 0.050633094
## 29 -0.1971177032 0.3387669553 -0.094110240
## 30 -0.0106056050 0.2810354582 0.135803381
## 31 -0.0697217978 0.1403912426 -0.054738964
## 32 0.2173953268 -0.2919884365 0.158753912
## 33 -0.1840084391 0.3411047720 0.024824536
## 34 -0.1327855745 0.1853348020 -0.096265251
## 35 -0.1796489032 0.6252502306 -0.033937800
## 36 0.0678833663 0.4074938856 0.397529236
## 37 -0.0272433396 0.2238673331 0.058004299
## 38 -0.1120642786 0.1766490045 0.145408478
## 39 -0.0158210172 0.0619280719 0.072936505
## 40 0.0442653903 0.0611840194 0.349700445
## 41 -0.0100377933 0.0269611204 -0.122379781
## 42 -0.2148869568 0.4136104531 -0.030486166
## 43 -0.1758429582 0.1965843301 -0.185418077
## 44 -0.0036532199 0.2000404005 0.153000065
## 45 0.2967771088 -0.1644281813 0.402481871
## 46 0.0704776576 -0.0337655528 0.196704986
## 47 0.0177604537 0.1030790845 0.166423297
## 48 -0.0376236147 0.0834241886 0.046247142
## 49 0.0560164943 -0.4613462421 -0.885085851
## 50 0.1765037578 -0.1122586181 0.268328014
## 51 -0.1244960251 0.3996141754 0.164007742
## 52 -0.0908968525 0.1521269997 -0.100537082
## 53 -0.0960830992 0.1167089739 -0.028187574
## 54 -0.1919247796 0.0570075661 -0.146572871
## 55 -0.3044116982 0.2976446341 0.193407340
## 56 0.0474772772 0.0651426681 0.423048938
## 57 0.0299612373 0.0813302760 0.004006171
## 58 -0.0336578911 0.2060566347 0.055154479
## 59 -0.0787545110 0.1332751102 0.050993558
## 60 -0.1864401452 0.1411550405 -0.325167353
## 61 0.0739921484 -0.0311319533 0.126288982
## 62 0.1410023712 -0.2410575687 0.063070925
## 63 0.0777889787 -0.0176180788 0.129000106
## 64 0.0994478284 0.0242973148 0.132253973
## 65 0.0643298684 -0.0642323117 -0.055120227
## 66 -0.0092050514 0.0670280781 -0.088167602
## 67 -0.2850408498 0.1880608876 -0.387192664
## 68 -0.0579377026 0.2391762840 -0.073180627
## 69 -0.1878391351 0.5828509914 0.008904502
## 70 -0.1678681016 0.0968797898 -0.165456733
## 71 -0.2456022716 0.3856166820 -0.092696256
## 72 -0.1899449714 0.2106870045 -0.031342216
## 73 -0.0167956431 -0.0216881476 -0.049714748
## 74 -0.1208772792 0.0616459727 -0.138313419
## 75 -0.1329177709 0.0663663531 -0.137697690
## 76 -0.0779171595 -0.0075192324 -0.207971767
## 77 -0.0234954862 -0.0507494297 -0.199948783
## 78 -0.0823419049 0.2521418593 0.053534975
## 79 -0.1599519060 0.2582799835 0.112949325
## 80 -0.0927125124 0.0632832064 -0.244032483
## 81 0.0506307621 0.0005301103 0.076297146
## 82 -0.1173782550 -0.0083509613 -0.346232581
## 83 -0.0048453280 -0.0550521718 -0.074351136
## 84 0.0958965321 -0.0336566463 0.163452005
## 85 0.0137629537 -0.0116690563 -0.085974638
## 86 -0.1604281754 0.0439402284 -0.340752757
## 87 0.0256168873 -0.0119566605 0.012944696
## 88 -0.0804838270 -0.1248322131 -0.247172585
## 89 -0.1743566368 0.0293915402 -0.293306506
## 90 -0.0841795191 -0.1417481238 -0.407763326
## 91 -0.0196269231 -0.0786772094 -0.132890261
## 92 -0.1431809698 0.0567291734 -0.151932750
## 93 -0.0731829845 0.5205331063 0.290833136
## 94 -0.1737220719 0.1933237265 -0.268592931
## 95 0.0118297609 -0.0653753757 0.140545793
## 96 -0.0171057767 0.0392012769 0.081498466
## 97 -0.1079569402 0.0891216439 0.014842582
## 98 -0.1650371237 0.1662110046 -0.173500853
## 99 -0.0157936394 0.0444069016 0.053157284
## 100 -0.0077842069 -0.0464531193 -0.184834567
## 101 -0.1184725344 0.1105945556 -0.019968121
## 102 0.1174429657 0.1260784400 0.345983014
## 103 0.0786477400 -0.0636227991 -0.138484301
## 104 0.1837508858 -0.0906820024 0.088260355
## 105 0.0205129513 0.0078072740 -0.141319495
## 106 0.1193319193 0.0409166377 0.170375988
## 107 -0.0072874808 0.0591530943 -0.064855524
## 108 0.1383391912 -0.1118515861 0.014342749
## 109 -0.0294117806 0.0507432971 -0.100030271
## 110 0.0753598672 -0.0157249054 0.143871521
## 111 0.0556300366 -0.3662132505 -0.552846698
## 112 0.0505883635 0.0050128626 0.001728604
## 113 -0.1110733699 0.0716866210 0.019020236
## 114 0.1472380155 0.1243949783 0.390215351
## 115 0.3390116079 -0.3313342600 0.060936855
## 116 0.0033995612 0.3442453837 0.408580632
## 117 0.2977925457 -0.2406464368 0.111098760
## 118 0.2583988824 -0.1761896766 0.193999408
## 119 0.0036480197 -0.0059007789 -0.163582622
## 120 0.1638550297 -0.1774560536 0.043469109
## 121 0.2164610364 -0.3080630939 0.012308132
## 122 -0.0376759895 -0.0316692876 -0.368529088
## 123 -0.0516754609 0.0672988969 -0.061124372
## 124 0.0973788186 -0.1190750967 0.225855226
## 125 0.1015139436 -0.0360056309 0.062719064
## 126 -0.0431486784 0.0160894929 -0.074166078
## 127 0.0355151849 -0.0406033536 0.037473350
## 128 0.1352562521 -0.0859133594 0.138623618
## 129 0.0080128545 -0.0671919351 -0.195518182
## 130 -0.0462774900 -0.0130945349 -0.268257183
## 131 0.1064450392 -0.0719289079 -0.055130918
## 132 0.0526997670 0.0088006615 -0.226776274
## 133 -0.0058746595 0.0538428166 -0.100777325
## 134 0.1006534121 -0.0928051841 0.066754066
## 135 0.0087195123 -0.0498424590 -0.162361729
## 136 0.0779909568 -0.1511208736 -0.026508952
## 137 -0.0472066580 0.1289741449 -0.012358907
## 138 0.1077768334 -0.1890818990 0.037034672
## 139 0.1396828848 -0.2811025436 0.254158367
## 140 0.1262474861 -0.1718979841 0.149507416
## 141 0.1457428958 -0.1816304599 0.002632915
## 142 0.2323345535 -0.2220649537 0.098889397
## 143 0.2574455193 0.0307718462 0.435438444
## 144 0.1717695455 -0.2916055735 0.004735884
## 145 -0.0454180955 -0.0403074237 -0.286382517
## 146 0.2094575076 -0.1985623195 0.077345934
## 147 -2.4806251088 -1.5452715585 1.324484896
## 148 -0.8140361346 -0.2283070354 -1.208012064
## 149 -0.6425831123 -0.1009854141 -0.815375576
## 150 -0.1312110952 -0.0487865196 -0.285965892
## 151 -0.1873664894 0.0483871985 0.114848433
## 152 -0.0901014344 0.0931132062 0.055095022
## 153 -0.1286831735 0.2405143731 -0.047125968
## 154 0.2979911952 -0.1450717628 0.344371930
## 155 -0.1816287903 0.1587986580 -0.130609332
## 156 -0.0305276569 0.0517350058 -0.108210502
## 157 0.1130492060 -0.0863017688 0.052802643
## 158 0.2331962793 -0.1927521584 0.171274959
## 159 0.1647483284 -0.3738445199 -0.145841696
## 160 0.0293534162 -0.0865460637 -0.087098586
## 161 -0.0027209646 0.0401847185 0.051333039
## 162 0.2192491750 -0.3170567925 -0.049458545
## 163 0.0152372575 -0.0196938556 -0.263548202
## 164 0.1155036747 -0.1857346664 -0.089694972
## 165 0.1735026397 -0.3727286174 -0.217326996
## 166 0.0657675868 -0.1700767180 -0.068825364
## 167 0.1831537947 -0.3141016121 -0.012452089
## 168 -0.0056989767 -0.0043989422 0.032565068
## 169 0.2511048496 -0.0625907077 0.424135706
## 170 0.2695712737 -0.2799830881 0.150788610
## 171 -0.0500562128 -0.0171289029 -0.080997058
## 172 0.1318108832 -0.0267083227 0.185137430
## 173 0.0793331640 -0.0821383050 0.107600707
## 174 0.3254309507 -0.5004660252 0.013660010
## 175 -0.0122773241 -0.1400394847 -0.176744863
## 176 0.3563139341 -0.5241940252 -0.023152983
## 177 0.4090748418 -0.5175434184 -0.008372562
## 178 0.2005064440 -0.2485664193 -0.062120049
## 179 0.4061864299 -0.4150799669 0.125097515
## 180 0.2275628925 -0.3204349591 -0.069454704
## 181 0.3186656251 -0.5196143357 -0.045944320
## 182 0.0579921513 -0.3889796664 -0.301932832
## 183 0.1840995629 -0.2586577656 -0.058019545
## 184 0.1687888921 -0.0834250436 0.149627796
## 185 0.0709839431 0.0343081044 0.157689116
## 186 0.0253657896 -0.1176629374 -0.235408391
## 187 0.1544681730 -0.2507189705 -0.004434491
## 188 0.0202790046 -0.0010358449 0.081103259
## 189 0.2080184113 -0.1757132297 0.102574097
## 190 -0.0279273517 -0.1053434096 -0.292646318
## 191 0.1931428038 -0.2352414898 0.065651309
## 192 -0.0196906120 -0.0277170029 -0.085017253
## attr(,"const")
## [1] 3.305679Canb.fitFull1920 <- envfit(Mic_canb1920 ~ ESD + TSF + Treatment + NH4_ppm + NO3_ppm + Moisture + P_ppm + K_ppm + Ca_ppm + Mg_ppm + TotalN_percent + TotalC_percent + TCNR, data = MicEnv1920_2, choices = c(1:3), perm=499, strata=MicEnv1920_2$YearLoc)
Canb.fitFull1920##
## ***VECTORS
##
## MDS1 MDS2 MDS3 r2 Pr(>r)
## NH4_ppm -0.23257 0.96215 -0.14208 0.0119 0.882
## NO3_ppm -0.85234 0.23187 -0.46877 0.0555 0.026 *
## Moisture -0.79984 0.53949 -0.26305 0.0261 0.188
## P_ppm -0.61550 0.30544 -0.72654 0.0485 0.172
## K_ppm -0.27680 -0.84664 -0.45451 0.0418 0.184
## Ca_ppm -0.04471 0.99290 0.11025 0.0891 0.002 **
## Mg_ppm -0.28634 0.91523 0.28347 0.0361 0.070 .
## TotalN_percent -0.84112 -0.39676 -0.36756 0.0411 0.204
## TotalC_percent -0.94541 0.14396 -0.29236 0.0648 0.010 **
## TCNR -0.55815 0.82691 -0.06849 0.0922 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## MDS1 MDS2 MDS3
## ESDClayey 0.0459 -0.0318 0.0156
## ESDLoamy 0.0643 0.0009 0.0290
## ESDSaline Lowland -0.0941 0.0133 -0.0507
## ESDSandy 0.0415 -0.0028 0.0137
## ESDThin Claypan -0.1336 0.1261 0.1966
## TSF1yr < -0.0083 0.0228 -0.0207
## TSF1yr - 2yr -0.0085 0.0513 0.0000
## TSF2yr - 3yr -0.0053 0.0085 -0.0564
## TSF3yr - 4yr 0.0361 -0.2293 0.0563
## TSFUnburned 0.0081 0.0640 0.0979
## TreatmentCattle 0.0138 0.0385 0.0109
## TreatmentSheep -0.0138 -0.0385 -0.0109
##
## Goodness of fit:
## r2 Pr(>r)
## ESD 0.0403 0.202
## TSF 0.0621 0.036 *
## Treatment 0.0105 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499canb.sigV1920 <- envfit(Mic_canb1920 ~ NO3_ppm + Ca_ppm +
TotalC_percent + TCNR, data = MicEnv1920_2,
choices = c(1:3), perm=499, strata=MicEnv1920_2$YearLoc)plot(Mic_canb1920)
text(Mic_canb1920, display = "species", col="black")
plot(Mic_canb1920)
text(Mic_canb1920, display = "species", col="black")
plot(canb.sigV1920)
Total Carbon and Total C:N are going in the same direction as the bacteria. This is odd at first considering that bacteria like/are more efficient at using lower C:N than fungi.
I’ll get the full range and means for these tomorrow, but if you sort by these values, they still are in the bacteria-friendly range (less than 20).
canb.sigF1920 <- envfit(Mic_canb1920 ~ TSF, data = MicEnv1920_2,
choices = c(1:3), perm=499, strata=MicEnv1920_2$YearLoc)
pairwise.factorfit(Mic_canb1920, fac=MicEnv1920_2$TSF, perm = 499, strata=MicEnv1920_2$YearLoc)##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic_canb1920 by MicEnv1920_2$TSF
## 999 permutations
##
## 1yr < 1yr - 2yr 2yr - 3yr 3yr - 4yr
## 1yr - 2yr 0.8037 - - -
## 2yr - 3yr 0.9150 0.6933 - -
## 3yr - 4yr 0.0050 0.0033 0.0033 -
## Unburned 0.7171 0.9150 0.6933 0.0033
##
## P value adjustment method: fdrTSF is significant…but it it is only 3yr-4yr from the others.
Is something else going on here? Probably!
plot(Mic_canb1920)
text(Mic_canb1920, display = "species", col="black")
ordihull(Mic_canb1920, MicEnv1920_2$TSF, scaling= "symmetric", draw="polygon", col= 1:4, label=TRUE)
The point in the lower left quadrant is probably making 3yr-4yr differnt from the others given there is not a lot of other spread from other TSF levels. I will take it out in the morning once I figure out which row it is and then rerun to see if that makes any difference.
point removed
#Removed row 147 as potential outlier
MicEnv1920_3 = MicEnv1920_2 [-147,]
MicBiomass1920_2 = MicBiomass1920 [-147,]
Mic_canb1920_2 <- capscale(MicBiomass1920_2 ~ 1, metaMDSdist = "true", dist="canb")## Square root transformation
## Wisconsin double standardizationsummary(Mic_canb1920_2) #broke 0.7 on the third axis##
## Call:
## capscale(formula = MicBiomass1920_2 ~ 1, distance = "canb", metaMDSdist = "true")
##
## Partitioning of squared Canberra distance:
## Inertia Proportion
## Total 0.5398 1
## Unconstrained 0.5398 1
##
## Eigenvalues, and their contribution to the squared Canberra distance
##
## Importance of components:
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6 MDS7
## Eigenvalue 0.2287 0.1042 0.04893 0.02140 0.02076 0.01549 0.01076
## Proportion Explained 0.4237 0.1930 0.09066 0.03965 0.03846 0.02869 0.01993
## Cumulative Proportion 0.4237 0.6167 0.70732 0.74697 0.78542 0.81411 0.83405
## MDS8 MDS9 MDS10 MDS11 MDS12 MDS13
## Eigenvalue 0.01005 0.00872 0.007257 0.006885 0.005997 0.005104
## Proportion Explained 0.01862 0.01615 0.013445 0.012756 0.011110 0.009455
## Cumulative Proportion 0.85267 0.86882 0.882266 0.895021 0.906131 0.915587
## MDS14 MDS15 MDS16 MDS17 MDS18 MDS19
## Eigenvalue 0.004508 0.004340 0.003474 0.003224 0.002822 0.002535
## Proportion Explained 0.008353 0.008041 0.006437 0.005974 0.005228 0.004696
## Cumulative Proportion 0.923939 0.931980 0.938417 0.944391 0.949619 0.954315
## MDS20 MDS21 MDS22 MDS23 MDS24 MDS25
## Eigenvalue 0.002211 0.001977 0.001794 0.001574 0.001460 0.001254
## Proportion Explained 0.004096 0.003662 0.003323 0.002917 0.002705 0.002323
## Cumulative Proportion 0.958411 0.962073 0.965396 0.968313 0.971018 0.973340
## MDS26 MDS27 MDS28 MDS29 MDS30 MDS31
## Eigenvalue 0.001236 0.001148 0.001051 0.0009363 0.0009154 0.0008916
## Proportion Explained 0.002291 0.002127 0.001948 0.0017346 0.0016959 0.0016517
## Cumulative Proportion 0.975631 0.977758 0.979706 0.9814410 0.9831369 0.9847887
## MDS32 MDS33 MDS34 MDS35 MDS36
## Eigenvalue 0.0008283 0.000737 0.0006485 0.0006175 0.0005848
## Proportion Explained 0.0015347 0.001365 0.0012014 0.0011440 0.0010835
## Cumulative Proportion 0.9863233 0.987689 0.9888901 0.9900342 0.9911176
## MDS37 MDS38 MDS39 MDS40 MDS41
## Eigenvalue 0.0004759 0.0004418 0.0004226 0.0003759 0.0003416
## Proportion Explained 0.0008817 0.0008186 0.0007828 0.0006964 0.0006329
## Cumulative Proportion 0.9919993 0.9928179 0.9936007 0.9942971 0.9949301
## MDS42 MDS43 MDS44 MDS45 MDS46
## Eigenvalue 0.0003045 0.0002638 0.0002477 0.0002182 0.0002096
## Proportion Explained 0.0005642 0.0004887 0.0004589 0.0004043 0.0003883
## Cumulative Proportion 0.9954943 0.9959829 0.9964418 0.9968461 0.9972345
## MDS47 MDS48 MDS49 MDS50 MDS51
## Eigenvalue 0.0001993 0.0001877 0.0001602 0.0001415 0.0001270
## Proportion Explained 0.0003692 0.0003477 0.0002968 0.0002621 0.0002353
## Cumulative Proportion 0.9976037 0.9979514 0.9982482 0.9985103 0.9987456
## MDS52 MDS53 MDS54 MDS55 MDS56
## Eigenvalue 0.0001163 0.0001089 8.675e-05 0.0000702 6.505e-05
## Proportion Explained 0.0002155 0.0002018 1.607e-04 0.0001301 1.205e-04
## Cumulative Proportion 0.9989611 0.9991629 9.993e-01 0.9994537 9.996e-01
## MDS57 MDS58 MDS59 MDS60 MDS61
## Eigenvalue 0.0000626 5.598e-05 4.403e-05 3.453e-05 1.841e-05
## Proportion Explained 0.0001160 1.037e-04 8.158e-05 6.397e-05 3.410e-05
## Cumulative Proportion 0.9996902 9.998e-01 9.999e-01 9.999e-01 1.000e+00
## MDS62 MDS63 MDS64
## Eigenvalue 1.067e-05 2.167e-06 1.444e-06
## Proportion Explained 1.977e-05 4.014e-06 2.675e-06
## Cumulative Proportion 1.000e+00 1.000e+00 1.000e+00
##
## Scaling 2 for species and site scores
## * Species are scaled proportional to eigenvalues
## * Sites are unscaled: weighted dispersion equal on all dimensions
## * General scaling constant of scores: 2.972498
##
##
## Species scores
##
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6
## AM_bio -0.4615 0.52710 0.7231 -0.39279 -0.23996 -0.06130
## GNB_bio -0.5576 -0.11163 -0.1289 0.06466 -0.17342 -0.41282
## Euk_bio 0.9544 -1.13026 0.3666 0.41482 -0.06738 0.38044
## Fungi_bio 1.5284 0.81517 -0.4167 -0.01184 0.05474 0.03222
## GPB_bio -0.5371 -0.08421 -0.4403 0.21427 -0.14783 0.10541
## Actino_bio -0.9266 -0.01617 -0.1038 -0.28912 0.57385 -0.04395
##
##
## Site scores (weighted sums of species scores)
##
## MDS1 MDS2 MDS3 MDS4 MDS5 MDS6
## 1 -0.0832498 0.069106 -0.2554030 0.1953423 -0.064281 -0.0214684
## 2 -0.1382824 0.081850 0.0635167 0.0074611 0.035954 0.0931791
## 3 0.0706632 0.007819 -0.2323273 -0.0337952 0.351332 -0.1078076
## 4 -0.2325108 0.386069 0.1415258 0.2288102 -0.012792 -0.3264760
## 5 -0.2437780 0.177084 -0.1370845 0.3624261 0.117733 -0.0319220
## 6 -0.0950629 0.064702 0.0627557 0.0009544 0.027970 0.0122110
## 7 -0.1424216 -0.014050 0.2324288 -0.2573650 -0.379771 0.2449190
## 8 -0.4307827 0.177771 0.1793140 -0.0523796 0.186462 0.2888524
## 9 -0.0237588 0.090579 0.1578783 -0.0384979 -0.103427 -0.1175345
## 10 -0.0577731 0.132832 0.1175332 0.0030043 -0.039903 -0.0655747
## 11 -0.3130585 0.286287 0.1579443 0.2049065 0.193747 -0.0851657
## 12 -0.2551989 0.312421 0.0460780 0.2312679 0.104373 -0.2393563
## 13 -0.2276249 0.368780 0.1596960 0.2406129 0.318865 -0.2963608
## 14 0.0946735 0.003465 0.0270397 -0.0442610 0.192867 -0.2043339
## 15 0.0608124 0.357752 -0.1576613 0.0161992 0.042210 0.0639619
## 16 -0.1245576 -0.076103 0.1654459 -0.2306976 0.143188 0.1072208
## 17 -0.3059888 0.280621 -0.0258742 0.3940385 0.555931 0.0171853
## 18 -0.2363138 0.326033 0.0447574 0.2557045 0.243333 -0.2540248
## 19 -0.2126048 0.311285 -0.0730652 0.2878521 0.292808 -0.2552212
## 20 -0.1504571 0.052245 0.1069973 -0.0605325 0.294504 0.2624414
## 21 -0.2394452 0.137532 0.1149248 0.0806520 0.015305 0.1572423
## 22 -0.0983574 -0.008380 0.1434057 -0.1065939 0.082587 0.0445989
## 23 0.1867117 0.034106 -0.2356126 -0.1578668 0.125481 -0.0709424
## 24 -0.0296447 0.108555 -0.0640850 0.0482790 0.067801 -0.0769264
## 25 -0.1556863 -0.119174 0.0122836 -0.2051002 0.092811 0.1138647
## 26 -0.1273677 -0.181732 0.2048876 -0.2900341 0.218809 -0.0205457
## 27 -0.0239853 -0.033899 0.2009096 -0.0904283 0.003385 -0.0606957
## 28 -0.0409156 -0.022508 -0.2132756 0.1986718 -0.268206 0.0185408
## 29 -0.3524814 -0.005065 0.0501566 -0.2975171 -0.218005 0.0971563
## 30 -0.1926810 0.241907 0.2000050 0.1443968 0.043511 -0.0317284
## 31 -0.1402015 -0.003348 0.0525053 -0.0784673 -0.178205 0.1374906
## 32 0.3275361 0.016622 -0.4412326 -0.2436335 0.045578 0.0760011
## 33 -0.3441464 0.053731 -0.0689835 0.0858479 -0.048291 0.2898660
## 34 -0.2105123 -0.053993 -0.0041802 -0.1841087 -0.145729 0.2161061
## 35 -0.5311969 0.232211 0.2672348 -0.0047351 -0.164871 0.1988989
## 36 -0.2243880 0.492566 -0.0455717 0.8067355 -1.980221 -0.1001359
## 37 -0.1668297 0.147108 0.1212539 0.0905792 -0.355237 0.1346015
## 38 -0.1878592 0.056901 -0.2349399 0.1918626 0.217618 0.3172916
## 39 -0.0525212 0.041203 -0.0987739 0.1005347 -0.115297 -0.0587049
## 40 -0.0108437 0.195049 -0.4380233 0.2522006 -0.085364 0.0155715
## 41 -0.0281151 -0.045219 0.1803044 -0.0246272 -0.217421 -0.0273909
## 42 -0.4126051 0.051182 -0.0097831 -0.0923170 -0.216208 0.1645550
## 43 -0.2461190 -0.119537 0.0614991 -0.3988282 -0.192462 -0.0744074
## 44 -0.1349554 0.187785 0.0142685 0.1564706 -0.192611 -0.0190134
## 45 0.2972383 0.290402 -0.4043272 -0.0792160 -0.115141 0.6150644
## 46 0.0663391 0.095753 -0.2827374 -0.0204565 0.001689 -0.0252765
## 47 -0.0571149 0.143221 -0.0735727 0.0972042 0.078795 -0.0513934
## 48 -0.0808747 0.024795 -0.0794137 0.0623267 -0.022694 -0.0022012
## 49 0.3227179 -0.662394 0.4899248 0.4268305 0.121221 1.4016833
## 50 0.1854581 0.163160 -0.3392230 -0.1027037 -0.048041 0.1989553
## 51 -0.3435902 0.207704 -0.0428514 0.3801990 0.093724 -0.0688649
## 52 -0.1620873 -0.035497 0.0612597 -0.1608560 -0.216530 0.1889878
## 53 -0.1410759 -0.042279 -0.0953094 0.0054819 -0.035935 0.2110760
## 54 -0.1642098 -0.238396 -0.3200026 -0.1134972 -0.005370 0.2886949
## 55 -0.3888043 -0.040488 -0.6533678 0.2943801 0.277620 0.8057901
## 56 -0.0105296 0.225652 -0.5608788 0.1443144 0.133567 0.0584569
## 57 -0.0371514 0.082045 0.1577244 -0.0438528 -0.187722 -0.0495480
## 58 -0.1587271 0.133039 0.1608351 0.0040132 0.112304 0.1383514
## 59 -0.1397470 0.020767 -0.1122502 0.0762982 0.080285 0.1404492
## 60 -0.2181752 -0.223963 0.1573813 -0.5497486 -0.147169 -0.3178602
## 61 0.0660506 0.079273 -0.1327249 -0.0597681 0.118210 -0.0770097
## 62 0.2458334 -0.036542 -0.2078593 -0.1141712 0.130469 -0.1775506
## 63 0.0597480 0.097420 -0.0818176 -0.0734733 0.148811 -0.0835746
## 64 0.0462154 0.159160 0.0657571 -0.0643452 -0.097521 -0.1028217
## 65 0.0801108 -0.009512 0.1669613 0.0382267 0.017943 -0.2273957
## 66 -0.0537893 -0.004500 0.1685922 -0.1293953 -0.080926 0.0172830
## 67 -0.3124425 -0.316508 0.0648506 -0.7307671 -0.208492 -0.6117265
## 68 -0.1983029 0.076445 0.2407038 -0.1826262 -0.138541 0.3094150
## 69 -0.5068820 0.220665 0.2415686 -0.0687952 0.171235 0.2556841
## 70 -0.1748606 -0.177633 -0.0628612 -0.2836331 0.195822 0.0478633
## 71 -0.4140391 -0.019972 0.0008088 -0.3955703 -0.185648 0.0381473
## 72 -0.2627090 -0.074719 -0.2215127 -0.0190556 -0.125941 0.3154218
## 73 0.0006195 -0.064390 -0.0143898 0.0958601 -0.067982 -0.1124551
## 74 -0.1220245 -0.152489 -0.1032361 -0.1270204 -0.090980 0.2023635
## 75 -0.1326578 -0.160331 -0.1198700 -0.1277545 -0.012732 0.1830748
## 76 -0.0495598 -0.175554 0.0915521 -0.0379800 0.114079 0.0570366
## 77 0.0134342 -0.148712 0.1483008 0.0736033 0.035085 0.0114950
## 78 -0.2204502 0.108524 0.0474793 0.0429417 -0.003417 0.2094604
## 79 -0.2730227 0.048503 -0.2498528 0.2565568 0.067745 0.3331921
## 80 -0.1062767 -0.153088 0.1676949 -0.2667183 -0.115853 0.0477504
## 81 0.0301272 0.067305 -0.0112495 -0.0296087 0.089174 -0.1311425
## 82 -0.0758643 -0.268298 0.1878417 -0.1313771 -0.041361 -0.0311736
## 83 0.0296301 -0.089214 -0.0161940 0.1023327 0.033162 -0.1060576
## 84 0.0820006 0.112751 -0.1503810 -0.0808883 0.087704 -0.0332286
## 85 0.0129252 -0.036003 0.1401065 0.0381479 -0.127558 -0.1039440
## 86 -0.1377299 -0.275135 0.1215858 -0.2636486 -0.140590 -0.1869739
## 87 0.0216927 0.007960 -0.0117301 0.0832746 -0.204010 -0.1300967
## 88 0.0250344 -0.291815 -0.1014944 0.2542734 0.010400 0.1818987
## 89 -0.1363401 -0.284536 -0.0018621 -0.2125491 0.170794 -0.0665209
## 90 0.0325847 -0.352510 0.2207824 0.1394621 0.033335 0.2779002
## 91 0.0352541 -0.141255 0.0250573 0.1728567 0.030250 -0.0621518
## 92 -0.1331206 -0.185776 -0.1560466 -0.1585915 -0.038529 0.2045017
## 93 -0.3892650 0.400153 0.0871712 0.3563120 0.315301 -0.2781703
## 94 -0.2444587 -0.160194 0.0955020 -0.6093034 -0.341008 -0.1540553
## 95 0.0492898 -0.012064 -0.4056267 0.2070349 -0.302489 -0.1074811
## 96 -0.0383420 0.023885 -0.1555188 0.0681498 0.114511 -0.0433745
## 97 -0.1296042 -0.058224 -0.2166680 0.0641842 0.091197 0.1499415
## 98 -0.2192050 -0.128737 0.0161059 -0.3265460 -0.126966 -0.0188188
## 99 -0.0411974 0.020993 -0.0903909 0.0475373 0.012921 -0.0661912
## 100 0.0210589 -0.118864 0.2012206 0.1778926 -0.214467 -0.0565556
## 101 -0.1506651 -0.061807 -0.1278508 -0.0583004 0.194659 0.2254987
## 102 -0.0066732 0.332530 -0.0640638 0.0481391 -0.017496 -0.0883470
## 103 0.0878925 -0.020431 0.3449003 0.0580645 -0.198547 -0.2234643
## 104 0.1747552 0.143754 0.1525289 -0.2520549 -0.100050 -0.1277132
## 105 0.0037283 -0.031668 0.2877366 -0.0754061 -0.006104 -0.1071437
## 106 0.0484844 0.208592 0.0935672 -0.0890334 -0.118376 -0.0760118
## 107 -0.0469237 0.002357 0.1563934 -0.0928225 0.058857 -0.0411281
## 108 0.1591280 0.055048 0.1477654 -0.0525803 -0.119882 -0.2151892
## 109 -0.0555771 -0.035910 0.1842888 -0.1266522 0.296282 0.0338671
## 110 0.0571924 0.101956 -0.1079408 -0.0497460 0.034381 -0.0773502
## 111 0.2693695 -0.394656 0.7315401 0.5383976 0.043777 0.6250721
## 112 0.0264159 0.047953 0.1347969 -0.0401844 -0.024347 -0.1843788
## 113 -0.1200859 -0.074742 -0.2722621 0.0911699 0.025415 0.1067990
## 114 0.0140879 0.381780 -0.0314879 -0.0451547 0.312801 -0.0455788
## 115 0.4301221 0.096394 0.0808007 -0.3057398 -0.079618 0.1011635
## 116 -0.2221436 0.399288 -0.0882256 0.2946432 0.405854 -0.4562424
## 117 0.3451490 0.143875 0.0682750 -0.4032828 0.019030 0.0595019
## 118 0.2786722 0.178808 -0.0755220 -0.3527827 0.145387 0.1753851
## 119 0.0018318 -0.067413 0.2706830 -0.0351469 0.086172 -0.1026469
## 120 0.2182302 0.032274 0.0007108 -0.2190690 0.289838 -0.1240382
## 121 0.3369872 -0.027008 -0.0462215 -0.0539307 0.122849 -0.0882305
## 122 -0.0100018 -0.204053 0.4284803 -0.1049527 -0.041527 0.0716028
## 123 -0.0803323 -0.037413 0.0508019 -0.0218878 0.029290 -0.0029757
## 124 0.1395205 0.061386 -0.4589090 -0.0627560 -0.066690 0.0197030
## 125 0.0863001 0.089470 0.0866929 -0.1326945 0.090476 -0.1669936
## 126 -0.0413208 -0.072094 0.0207927 -0.0189880 0.159978 -0.0373426
## 127 0.0471990 0.005802 -0.0563152 0.0135454 0.003288 -0.1638916
## 128 0.1410074 0.105525 -0.0871289 -0.2119591 0.286813 -0.0423123
## 129 0.0445731 -0.121037 0.2553625 0.0790352 0.340701 -0.1099948
## 130 -0.0264842 -0.165014 0.2696337 -0.0519630 -0.072392 0.0378042
## 131 0.1119278 0.030210 0.2533302 0.0027480 -0.207530 -0.2434579
## 132 0.0220568 -0.031130 0.4560065 -0.2002587 -0.018459 0.0004955
## 133 -0.0429725 -0.012554 0.2096365 -0.1374561 0.104736 -0.0252801
## 134 0.1230584 0.042778 -0.0414090 -0.0251802 -0.102793 -0.1614631
## 135 0.0340687 -0.095071 0.2158954 0.1253942 -0.101710 -0.1000725
## 136 0.1461238 -0.056226 -0.0065438 0.1570796 -0.039886 -0.2035751
## 137 -0.1176703 0.029893 0.0547589 0.0079332 -0.187033 0.0756108
## 138 0.1903933 -0.038341 -0.1531861 0.0861532 -0.081775 -0.1618722
## 139 0.2726885 -0.020860 -0.7482829 0.0194132 -0.423392 0.0317759
## 140 0.1917760 0.026979 -0.3275830 -0.1254434 -0.069885 -0.0710481
## 141 0.2092286 -0.000935 0.0455843 -0.0669936 0.192348 -0.1769700
## 142 0.2914378 0.085864 -0.0333891 -0.2180696 -0.072320 0.0030600
## 143 0.1463138 0.444200 0.0167613 -0.1222103 0.095389 0.2259300
## 144 0.2978820 -0.062940 -0.1084788 0.1232171 0.026517 -0.1114769
## 145 -0.0082835 -0.192316 0.2507615 0.0063480 -0.110858 0.0744930
## 146 0.2614228 0.075740 0.0127577 -0.1772712 -0.010185 -0.0765442
## 148 -0.3839616 -1.495938 -0.5812760 0.4382937 -0.136465 -0.3263289
## 149 -0.3549567 -1.088171 -0.6912563 -0.0711184 0.010080 -0.5847358
## 150 -0.0573186 -0.296405 -0.0498354 -0.0136548 -0.290107 0.1208882
## 151 -0.1514067 -0.134275 -0.5767439 0.1888948 0.225459 -0.2832764
## 152 -0.1204410 -0.022012 -0.2223389 0.0999475 0.107754 0.1492788
## 153 -0.2427912 0.023639 0.1316947 -0.1766554 0.131600 0.2859032
## 154 0.2852247 0.297676 -0.1841391 -0.1812755 -0.173540 0.4808864
## 155 -0.2239798 -0.132524 -0.0565404 -0.2986398 0.119358 0.0395268
## 156 -0.0573180 -0.043653 0.1515560 -0.1178594 0.106468 0.0057735
## 157 0.1264602 0.056551 0.0250300 -0.0429290 -0.078174 -0.1672782
## 158 0.2732396 0.128829 -0.1613943 -0.1965566 -0.272277 0.0812720
## 159 0.3469970 -0.166362 0.1775337 0.4363229 0.223914 -0.1742377
## 160 0.0722728 -0.075083 0.1023383 0.1536564 0.027644 -0.1909934
## 161 -0.0300465 0.032830 -0.0465868 0.0570831 -0.038671 -0.1049983
## 162 0.3445655 -0.042535 0.1260538 0.1339410 -0.038025 -0.1321093
## 163 0.0169149 -0.102005 0.4124264 -0.0935530 -0.078780 -0.0099743
## 164 0.1922099 -0.059846 0.1791277 0.2305348 -0.115102 -0.2293994
## 165 0.3519169 -0.166306 0.4232750 0.5873549 -0.028499 -0.1548967
## 166 0.1504848 -0.096329 0.0257663 0.2345976 0.019956 -0.2142634
## 167 0.3198201 -0.072222 -0.0685385 0.1671509 0.014265 -0.1092551
## 168 -0.0028594 -0.012991 -0.1131245 0.1033243 -0.142248 -0.1212977
## 169 0.2025720 0.344571 -0.2574321 -0.0382474 -0.085698 0.3853518
## 170 0.3531424 0.088187 -0.1994712 -0.2839118 0.008839 0.1153753
## 171 -0.0237374 -0.105282 -0.0127079 0.0381056 0.313518 -0.0504309
## 172 0.1006820 0.167861 -0.0544549 -0.0849898 -0.049955 -0.0198507
## 173 0.1026365 0.036186 -0.1931676 -0.0684956 0.107734 -0.0948289
## 174 0.5317726 -0.074838 -0.2031998 -0.0008209 -0.110435 -0.0170211
## 175 0.0797338 -0.196408 0.0348025 0.2920439 0.305120 -0.0855557
## 176 0.5662766 -0.076068 -0.1240861 -0.0053637 0.055636 0.1687640
## 177 0.5954181 -0.010243 -0.0140860 -0.0505070 -0.121130 0.1347734
## 178 0.2877213 -0.009197 0.2385939 0.0294931 0.007897 -0.2243516
## 179 0.5272075 0.103861 -0.1577547 -0.3863661 -0.012078 0.3354170
## 180 0.3516144 -0.045502 0.1642844 0.0294898 0.199937 -0.1542526
## 181 0.5410980 -0.091311 0.0670675 0.3061289 -0.167237 -0.0146277
## 182 0.2877667 -0.340473 0.1969871 0.8191536 0.282558 0.0037740
## 183 0.2839789 -0.034020 0.1689356 0.1865303 -0.164581 -0.2055024
## 184 0.1609213 0.149760 -0.0013082 -0.2088840 0.063214 -0.0380010
## 185 0.0217968 0.143726 -0.0349625 -0.0230376 0.115810 -0.0701132
## 186 0.0884858 -0.153407 0.2898174 0.2505785 -0.108362 -0.0720025
## 187 0.2601429 -0.048527 -0.0349529 0.0723286 0.093846 -0.1714184
## 188 0.0118523 0.032589 -0.1267709 0.0222881 0.007273 -0.1083310
## 189 0.2457239 0.099951 -0.0021629 -0.2291568 0.015761 -0.0552401
## 190 0.0457479 -0.222758 0.2521257 0.1687477 0.024494 0.0551591
## 191 0.2749944 0.023944 -0.0792762 -0.0872550 -0.026324 -0.0809417
## 192 0.0022875 -0.084438 0.0314884 0.0531752 0.075973 -0.0840015plot(Mic_canb1920_2)
#use Mic_e1920_2
Mic_e1920_2 <- capscale(MicBiomass1920_2 ~ 1, metaMDSdist = "true", dist="euclidean")## Square root transformation
## Wisconsin double standardizationsummary(Mic_e1920_2) #way better! first axis explains 50%, hits 0.9245 through third axis##
## Call:
## capscale(formula = MicBiomass1920_2 ~ 1, distance = "euclidean", metaMDSdist = "true")
##
## Partitioning of squared Euclidean distance:
## Inertia Proportion
## Total 0.3724 1
## Unconstrained 0.3724 1
##
## Eigenvalues, and their contribution to the squared Euclidean distance
##
## Importance of components:
## MDS1 MDS2 MDS3 MDS4 MDS5
## Eigenvalue 0.1888 0.1070 0.04839 0.02105 0.007059
## Proportion Explained 0.5071 0.2874 0.12995 0.05654 0.018957
## Cumulative Proportion 0.5071 0.7945 0.92450 0.98104 1.000000
##
## Scaling 2 for species and site scores
## * Species are scaled proportional to eigenvalues
## * Sites are unscaled: weighted dispersion equal on all dimensions
## * General scaling constant of scores: 2.900195
##
##
## Species scores
##
## MDS1 MDS2 MDS3 MDS4 MDS5
## AM_bio -0.4582 0.32348 -0.8881 0.007184 0.055151
## GNB_bio -0.4741 -0.01545 0.1410 0.292572 -0.304727
## Euk_bio 0.8051 -1.26207 -0.1046 -0.073412 0.013921
## Fungi_bio 1.4763 0.84365 0.1425 -0.063565 -0.012314
## GPB_bio -0.4585 0.02271 0.3829 0.347135 0.251375
## Actino_bio -0.8905 0.08768 0.3264 -0.509915 -0.003406
##
##
## Site scores (weighted sums of species scores)
##
## MDS1 MDS2 MDS3 MDS4 MDS5
## 1 -0.067628 7.130e-02 0.216253 0.096703 -0.046997
## 2 -0.143840 6.672e-02 -0.052511 -0.125041 0.109358
## 3 0.053492 2.783e-02 0.219443 -0.301600 0.249847
## 4 -0.185944 3.602e-01 -0.167866 0.090495 -0.132267
## 5 -0.206228 2.101e-01 0.168000 0.064234 -0.019178
## 6 -0.103653 4.053e-02 -0.050671 -0.102041 0.023468
## 7 -0.163550 -3.118e-02 -0.358371 0.181489 -0.133657
## 8 -0.367457 2.223e-01 -0.114628 -0.153504 -0.096356
## 9 -0.034779 3.961e-02 -0.171777 -0.049515 -0.188821
## 10 -0.064683 8.748e-02 -0.122062 -0.113660 -0.077491
## 11 -0.259268 3.032e-01 -0.076707 -0.069647 -0.147755
## 12 -0.204138 3.205e-01 -0.026413 0.008556 0.032937
## 13 -0.203227 3.405e-01 -0.038852 -0.220531 -0.277354
## 14 0.068571 -1.497e-02 0.013001 -0.223613 -0.039633
## 15 0.092787 3.288e-01 0.077021 0.004479 0.120636
## 16 -0.160285 -7.897e-02 -0.111142 -0.220712 -0.102307
## 17 -0.295886 2.995e-01 0.235698 -0.342852 -0.119016
## 18 -0.200972 3.193e-01 0.035677 -0.125845 -0.154445
## 19 -0.181380 3.120e-01 0.124432 -0.106614 -0.071838
## 20 -0.198355 3.531e-02 0.025503 -0.429132 -0.036643
## 21 -0.219749 1.338e-01 -0.070373 -0.103213 -0.157255
## 22 -0.119415 -2.396e-02 -0.105979 -0.164350 -0.151354
## 23 0.190179 7.723e-02 0.190412 -0.075871 0.206922
## 24 -0.029592 8.951e-02 0.069635 -0.104094 -0.143204
## 25 -0.184266 -1.071e-01 0.003782 -0.076038 0.079260
## 26 -0.174971 -1.729e-01 -0.089931 -0.220244 -0.204558
## 27 -0.051386 -7.126e-02 -0.163026 -0.086671 -0.057467
## 28 -0.045614 -1.397e-02 0.161237 0.349829 0.188526
## 29 -0.327463 5.795e-03 -0.198803 0.083465 -0.096595
## 30 -0.173733 2.106e-01 -0.182031 -0.138428 -0.285672
## 31 -0.142716 -1.482e-02 -0.090746 0.148539 0.081216
## 32 0.370369 1.611e-01 0.313237 -0.008069 0.468948
## 33 -0.297484 1.058e-01 0.082088 0.129540 0.024621
## 34 -0.216745 -4.097e-02 -0.049649 0.109122 0.279745
## 35 -0.406033 3.502e-01 -0.367405 0.300726 -0.245918
## 36 0.014362 2.231e-01 -0.729977 1.840895 0.020831
## 37 -0.146956 1.133e-01 -0.204729 0.253798 -0.086647
## 38 -0.204053 7.548e-02 0.283999 -0.229083 0.132736
## 39 -0.048455 2.624e-02 0.079053 0.135561 -0.012456
## 40 0.007686 2.059e-01 0.297314 0.193667 0.279008
## 41 -0.042943 -8.532e-02 -0.175551 0.187521 -0.142035
## 42 -0.345277 1.007e-01 -0.085695 0.217827 0.017495
## 43 -0.261869 -1.090e-01 -0.140510 0.121132 -0.206175
## 44 -0.118646 1.599e-01 -0.056640 0.108309 0.272735
## 45 0.393449 3.590e-01 0.182652 0.167953 0.292196
## 46 0.075405 1.082e-01 0.202106 0.036235 0.203699
## 47 -0.058130 1.234e-01 0.072049 -0.127239 0.106360
## 48 -0.083114 1.744e-02 0.080758 0.038374 0.081377
## 49 0.381848 -1.040e+00 -0.212273 -0.220117 0.267706
## 50 0.212490 2.001e-01 0.172832 0.069029 0.430282
## 51 -0.269682 2.796e-01 0.119945 0.210182 -0.055762
## 52 -0.169195 -3.921e-02 -0.123767 0.161550 0.153279
## 53 -0.157704 -1.964e-02 0.098249 0.069078 0.371904
## 54 -0.175979 -1.549e-01 0.312873 0.125383 0.096081
## 55 -0.328938 5.450e-02 0.697082 -0.082312 0.336106
## 56 0.034265 2.459e-01 0.393381 0.020452 0.120438
## 57 -0.051509 2.901e-02 -0.210780 0.046144 0.065893
## 58 -0.172238 1.043e-01 -0.116704 -0.262328 0.026914
## 59 -0.146615 3.190e-02 0.136065 -0.061597 0.139053
## 60 -0.266368 -2.077e-01 -0.232518 0.049013 0.058239
## 61 0.058037 7.541e-02 0.096373 -0.124165 0.320601
## 62 0.251877 2.771e-02 0.226597 -0.049988 -0.224053
## 63 0.049317 8.649e-02 0.064940 -0.175509 0.161281
## 64 0.044657 1.123e-01 -0.095731 0.006963 -0.088279
## 65 0.051943 -6.221e-02 -0.117645 -0.106882 0.130900
## 66 -0.079980 -3.908e-02 -0.188014 -0.027333 0.157408
## 67 -0.364511 -2.650e-01 -0.196808 0.110636 -0.087065
## 68 -0.206307 6.088e-02 -0.328615 -0.056988 -0.058944
## 69 -0.408666 2.958e-01 -0.255407 -0.052860 -0.084605
## 70 -0.220545 -1.536e-01 0.088268 -0.140094 0.016858
## 71 -0.389619 -1.779e-02 -0.214593 0.003586 0.134127
## 72 -0.257577 -1.898e-02 0.184971 0.221808 0.280635
## 73 -0.008531 -8.812e-02 0.039733 0.125566 -0.148013
## 74 -0.156498 -1.134e-01 0.100595 0.152665 0.424265
## 75 -0.159800 -1.238e-01 0.119762 0.092577 0.208044
## 76 -0.080960 -1.817e-01 -0.009362 -0.055426 0.070376
## 77 -0.016905 -1.763e-01 -0.079964 -0.014227 0.398154
## 78 -0.210212 1.102e-01 -0.035664 -0.082517 0.230314
## 79 -0.252404 9.943e-02 0.263359 0.071518 0.187405
## 80 -0.141375 -1.598e-01 -0.167136 0.060951 0.195793
## 81 0.017039 4.483e-02 0.020507 -0.139997 0.010176
## 82 -0.114009 -2.731e-01 -0.116277 0.064124 0.167864
## 83 0.005302 -1.066e-01 0.048982 -0.010537 0.336342
## 84 0.080578 1.104e-01 0.096297 -0.090772 0.316522
## 85 -0.004496 -8.443e-02 -0.124397 0.105311 0.057926
## 86 -0.181893 -2.554e-01 -0.099341 0.142505 0.163703
## 87 0.017061 -2.678e-02 -0.013846 0.202755 0.059784
## 88 -0.007760 -2.612e-01 0.160848 0.088110 0.502013
## 89 -0.184191 -2.485e-01 0.057767 -0.061730 0.059768
## 90 0.022006 -4.128e-01 -0.086040 0.041879 0.046803
## 91 0.015731 -1.695e-01 0.033109 0.035009 0.163125
## 92 -0.168823 -1.358e-01 0.151367 0.121238 0.373743
## 93 -0.305782 4.471e-01 -0.001120 -0.025099 0.088402
## 94 -0.287729 -1.417e-01 -0.317673 0.126414 0.323576
## 95 0.061232 1.379e-02 0.289118 0.396968 0.020874
## 96 -0.051822 2.221e-02 0.153761 -0.136057 0.217945
## 97 -0.130548 -3.164e-02 0.232290 -0.022444 -0.123639
## 98 -0.236680 -1.180e-01 -0.082769 0.103804 0.029328
## 99 -0.046965 9.290e-03 0.093401 -0.020115 0.059626
## 100 0.009778 -1.632e-01 -0.142386 0.253027 -0.247577
## 101 -0.175533 -4.420e-02 0.168946 -0.165714 -0.007311
## 102 0.021445 2.925e-01 0.020027 0.042740 -0.106011
## 103 0.056971 -9.474e-02 -0.300872 -0.002807 -0.129037
## 104 0.163513 1.029e-01 -0.180723 -0.046650 -0.247498
## 105 -0.024813 -7.648e-02 -0.232789 -0.140089 -0.215094
## 106 0.050622 1.529e-01 -0.130444 -0.002914 -0.230249
## 107 -0.072429 -2.899e-02 -0.130319 -0.157492 -0.012715
## 108 0.142593 5.022e-03 -0.148468 0.079474 -0.103525
## 109 -0.102502 -5.431e-02 -0.080859 -0.383578 -0.111353
## 110 0.059985 9.247e-02 0.082316 -0.036487 -0.074947
## 111 0.295615 -7.029e-01 -0.411190 -0.169737 -0.016040
## 112 0.009926 2.323e-03 -0.117407 -0.096085 -0.195534
## 113 -0.110790 -3.878e-02 0.279219 0.062789 -0.212096
## 114 0.029903 3.380e-01 0.019623 -0.231804 -0.097266
## 115 0.440472 1.722e-01 -0.105351 -0.020042 -0.335928
## 116 -0.181858 4.036e-01 0.132004 -0.046507 -0.289437
## 117 0.354753 1.893e-01 -0.100685 -0.150739 -0.361045
## 118 0.300157 2.302e-01 0.019671 -0.212404 -0.209181
## 119 -0.025305 -1.043e-01 -0.179562 -0.181888 -0.257061
## 120 0.195761 5.157e-02 0.004894 -0.332373 -0.277956
## 121 0.314112 2.115e-02 0.035466 -0.117750 -0.206814
## 122 -0.046962 -2.320e-01 -0.297186 -0.093725 -0.150947
## 123 -0.093744 -5.068e-02 -0.013310 -0.013095 -0.200712
## 124 0.161925 1.160e-01 0.324652 0.140266 0.255729
## 125 0.068450 5.785e-02 -0.078683 -0.187989 -0.143897
## 126 -0.065457 -7.978e-02 0.046474 -0.142747 -0.117913
## 127 0.039762 -1.203e-02 0.065287 -0.001906 -0.136951
## 128 0.131632 1.149e-01 0.065688 -0.291107 0.121346
## 129 0.004872 -1.536e-01 -0.111020 -0.361055 0.056099
## 130 -0.055660 -1.954e-01 -0.188855 0.035378 -0.024262
## 131 0.082547 -4.286e-02 -0.247618 0.060551 0.124694
## 132 -0.036521 -6.724e-02 -0.431910 -0.281709 0.061267
## 133 -0.076011 -4.192e-02 -0.168337 -0.232689 -0.046968
## 134 0.122722 2.296e-02 0.007231 0.144540 -0.228600
## 135 0.017010 -1.498e-01 -0.153214 0.104115 -0.094369
## 136 0.133434 -8.578e-02 0.020897 0.088047 -0.113538
## 137 -0.114554 8.282e-03 -0.077956 0.176450 -0.113783
## 138 0.189208 -3.168e-02 0.118100 0.169696 -0.031397
## 139 0.269324 1.024e-01 0.467300 0.516121 0.610675
## 140 0.222027 8.108e-02 0.251264 0.159792 -0.086143
## 141 0.180592 -4.050e-03 -0.015588 -0.212664 0.083067
## 142 0.301808 1.195e-01 -0.011101 0.073677 -0.267909
## 143 0.186724 3.974e-01 -0.031075 -0.142721 -0.095438
## 144 0.277363 -4.862e-02 0.068569 0.053899 0.199888
## 145 -0.036770 -2.282e-01 -0.177690 0.088979 0.127600
## 146 0.254505 8.646e-02 -0.037501 0.016315 0.031408
## 148 -0.150258 -9.914e-01 1.101603 0.450326 -0.905521
## 149 -0.319597 -6.374e-01 0.894343 0.304443 -0.749639
## 150 -0.098553 -2.354e-01 0.101215 0.349308 -0.605673
## 151 -0.081568 -6.953e-02 0.675016 -0.118474 -0.228971
## 152 -0.127788 -3.234e-05 0.235283 -0.058141 0.124214
## 153 -0.258493 2.149e-02 -0.060612 -0.268740 -0.167151
## 154 0.370955 3.335e-01 0.058506 0.186942 -0.369750
## 155 -0.257742 -1.165e-01 0.046972 -0.105829 0.056071
## 156 -0.088817 -6.449e-02 -0.104287 -0.175151 0.025358
## 157 0.112021 2.455e-02 -0.052043 0.060199 0.216414
## 158 0.310024 1.489e-01 0.016649 0.333157 0.113772
## 159 0.297866 -2.915e-01 -0.139662 -0.223351 0.171532
## 160 0.052267 -1.197e-01 -0.034396 -0.046099 -0.098612
## 161 -0.032265 1.141e-02 0.049486 0.027669 -0.123366
## 162 0.311106 -8.450e-02 -0.141149 0.063985 0.066785
## 163 -0.025839 -1.444e-01 -0.337345 -0.112963 -0.053357
## 164 0.173611 -1.322e-01 -0.149488 0.121401 -0.180210
## 165 0.319537 -3.837e-01 -0.320386 -0.050094 0.015271
## 166 0.131933 -1.382e-01 0.012761 0.020788 -0.101659
## 167 0.295237 -7.470e-02 0.024886 0.073754 0.147428
## 168 -0.002351 -2.960e-02 0.094338 0.177903 -0.104844
## 169 0.279469 3.562e-01 0.128512 0.148935 -0.160635
## 170 0.387585 1.933e-01 0.135292 0.040840 -0.062250
## 171 -0.054199 -1.029e-01 0.121020 -0.269637 -0.302293
## 172 0.107217 1.461e-01 0.003807 0.027171 0.054145
## 173 0.094904 4.917e-02 0.148045 -0.086967 0.344981
## 174 0.548595 9.020e-02 0.150816 0.157786 -0.186347
## 175 0.056336 -2.254e-01 0.068479 -0.224412 0.278157
## 176 0.561701 1.151e-01 0.096930 -0.076383 -0.094067
## 177 0.603248 1.531e-01 -0.045164 0.036372 -0.165635
## 178 0.247017 -6.212e-02 -0.206974 -0.092361 -0.062005
## 179 0.590611 3.122e-01 0.086099 -0.052584 -0.145520
## 180 0.303422 -5.833e-02 -0.142317 -0.277833 -0.011666
## 181 0.500735 -1.476e-01 -0.174127 0.148842 -0.283891
## 182 0.284505 -5.464e-01 -0.064046 -0.244475 0.419152
## 183 0.263051 -1.067e-01 -0.175543 0.198817 0.018758
## 184 0.158433 1.412e-01 -0.027577 -0.117905 -0.014395
## 185 0.015229 1.194e-01 0.028389 -0.165019 0.050635
## 186 0.071195 -2.366e-01 -0.205438 0.107646 0.126482
## 187 0.234287 -4.938e-02 0.032519 -0.039975 0.031262
## 188 0.005148 2.248e-02 0.110954 -0.013020 0.163013
## 189 0.243300 1.160e-01 -0.027858 -0.037640 -0.098152
## 190 0.025687 -2.813e-01 -0.135671 0.016334 0.061052
## 191 0.273078 5.127e-02 0.044171 0.081882 -0.092822
## 192 -0.019426 -1.071e-01 0.025135 -0.043795 0.060637plot(Mic_e1920_2)
text(Mic_e1920_2, display = "species", col="black")
e.fitFull1920 <- envfit(Mic_e1920_2 ~ ESD + TSF + Treatment + NH4_ppm + NO3_ppm + Moisture + P_ppm + K_ppm + Ca_ppm + Mg_ppm +
TotalN_percent + TotalC_percent + TCNR, data = MicEnv1920_3, choices = c(1:3), perm=499, strata=MicEnv1920_3$YearLoc)
e.fitFull1920##
## ***VECTORS
##
## MDS1 MDS2 MDS3 r2 Pr(>r)
## NH4_ppm -0.95265 -0.05490 0.29907 0.0123 0.892
## NO3_ppm -0.79958 -0.55604 0.22692 0.0540 0.038 *
## Moisture -0.88783 -0.18987 -0.41916 0.0308 0.082 .
## P_ppm -0.61555 -0.70458 0.35308 0.0648 0.046 *
## K_ppm 0.38812 -0.54814 -0.74088 0.0821 0.006 **
## Ca_ppm -0.55538 0.47171 -0.68487 0.1560 0.002 **
## Mg_ppm -0.70938 0.68867 0.15005 0.0386 0.130
## TotalN_percent -0.24891 -0.78055 -0.57340 0.0292 0.420
## TotalC_percent -0.62367 -0.34344 -0.70220 0.0711 0.002 **
## TCNR -0.79115 0.19023 -0.58129 0.1233 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## MDS1 MDS2 MDS3
## ESDClayey 0.0410 0.0129 0.0017
## ESDLoamy 0.0491 0.0197 -0.1097
## ESDSaline Lowland -0.0639 -0.0443 0.0307
## ESDSandy 0.0232 0.0192 -0.0212
## ESDThin Claypan -0.1260 0.0577 0.5002
## TSF1yr < -0.0287 -0.0154 -0.0008
## TSF1yr - 2yr -0.0380 0.0034 -0.0156
## TSF2yr - 3yr -0.0169 -0.0485 -0.0205
## TSF3yr - 4yr 0.2080 0.0361 -0.0122
## TSFUnburned -0.0322 0.0865 0.0856
## TreatmentCattle -0.0178 0.0218 -0.0386
## TreatmentSheep 0.0180 -0.0220 0.0390
##
## Goodness of fit:
## r2 Pr(>r)
## ESD 0.0768 0.020 *
## TSF 0.0669 0.024 *
## Treatment 0.0174 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499e.sigV1920 <- envfit(Mic_e1920_2 ~ K_ppm + Ca_ppm +
TotalC_percent + TCNR, data = MicEnv1920_3,
choices = c(1:3), perm=499, strata=MicEnv1920_3$YearLoc)
plot(Mic_e1920_2, main="Euclidean", display="sites")
plot(e.sigV1920)
e.sigTSF1920 <- envfit(Mic_e1920_2 ~ TSF, data = MicEnv1920_3,
choices = c(1:3), perm=499, strata=MicEnv1920_3$YearLoc)
pairwise.factorfit(Mic_e1920_2, fac=MicEnv1920_3$TSF, perm = 499, strata=MicEnv1920_3$YearLoc)##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic_e1920_2 by MicEnv1920_3$TSF
## 999 permutations
##
## 1yr < 1yr - 2yr 2yr - 3yr 3yr - 4yr
## 1yr - 2yr 0.8300 - - -
## 2yr - 3yr 0.7956 0.5463 - -
## 3yr - 4yr 0.0025 0.0025 0.0025 -
## Unburned 0.1350 0.3229 0.0740 0.0025
##
## P value adjustment method: fdrplot(Mic_e1920_2, main="Euclidean", display="sites")
ordispider(Mic_e1920_2, MicEnv1920_3$TSF, label=TRUE)
e.sigESD1920 <- envfit(Mic_e1920_2 ~ ESD, data = MicEnv1920_3,
choices = c(1:3), perm=499, strata=MicEnv1920_3$YearLoc)
pairwise.factorfit(Mic_e1920_2, fac=MicEnv1920_3$ESD, perm = 499, strata=MicEnv1920_3$YearLoc)##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic_e1920_2 by MicEnv1920_3$ESD
## 999 permutations
##
## Clayey Loamy Saline Lowland Sandy
## Loamy 0.983 - - -
## Saline Lowland 0.095 0.217 - -
## Sandy 0.983 0.983 0.095 -
## Thin Claypan 0.445 0.592 0.717 0.630
##
## P value adjustment method: fdrplot(Mic_e1920_2, main="Euclidean", display="sites")
ordispider(Mic_e1920_2, MicEnv1920_3$ESD, label=TRUE)