chapter 3 pca topsoil
James Lin
8/11/2021
1 Biplot Setup
2 Set up
2.1 1) Load packages
2.2 2) Import data
## [1] "sample_name" "location" "treatment"
## [4] "clay" "t_np" "to_cp"
## [7] "ca" "cu" "mg"
## [10] "mn" "na" "p"
## [13] "p_h" "k" "zn"
## [16] "fe" "cec" "gwc"
## [19] "bd" "ac" "x20wsa2000"
## [22] "respiration" "mb" "gramp"
## [25] "gramn" "actin" "amf"
## [28] "fungi" "fb" "glucosidase"
## [31] "glucosaminidase" "acidphosphotase" "alkphosphatase"
## [34] "arylsulfatase" "phosphodiesterase" "protein"## [1] "sample_name" "location" "treatment" "Clay" "TN"
## [6] "SOC" "Ca" "Cu" "Mg" "Mn"
## [11] "Na" "P" "pH" "K" "Zn"
## [16] "Fe" "CEC" "GWC" "BD" "POXC"
## [21] "MWD" "Resp" "MB" "GmP" "GmN"
## [26] "Act" "AMF" "Fun" "FB" "bG"
## [31] "NAG" "AP" "ALK" "ARY" "PHO"
## [36] "Pro"2.3 4) Theme James
2.4 Overall PCA
## Standard deviations (1, .., p=33):
## [1] 3.615159e+00 2.418593e+00 1.945146e+00 1.440160e+00 1.217822e+00
## [6] 1.053898e+00 9.659879e-01 9.134885e-01 8.359385e-01 7.578631e-01
## [11] 6.534546e-01 6.180760e-01 5.785962e-01 5.183776e-01 4.641616e-01
## [16] 3.842594e-01 3.743173e-01 3.631148e-01 3.449183e-01 2.704280e-01
## [21] 2.550464e-01 2.359468e-01 2.177108e-01 2.000767e-01 1.813732e-01
## [26] 1.762910e-01 1.590204e-01 1.354248e-01 1.234781e-01 9.618431e-02
## [31] 7.227879e-02 6.079750e-02 3.665045e-16
##
## Rotation (n x k) = (33 x 33):
## PC1 PC2 PC3 PC4 PC5
## Clay -0.0763302839 -0.285472857 0.054966695 -0.057845085 0.035819131
## TN -0.2431068930 0.113620298 -0.099521649 0.091626726 0.037468099
## SOC -0.2555224984 0.065372278 -0.086651555 -0.008639296 0.013872651
## Ca -0.0235374295 -0.351019373 -0.195101340 0.057903378 0.154276259
## Cu -0.0627234025 0.009318035 0.316157281 -0.080577266 0.447140465
## Mg -0.0484038078 -0.016923672 0.401583035 0.146274996 -0.200161801
## Mn -0.0478045471 0.325639548 -0.046019083 -0.154866657 0.281345272
## Na -0.0719569820 -0.141668078 0.255466337 -0.330664653 -0.061525699
## P 0.1153645930 0.222144158 -0.267378312 -0.260041396 0.173224678
## pH -0.0164468048 -0.320503889 -0.279357155 0.065009156 -0.104207669
## K 0.0629815910 0.284019348 -0.241894819 -0.045950687 0.129705679
## Zn -0.2111979853 0.144817667 -0.110451181 0.084128455 0.102662451
## Fe -0.0943690234 0.125923593 0.347899730 -0.234668215 -0.006134716
## CEC -0.0277757830 -0.353453286 -0.166879087 0.077098305 0.147528248
## GWC -0.1045501499 -0.170436681 0.012319224 -0.386493578 -0.183303754
## BD 0.0955162297 -0.179231490 0.125514723 0.050766289 0.252582454
## POXC -0.0002862881 0.026435035 0.295544913 0.521721450 -0.011277482
## MWD -0.1999298246 0.084321299 -0.018372408 0.018114554 -0.363920745
## Resp -0.2400311188 0.010103061 -0.005153055 0.147116748 0.215616549
## MB -0.2570614607 -0.073250460 0.019162023 -0.114628399 0.104081288
## GmP -0.2460119169 -0.063047337 0.072296229 -0.136936343 0.063965209
## GmN -0.2447322393 -0.074853571 -0.043987196 -0.062242051 0.152726152
## Act -0.1345037027 -0.131293582 0.201006055 0.139204451 0.206851906
## AMF -0.2511261026 -0.123596334 0.013773325 -0.068338627 0.143507532
## Fun -0.2166773591 -0.042447229 0.069750235 -0.179549759 0.036987921
## FB -0.0822884448 -0.107862678 -0.115675735 -0.039695445 0.117772486
## bG -0.1779859107 0.104165385 -0.069998950 0.283976708 0.185772527
## NAG -0.2361438648 0.159873589 0.030984725 0.007738284 -0.034720848
## AP -0.2316847097 0.146988125 -0.017564692 0.189741006 -0.112786853
## ALK -0.2248120118 -0.047975178 -0.240021344 0.139894614 -0.105759756
## ARY -0.2447724768 -0.018776633 0.011415478 -0.050892835 -0.296999066
## PHO -0.2520702279 -0.077918350 -0.098382782 -0.001520702 -0.129340295
## Pro -0.1718471784 0.245782651 -0.014008715 -0.054364001 -0.049632755
## PC6 PC7 PC8 PC9 PC10
## Clay -0.02086106 0.2249699635 -0.21009163 0.331259031 -0.516289465
## TN -0.08435706 0.0109950831 -0.13474356 -0.080982549 0.027997180
## SOC -0.16938646 0.0397449871 -0.09670616 -0.089511588 0.035312627
## Ca -0.07365511 0.0270973834 -0.08147922 -0.125476905 0.190114457
## Cu -0.12145856 0.0478888510 -0.31638089 0.214415054 -0.116519789
## Mg -0.25424489 0.1459502891 0.26346008 -0.113232526 -0.199468587
## Mn 0.10243693 0.1271499263 -0.04930112 0.312224900 0.072594994
## Na 0.05830157 -0.2645060503 -0.11291599 -0.319121396 -0.240414612
## P -0.08630585 0.0146185885 0.03877671 -0.162243560 0.039857453
## pH 0.02722043 0.0071666956 -0.12148917 -0.060633430 -0.078717207
## K 0.03639169 0.2084125435 0.23194563 -0.062497014 -0.333505449
## Zn -0.23046132 0.0463711960 -0.09730489 -0.240764162 -0.068868299
## Fe -0.16754818 -0.1981937814 -0.20481211 -0.149098036 0.293566233
## CEC -0.11906685 0.0752365501 -0.01694076 -0.169513015 0.127839528
## GWC -0.35197487 0.2382982791 0.06664196 -0.115445937 -0.065532031
## BD -0.32222048 0.3717230896 0.21257693 0.231072398 0.307620237
## POXC -0.04579081 -0.0000631283 -0.04155606 -0.063074441 0.184908770
## MWD 0.14632322 0.0173628609 -0.11649403 0.286262400 0.160566893
## Resp 0.03820870 -0.0045046522 -0.18039885 0.019229745 -0.089640187
## MB 0.16541124 0.0461810822 0.05835380 -0.044042818 0.080102806
## GmP 0.25595112 0.0364546545 -0.09140108 -0.029822350 0.037047724
## GmN 0.18883257 0.0532589174 0.09056703 -0.097919272 0.228110349
## Act 0.31476149 0.0613343958 0.41032009 -0.132556523 -0.200294445
## AMF 0.06088742 -0.1113799580 0.02221333 0.052895702 0.046518314
## Fun 0.19045558 0.0091604175 0.42856284 -0.001015258 0.138639626
## FB -0.34626694 -0.6665167171 0.34438060 0.395331368 -0.062484600
## bG -0.14497537 -0.2068712419 -0.01589960 -0.207306433 -0.230564054
## NAG -0.08984146 0.0612139062 0.10474445 0.007452116 -0.041373675
## AP 0.07600283 -0.0290407901 -0.02718157 0.114284054 -0.031338745
## ALK -0.06038836 0.0368442251 0.01169307 0.001417594 -0.008376931
## ARY -0.03829034 0.0792409537 0.02500176 0.192900970 -0.031173282
## PHO -0.06884595 0.0568151404 -0.02567387 0.125806768 0.058685607
## Pro -0.27438533 0.1615709148 0.11542679 -0.088165998 0.007496480
## PC11 PC12 PC13 PC14 PC15
## Clay 0.2148436711 -0.0007170844 -0.056337589 0.563005316 -0.0953808629
## TN 0.1784825601 0.2433401634 -0.061874462 -0.003800405 0.0480523789
## SOC 0.2019462498 0.1885442935 -0.068911552 0.009978064 0.0084512173
## Ca -0.0072610776 -0.0207471235 -0.317779444 -0.017922301 -0.0449468859
## Cu -0.1733122210 -0.2868989800 -0.144621971 -0.396445424 -0.1153460031
## Mg 0.1135836547 -0.0366550936 0.002822752 -0.161902714 -0.3907055397
## Mn 0.0543625088 0.0536206257 -0.201893661 0.034713505 0.0230329385
## Na -0.3003005594 0.4769904484 -0.038038014 0.010033480 -0.1622304439
## P -0.0228726096 0.0325334021 -0.014772434 0.190867261 -0.0343014364
## pH -0.1668243743 -0.0398765147 0.200009783 -0.055949557 -0.0806889759
## K -0.0534012079 0.1404419922 0.035176643 -0.257726117 -0.2582270225
## Zn 0.2811734700 0.1745665185 0.006166026 -0.091758221 -0.1325794900
## Fe 0.1236902032 0.0186232704 -0.052959659 0.262196185 0.0761522165
## CEC 0.0001173003 -0.0035930499 -0.341864980 -0.078492447 -0.1509134485
## GWC 0.1302998524 -0.2221531655 0.152710791 -0.239509788 0.4803355165
## BD -0.3033947657 0.4523697861 0.324702554 0.125220384 0.0385724172
## POXC 0.0902560080 -0.0586433975 -0.024275695 0.061403470 -0.0658409544
## MWD -0.2794252180 0.2023519272 -0.240141469 -0.124216298 -0.0371617727
## Resp 0.1610554991 0.2117899557 0.224487782 -0.184911942 0.1518368790
## MB 0.0016758284 -0.1097887288 0.151347427 -0.022704844 -0.0747778900
## GmP -0.1330460836 -0.0228975710 0.165944480 -0.029192243 -0.0796940561
## GmN 0.0164336290 -0.1769207510 0.148939447 0.035275808 -0.1753159961
## Act -0.0060801955 0.1496383960 -0.369648748 -0.017651456 0.4984083731
## AMF -0.0540317360 -0.0411045339 0.120553604 -0.049080329 -0.0255166644
## Fun 0.2021574869 -0.1234325411 0.054017376 0.169845778 -0.2757288578
## FB 0.0853340757 0.0541419649 -0.039601702 -0.077672139 -0.0259126209
## bG -0.4209002593 -0.2580897236 0.209418218 0.243584504 0.1233983355
## NAG -0.1496121345 -0.0361799000 -0.035091954 0.105612071 0.0781809845
## AP 0.0723018340 0.0572721254 0.225023116 -0.005099303 0.1294133470
## ALK -0.0863028863 0.0300438491 -0.105220740 0.048679927 -0.0146671479
## ARY -0.1200470216 -0.0263183342 -0.061876138 -0.150249674 -0.0003755959
## PHO 0.0101753903 -0.0485894972 -0.048651105 0.025702540 -0.0669126173
## Pro -0.3201760173 -0.1817604599 -0.290309158 0.214061766 -0.0312804902
## PC16 PC17 PC18 PC19 PC20
## Clay -0.006498226 -0.0723282496 0.1347314093 0.003928476 0.061465724
## TN -0.045579749 0.0769528480 -0.0859492784 0.206331897 -0.152707375
## SOC -0.054601744 0.1108140448 0.0182371330 0.039434136 -0.215359152
## Ca -0.163534717 0.0450767546 0.0256839220 -0.097887866 -0.088492137
## Cu 0.107417325 -0.0306139537 0.0666929494 0.369290069 -0.128914773
## Mg -0.132620503 0.2507546394 0.0421858063 -0.238894513 0.213388384
## Mn -0.059375509 -0.2238752272 -0.2629585113 -0.547178882 -0.066569018
## Na -0.014744675 -0.2914926404 -0.1564194868 -0.040332133 -0.141326247
## P -0.022349973 -0.0709891589 0.2019528947 0.257065996 0.505893631
## pH 0.022761432 -0.1659905027 0.0666011087 0.136986310 0.056880324
## K -0.225876019 -0.2411008839 0.0255010434 0.012221099 0.002894847
## Zn 0.493882811 0.0467806412 0.0538421026 -0.042011718 0.055896691
## Fe -0.124037455 0.0184616970 0.0377808182 0.002315550 0.125626695
## CEC -0.228505985 0.0586063115 0.0355792167 -0.147432018 -0.061313381
## GWC -0.017772550 -0.3308788653 0.1234336249 -0.162070409 -0.067314112
## BD 0.088115885 0.0487195985 -0.0280739296 0.044894035 -0.040828724
## POXC -0.049325884 -0.6592401157 -0.0046213296 0.052107362 0.162151114
## MWD 0.105094973 -0.0433042606 0.6107715147 -0.157986097 0.044355741
## Resp -0.108832546 0.0341796631 0.2807524815 -0.142776296 0.172317608
## MB 0.010734607 0.0080279396 -0.0345834584 -0.070437512 0.099790024
## GmP 0.003669583 0.1240842729 -0.0729396432 0.002581420 0.193195492
## GmN 0.016724589 -0.1488989769 0.0595999573 -0.032385385 0.111231079
## Act 0.139913311 0.0447173648 0.0008134444 0.116653313 0.173829953
## AMF -0.124486472 0.0807414444 -0.0605631752 -0.110261075 0.224391453
## Fun 0.155817027 -0.1048152927 0.2098153729 0.118336607 -0.442185885
## FB 0.003085901 -0.0945555014 0.0482270095 0.020134297 0.100252345
## bG 0.095466001 0.0816724322 0.0730478450 -0.339299220 -0.167480466
## NAG -0.623072814 0.0550865937 0.0903840377 0.215639594 -0.063538906
## AP -0.164716376 -0.0002967628 -0.0903010076 0.190967976 -0.212036936
## ALK 0.087792439 -0.2213093897 -0.1722759178 0.102322758 0.009928299
## ARY 0.122871636 0.0671335429 -0.3148531710 0.062108895 0.124386632
## PHO 0.015097932 -0.0105647720 -0.3789654983 0.040903403 0.217779433
## Pro 0.176231452 0.0084390474 0.0090856022 0.081646661 0.017225557
## PC21 PC22 PC23 PC24 PC25
## Clay 0.015938733 0.036138675 -0.134824579 -0.002859878 -0.052965316
## TN 0.123210724 -0.342910365 -0.331353124 -0.078432422 0.102340993
## SOC 0.072878219 -0.175831179 -0.091479527 -0.055373142 0.088582377
## Ca -0.024595171 0.052506488 0.003593264 0.007975998 0.004593207
## Cu -0.124521127 0.027129207 0.003891066 0.076960138 0.065965606
## Mg 0.006142689 -0.008582279 0.019166633 0.129052200 0.074851057
## Mn 0.076201169 0.059114136 0.157218236 -0.110998608 0.125935407
## Na 0.092348138 0.094441916 0.090086647 0.151635101 0.125479283
## P -0.088554459 -0.021804243 0.004326672 0.159293883 0.403072121
## pH 0.025764925 -0.020617610 0.345139838 -0.440077007 -0.132206842
## K -0.285462763 -0.121173578 -0.188515380 -0.156101147 -0.386071677
## Zn -0.029694591 0.466363127 0.047576539 -0.266082655 0.064776827
## Fe -0.402862418 -0.075291328 -0.001348548 -0.147803809 -0.451390961
## CEC -0.058334698 0.042791275 -0.013780046 0.015129884 -0.026081162
## GWC 0.002541101 0.007584349 -0.105450359 0.007364000 0.060819950
## BD -0.063193000 0.021482991 -0.042764762 -0.010500805 -0.012343023
## POXC 0.094599539 -0.092760921 -0.064441565 -0.165772475 0.142148351
## MWD -0.158494979 0.078134454 -0.132264590 -0.020917237 0.044454235
## Resp 0.118978952 -0.323747276 0.485875066 0.288792295 -0.104791783
## MB 0.042002129 0.048470303 -0.109332754 0.009695655 -0.032832993
## GmP 0.191076223 -0.165970655 -0.156273624 -0.283360121 -0.026258099
## GmN 0.170256933 0.206355269 -0.216578816 0.296797978 -0.129239278
## Act -0.112497647 0.048971615 0.016302798 -0.089318466 -0.053234582
## AMF 0.034578189 0.110068074 -0.166828007 -0.133225407 -0.015436819
## Fun -0.168476923 -0.210342287 0.246810642 -0.049204453 0.162366658
## FB 0.130746517 0.002181195 -0.059238963 -0.058086110 -0.079427578
## bG -0.275869223 -0.120814426 -0.121046101 -0.011777668 0.167040430
## NAG 0.080448809 0.249563901 0.138158106 -0.191791425 0.255666156
## AP -0.041213694 0.456157996 0.031454518 0.182788943 -0.163037504
## ALK -0.130769871 -0.076913405 -0.116264201 0.449753936 -0.132759830
## ARY -0.016557533 -0.218567620 -0.078052559 -0.093838101 0.164670300
## PHO -0.443418570 0.005956114 0.338980636 0.057516427 0.100298497
## Pro 0.463795458 -0.060574977 0.239951616 0.018061249 -0.365769777
## PC26 PC27 PC28 PC29 PC30
## Clay -0.045463114 -0.056440075 0.034940293 0.029152497 0.0006269166
## TN -0.092094013 0.366333020 0.209772608 -0.307316691 -0.1048106381
## SOC -0.089220722 -0.083384976 -0.109219233 0.073970735 0.1659162449
## Ca -0.111648143 -0.044335739 -0.047275203 0.161180087 -0.0308590277
## Cu 0.032306176 0.089562083 -0.006209569 -0.008718812 0.0104324520
## Mg 0.066617829 0.373157801 -0.035928601 0.012544353 -0.0480295701
## Mn 0.120133083 0.308431053 0.018121220 0.077348209 -0.0161272177
## Na -0.082789661 -0.022593699 0.030287907 -0.015310944 0.0151646559
## P -0.139471045 0.217582718 -0.108332018 0.211477279 0.0627166455
## pH 0.152639977 0.467815973 0.148966899 0.035142377 0.0887582800
## K -0.122641403 -0.169034394 0.030190688 0.017605756 0.0063260192
## Zn 0.170834824 -0.181480784 0.020842473 0.026464333 -0.0485418985
## Fe 0.136452049 0.088022490 0.091467111 0.159651253 0.0244570571
## CEC -0.126125587 -0.003936428 -0.053553720 0.179471281 -0.0409292064
## GWC -0.062210651 0.040989655 -0.066508131 -0.052249059 -0.0856296135
## BD 0.013216980 -0.007668813 0.008943808 0.017071491 -0.0166957993
## POXC -0.125959830 -0.114833541 -0.099578524 0.038438435 0.0367748997
## MWD -0.070139865 0.040793879 -0.014848178 -0.094861599 -0.0350353137
## Resp 0.010865663 -0.168443969 0.065835389 0.078081316 0.0290399496
## MB 0.007042866 -0.131867181 -0.204684432 0.051392453 0.0962968230
## GmP 0.021790928 -0.023091936 -0.395952720 0.136218299 -0.5374083753
## GmN -0.016318689 0.030728004 0.601386959 -0.035564508 -0.1473156811
## Act 0.010117994 0.123244995 0.064767927 0.013285761 -0.0117640805
## AMF -0.055914758 0.025215984 -0.183735342 -0.341377171 0.6613642743
## Fun 0.003046567 0.030045884 -0.089735459 0.042038492 0.0800575106
## FB -0.016610407 -0.005786716 0.001192895 0.047018675 -0.1788472176
## bG -0.073484563 0.026739995 0.069459104 0.066005974 -0.0440436751
## NAG 0.354178103 -0.222994374 0.130875747 -0.075341094 -0.0937985072
## AP -0.374949416 0.304062327 -0.205386983 0.326919980 0.0007224411
## ALK 0.614244699 0.090788230 -0.293042048 -0.007787326 0.0213150158
## ARY -0.010836076 -0.170783345 0.331131282 0.556306315 0.2439453717
## PHO -0.312187662 -0.118722689 0.026739128 -0.406688440 -0.2441427152
## Pro -0.212597242 -0.018200644 -0.076375756 -0.086877488 0.0639173242
## PC31 PC32 PC33
## Clay 3.105705e-02 0.009614304 0.000000e+00
## TN 3.045723e-01 0.230178127 -5.073813e-16
## SOC -7.539875e-01 -0.212481381 4.557855e-16
## Ca 1.311742e-01 0.008826359 7.289232e-01
## Cu -5.832655e-02 -0.005155952 3.654456e-17
## Mg -6.942920e-02 0.009886825 1.166931e-01
## Mn -3.540812e-02 0.005467538 -1.295359e-16
## Na 1.715675e-02 0.017633904 1.195006e-02
## P 1.138698e-05 -0.006321490 1.537687e-16
## pH -1.907801e-01 0.060618705 4.992630e-16
## K 1.942732e-02 -0.022454242 8.041946e-02
## Zn 1.620812e-01 -0.013579660 2.450434e-16
## Fe 2.811088e-02 0.016360875 -1.438994e-17
## CEC 1.333236e-01 0.008948476 -6.696593e-01
## GWC 6.492429e-02 -0.037402194 -5.565015e-17
## BD -1.317832e-03 0.008892750 2.932853e-16
## POXC -7.943478e-03 -0.006778343 5.931477e-17
## MWD -2.987538e-02 0.036804940 -8.981211e-17
## Resp 1.487368e-01 -0.005595816 -2.773646e-16
## MB -1.876606e-01 0.825766289 1.935370e-15
## GmP 6.328646e-02 -0.283432311 -7.122570e-16
## GmN -1.685836e-01 -0.185363418 -1.684147e-16
## Act -1.176610e-01 -0.015624714 1.111357e-16
## AMF 1.895246e-01 -0.278802639 -1.980288e-16
## Fun 1.834686e-01 -0.087682985 -2.879613e-16
## FB -5.029521e-02 0.047810433 3.636857e-17
## bG -9.432641e-03 -0.004269481 4.836532e-17
## NAG 4.025449e-02 0.036867836 2.902767e-16
## AP 8.840100e-02 -0.031226506 -2.399837e-16
## ALK 1.952869e-02 -0.076761614 2.690181e-16
## ARY 1.563570e-01 -0.015876602 8.614383e-17
## PHO -1.040811e-01 -0.004413650 6.158793e-17
## Pro 5.576237e-02 0.022897327 -1.998972e-16## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6 PC7
## Standard deviation 3.615 2.4186 1.9451 1.44016 1.21782 1.05390 0.96599
## Proportion of Variance 0.396 0.1773 0.1147 0.06285 0.04494 0.03366 0.02828
## Cumulative Proportion 0.396 0.5733 0.6880 0.75081 0.79575 0.82941 0.85768
## PC8 PC9 PC10 PC11 PC12 PC13 PC14
## Standard deviation 0.91349 0.83594 0.7579 0.65345 0.61808 0.57860 0.51838
## Proportion of Variance 0.02529 0.02118 0.0174 0.01294 0.01158 0.01014 0.00814
## Cumulative Proportion 0.88297 0.90415 0.9215 0.93449 0.94607 0.95621 0.96435
## PC15 PC16 PC17 PC18 PC19 PC20 PC21
## Standard deviation 0.46416 0.38426 0.37432 0.3631 0.34492 0.27043 0.25505
## Proportion of Variance 0.00653 0.00447 0.00425 0.0040 0.00361 0.00222 0.00197
## Cumulative Proportion 0.97088 0.97536 0.97960 0.9836 0.98720 0.98942 0.99139
## PC22 PC23 PC24 PC25 PC26 PC27 PC28
## Standard deviation 0.23595 0.21771 0.20008 0.1814 0.17629 0.15902 0.13542
## Proportion of Variance 0.00169 0.00144 0.00121 0.0010 0.00094 0.00077 0.00056
## Cumulative Proportion 0.99308 0.99451 0.99573 0.9967 0.99767 0.99843 0.99899
## PC29 PC30 PC31 PC32 PC33
## Standard deviation 0.12348 0.09618 0.07228 0.06080 3.665e-16
## Proportion of Variance 0.00046 0.00028 0.00016 0.00011 0.000e+00
## Cumulative Proportion 0.99945 0.99973 0.99989 1.00000 1.000e+00
2.5 Less variables- biologicals
## [1] "sample_name" "location" "treatment" "Resp" "MB"
## [6] "GmP" "GmN" "Act" "AMF" "Fun"
## [11] "bG" "NAG" "AP" "ALK" "ARY"
## [16] "PHO" "Pro"2.6 Less PCA- subset by location
## Standard deviations (1, .., p=14):
## [1] 3.08173598 1.26228497 0.89723179 0.84222540 0.63866923 0.58132238
## [7] 0.46003241 0.38379076 0.31323615 0.28387328 0.21655061 0.17174994
## [13] 0.16442586 0.09101219
##
## Rotation (n x k) = (14 x 14):
## PC1 PC2 PC3 PC4 PC5 PC6
## Resp -0.2793812 -0.02486202 0.29051594 -0.28115029 0.13807424 -0.436831954
## MB -0.3070801 0.21193467 -0.05564918 0.03501593 0.22506875 0.009755181
## GmP -0.2924982 0.22473237 -0.05090488 0.07293425 0.23859381 -0.232977931
## GmN -0.2961093 0.19986562 -0.04172352 -0.05039611 0.32571499 0.197766168
## Act -0.1695054 0.42092409 0.56344153 0.19006048 -0.60617258 0.144763382
## AMF -0.2977739 0.22626088 -0.01381352 -0.14189101 0.18095745 0.013475682
## Fun -0.2620103 0.26827121 -0.09446396 0.40347819 0.09735191 0.226177698
## bG -0.2121104 -0.35608128 0.51992011 -0.26956760 0.18459567 0.359038982
## NAG -0.2750684 -0.29361030 0.07504938 0.33065864 -0.01857088 -0.177290495
## AP -0.2700601 -0.29099381 0.10370681 -0.01456582 -0.18951969 -0.474585804
## ALK -0.2647955 -0.15359245 -0.20782987 -0.44625536 -0.27951091 0.387877313
## ARY -0.2822555 -0.05921448 -0.37343307 0.07289287 -0.39500400 -0.149933024
## PHO -0.2939780 -0.01309293 -0.33451355 -0.22413873 -0.21623487 0.091431030
## Pro -0.1963859 -0.48859743 -0.01848312 0.50587464 0.07964877 0.276653527
## PC7 PC8 PC9 PC10 PC11 PC12
## Resp 0.05802612 -0.50207543 0.34790201 -0.351590012 0.15925803 -0.061608687
## MB -0.06116865 -0.01256922 -0.12100260 0.005908766 -0.01587731 0.034106631
## GmP -0.35608388 0.09462334 -0.44142737 -0.066552970 0.33442029 0.429356900
## GmN 0.23056691 -0.16212547 -0.36988259 0.128072051 -0.31764292 -0.321196687
## Act -0.09919723 -0.14118411 -0.10613837 0.035092585 -0.09427158 0.029892303
## AMF -0.25957767 0.09787748 0.33338318 0.279419700 -0.23712521 -0.346637165
## Fun 0.52555960 0.24640191 0.35691640 -0.283710594 0.24066839 0.086029795
## bG -0.16449165 0.49267293 0.05857575 -0.125686893 0.06286241 0.042674857
## NAG 0.02290150 -0.04545760 0.21050241 0.719901685 0.25228676 0.064512208
## AP 0.45619381 0.28499901 -0.31771602 -0.046711050 -0.31575457 -0.005930972
## ALK 0.23844920 -0.25834481 -0.20308811 0.124370374 0.43245097 -0.024012408
## ARY -0.33722368 0.26901402 0.02099782 -0.262163774 0.15982130 -0.478858765
## PHO -0.08777183 -0.01356980 0.28984167 -0.002251208 -0.46678579 0.585470726
## Pro -0.21336466 -0.39621334 -0.09204655 -0.274369799 -0.20215628 -0.019950428
## PC13 PC14
## Resp 0.130119564 -0.042525269
## MB 0.018469231 0.886216020
## GmP -0.132189017 -0.310046461
## GmN 0.457918630 -0.276542127
## Act 0.004135394 -0.005672800
## AMF -0.584588501 -0.150252906
## Fun -0.067275666 -0.111234556
## bG 0.165651742 0.004624773
## NAG 0.241642293 -0.004902870
## AP -0.277880322 0.029278569
## ALK -0.259353700 0.014588455
## ARY 0.288767540 -0.007575280
## PHO 0.200345391 -0.058705413
## Pro -0.235455445 -0.024657132## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6 PC7
## Standard deviation 3.0817 1.2623 0.8972 0.84223 0.63867 0.58132 0.46003
## Proportion of Variance 0.6784 0.1138 0.0575 0.05067 0.02914 0.02414 0.01512
## Cumulative Proportion 0.6784 0.7922 0.8497 0.90034 0.92948 0.95362 0.96874
## PC8 PC9 PC10 PC11 PC12 PC13 PC14
## Standard deviation 0.38379 0.31324 0.28387 0.21655 0.17175 0.16443 0.09101
## Proportion of Variance 0.01052 0.00701 0.00576 0.00335 0.00211 0.00193 0.00059
## Cumulative Proportion 0.97926 0.98626 0.99202 0.99537 0.99748 0.99941 1.00000
2.7 Less PCA-subset by land use
## Standard deviations (1, .., p=14):
## [1] 3.08173598 1.26228497 0.89723179 0.84222540 0.63866923 0.58132238
## [7] 0.46003241 0.38379076 0.31323615 0.28387328 0.21655061 0.17174994
## [13] 0.16442586 0.09101219
##
## Rotation (n x k) = (14 x 14):
## PC1 PC2 PC3 PC4 PC5 PC6
## Resp -0.2793812 -0.02486202 0.29051594 -0.28115029 0.13807424 -0.436831954
## MB -0.3070801 0.21193467 -0.05564918 0.03501593 0.22506875 0.009755181
## GmP -0.2924982 0.22473237 -0.05090488 0.07293425 0.23859381 -0.232977931
## GmN -0.2961093 0.19986562 -0.04172352 -0.05039611 0.32571499 0.197766168
## Act -0.1695054 0.42092409 0.56344153 0.19006048 -0.60617258 0.144763382
## AMF -0.2977739 0.22626088 -0.01381352 -0.14189101 0.18095745 0.013475682
## Fun -0.2620103 0.26827121 -0.09446396 0.40347819 0.09735191 0.226177698
## bG -0.2121104 -0.35608128 0.51992011 -0.26956760 0.18459567 0.359038982
## NAG -0.2750684 -0.29361030 0.07504938 0.33065864 -0.01857088 -0.177290495
## AP -0.2700601 -0.29099381 0.10370681 -0.01456582 -0.18951969 -0.474585804
## ALK -0.2647955 -0.15359245 -0.20782987 -0.44625536 -0.27951091 0.387877313
## ARY -0.2822555 -0.05921448 -0.37343307 0.07289287 -0.39500400 -0.149933024
## PHO -0.2939780 -0.01309293 -0.33451355 -0.22413873 -0.21623487 0.091431030
## Pro -0.1963859 -0.48859743 -0.01848312 0.50587464 0.07964877 0.276653527
## PC7 PC8 PC9 PC10 PC11 PC12
## Resp 0.05802612 -0.50207543 0.34790201 -0.351590012 0.15925803 -0.061608687
## MB -0.06116865 -0.01256922 -0.12100260 0.005908766 -0.01587731 0.034106631
## GmP -0.35608388 0.09462334 -0.44142737 -0.066552970 0.33442029 0.429356900
## GmN 0.23056691 -0.16212547 -0.36988259 0.128072051 -0.31764292 -0.321196687
## Act -0.09919723 -0.14118411 -0.10613837 0.035092585 -0.09427158 0.029892303
## AMF -0.25957767 0.09787748 0.33338318 0.279419700 -0.23712521 -0.346637165
## Fun 0.52555960 0.24640191 0.35691640 -0.283710594 0.24066839 0.086029795
## bG -0.16449165 0.49267293 0.05857575 -0.125686893 0.06286241 0.042674857
## NAG 0.02290150 -0.04545760 0.21050241 0.719901685 0.25228676 0.064512208
## AP 0.45619381 0.28499901 -0.31771602 -0.046711050 -0.31575457 -0.005930972
## ALK 0.23844920 -0.25834481 -0.20308811 0.124370374 0.43245097 -0.024012408
## ARY -0.33722368 0.26901402 0.02099782 -0.262163774 0.15982130 -0.478858765
## PHO -0.08777183 -0.01356980 0.28984167 -0.002251208 -0.46678579 0.585470726
## Pro -0.21336466 -0.39621334 -0.09204655 -0.274369799 -0.20215628 -0.019950428
## PC13 PC14
## Resp 0.130119564 -0.042525269
## MB 0.018469231 0.886216020
## GmP -0.132189017 -0.310046461
## GmN 0.457918630 -0.276542127
## Act 0.004135394 -0.005672800
## AMF -0.584588501 -0.150252906
## Fun -0.067275666 -0.111234556
## bG 0.165651742 0.004624773
## NAG 0.241642293 -0.004902870
## AP -0.277880322 0.029278569
## ALK -0.259353700 0.014588455
## ARY 0.288767540 -0.007575280
## PHO 0.200345391 -0.058705413
## Pro -0.235455445 -0.024657132## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6 PC7
## Standard deviation 3.0817 1.2623 0.8972 0.84223 0.63867 0.58132 0.46003
## Proportion of Variance 0.6784 0.1138 0.0575 0.05067 0.02914 0.02414 0.01512
## Cumulative Proportion 0.6784 0.7922 0.8497 0.90034 0.92948 0.95362 0.96874
## PC8 PC9 PC10 PC11 PC12 PC13 PC14
## Standard deviation 0.38379 0.31324 0.28387 0.21655 0.17175 0.16443 0.09101
## Proportion of Variance 0.01052 0.00701 0.00576 0.00335 0.00211 0.00193 0.00059
## Cumulative Proportion 0.97926 0.98626 0.99202 0.99537 0.99748 0.99941 1.00000
2.8 Less PCA- subset by land use with C and N
## Standard deviations (1, .., p=16):
## [1] 3.33015629 1.32745203 0.90153038 0.84911178 0.64259303 0.60224871
## [7] 0.50569455 0.44735680 0.32909163 0.28970514 0.25943310 0.21410430
## [13] 0.17117855 0.15870662 0.12964562 0.07761118
##
## Rotation (n x k) = (16 x 16):
## PC1 PC2 PC3 PC4 PC5 PC6
## TN -0.2677758 -0.245511420 -0.035984542 0.11486974 -0.08034124 0.27191938
## SOC -0.2778839 -0.175690702 0.092215419 0.05731012 -0.12581784 0.17039065
## Resp -0.2621482 -0.006616583 -0.286043783 0.28865180 -0.19664248 0.39253376
## MB -0.2787346 0.244726896 0.054593969 -0.03447562 -0.21015745 -0.06729087
## GmP -0.2646693 0.256122777 0.048081881 -0.06920994 -0.23914893 0.11055132
## GmN -0.2691429 0.229232236 0.040651121 0.05022275 -0.29144644 -0.22534061
## Act -0.1453383 0.434083090 -0.561489078 -0.16582107 0.57227462 0.04561454
## AMF -0.2700299 0.254780886 0.015202865 0.13884947 -0.15614581 -0.09772044
## Fun -0.2349928 0.299957333 0.091587624 -0.39277905 -0.09361773 -0.14853814
## bG -0.2008270 -0.293766067 -0.527099730 0.21547953 -0.07131728 -0.52944152
## NAG -0.2591588 -0.229786056 -0.086758937 -0.35835147 0.01677500 0.11535290
## AP -0.2555415 -0.238128951 -0.116762920 -0.01264269 0.16814108 0.38223849
## ALK -0.2491785 -0.118248178 0.201472379 0.40913026 0.34459970 -0.32723379
## ARY -0.2602273 -0.006695749 0.360622025 -0.10573570 0.41673756 0.09026262
## PHO -0.2721212 0.025494076 0.328469956 0.19624896 0.25422981 -0.10737239
## Pro -0.1904176 -0.420686128 0.004404824 -0.54640665 -0.03758373 -0.27430553
## PC7 PC8 PC9 PC10 PC11
## TN -0.36182823 0.10593697 -0.06489674 0.2118618281 -0.426767457
## SOC -0.35154424 0.24522111 0.26405736 0.0866283093 -0.218623768
## Resp -0.02588831 0.13698799 0.12706575 -0.0001835356 0.664384348
## MB 0.07636513 0.02499022 -0.11971026 0.0044953926 0.007581183
## GmP 0.37094180 0.18198681 -0.35410726 0.2316691090 -0.266728760
## GmN -0.15363761 -0.17587457 -0.43742049 -0.1501643266 0.135700728
## Act -0.20036696 0.21649539 -0.10412713 -0.0046696974 -0.056673318
## AMF 0.19971748 0.17008457 0.30283673 -0.2682836728 -0.131969935
## Fun -0.32534158 -0.47490628 0.41558524 0.2437686947 0.062477034
## bG 0.29968464 -0.10533100 0.22910980 0.2297940023 -0.137731135
## NAG 0.13119308 -0.05836503 0.09671768 -0.7365729382 -0.180141501
## AP 0.19735073 -0.62210313 -0.21330820 0.0893091662 0.026832827
## ALK -0.28625289 -0.09753654 -0.28993608 -0.1525323786 -0.008113886
## ARY 0.39065245 0.11795360 0.11361138 0.2919656757 0.039830971
## PHO 0.06106878 0.06786213 0.22088141 -0.1036852223 0.203547769
## Pro -0.08753516 0.33811624 -0.22469654 0.1317840478 0.345389721
## PC12 PC13 PC14 PC15 PC16
## TN 0.123658800 -0.0169094659 -0.091625268 -0.54069008 0.288872393
## SOC 0.040358923 -0.0319272587 -0.098193093 0.64026120 -0.322945399
## Resp -0.285799310 -0.0004515216 -0.011209781 -0.12058376 -0.002617374
## MB 0.005787031 0.0361190200 -0.006316851 0.40134246 0.791349700
## GmP -0.270869775 0.3927065166 0.195612073 -0.05538442 -0.313035908
## GmN 0.246296496 -0.2290411805 -0.508046781 -0.07163455 -0.268176234
## Act 0.107396613 0.0224178686 -0.024717784 0.05775299 -0.032044025
## AMF 0.284294228 -0.4569772153 0.483485099 -0.16649331 -0.087647491
## Fun -0.228012675 0.0790507802 0.101145447 -0.14992087 -0.054278809
## bG -0.041171873 0.0670567959 -0.178170562 0.02393785 -0.005340188
## NAG -0.267350592 0.1198841263 -0.188398809 -0.06152802 0.020324443
## AP 0.314444054 -0.0660004931 0.257520752 0.19155540 -0.058518336
## ALK -0.438941921 -0.0576013566 0.306604665 0.03528823 -0.005407372
## ARY -0.188362303 -0.4119725799 -0.366072008 -0.05777331 0.019556671
## PHO 0.444539531 0.6131664160 -0.083667092 -0.11285321 -0.010112074
## Pro 0.158660695 -0.0538018658 0.268796248 -0.04474286 -0.008531989## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6 PC7
## Standard deviation 3.3302 1.3275 0.9015 0.84911 0.64259 0.60225 0.50569
## Proportion of Variance 0.6931 0.1101 0.0508 0.04506 0.02581 0.02267 0.01598
## Cumulative Proportion 0.6931 0.8033 0.8540 0.89911 0.92492 0.94759 0.96357
## PC8 PC9 PC10 PC11 PC12 PC13 PC14
## Standard deviation 0.44736 0.32909 0.28971 0.25943 0.21410 0.17118 0.15871
## Proportion of Variance 0.01251 0.00677 0.00525 0.00421 0.00287 0.00183 0.00157
## Cumulative Proportion 0.97608 0.98285 0.98810 0.99230 0.99517 0.99700 0.99857
## PC15 PC16
## Standard deviation 0.12965 0.07761
## Proportion of Variance 0.00105 0.00038
## Cumulative Proportion 0.99962 1.00000
