> library(vegan) 要求されたパッケージ permute をロード中です This is vegan 2.0-4 > data(varechem) > data(varespec) > varechem N P K Ca Mg S Al Fe Mn Zn Mo Baresoil 18 19.8 42.1 139.9 519.4 90.0 32.3 39.0 40.9 58.1 4.5 0.30 43.90 15 13.4 39.1 167.3 356.7 70.7 35.2 88.1 39.0 52.4 5.4 0.30 23.60 24 20.2 67.7 207.1 973.3 209.1 58.1 138.0 35.4 32.1 16.8 0.80 21.20 27 20.6 60.8 233.7 834.0 127.2 40.7 15.4 4.4 132.0 10.7 0.20 18.70 23 23.8 54.5 180.6 777.0 125.8 39.5 24.2 3.0 50.1 6.6 0.30 46.00 19 22.8 40.9 171.4 691.8 151.4 40.8 104.8 17.6 43.6 9.1 0.40 40.50 22 26.6 36.7 171.4 738.6 94.9 33.8 20.7 2.5 77.6 7.4 0.30 23.00 16 24.2 31.0 138.2 394.6 45.3 27.1 74.2 9.8 24.4 5.2 0.30 29.80 28 29.8 73.5 260.0 748.6 105.3 42.5 17.9 2.4 106.6 9.3 0.30 17.60 13 28.1 40.5 313.8 540.7 118.9 60.2 329.7 109.9 61.7 9.1 0.50 29.90 14 21.8 38.1 146.8 512.2 75.0 36.6 92.3 4.6 29.0 8.1 0.50 33.30 20 26.2 61.9 202.2 741.2 86.3 48.6 124.3 23.6 94.5 10.2 0.60 56.90 25 22.8 50.6 151.7 648.0 64.8 30.2 12.1 2.3 122.9 8.1 0.20 23.70 7 30.5 24.6 78.7 188.5 55.5 25.3 294.9 123.8 10.1 3.0 0.40 18.60 5 33.1 22.7 43.6 240.3 25.7 14.9 39.0 8.4 26.8 8.4 0.20 8.10 6 19.1 26.4 61.1 259.1 37.0 21.4 155.1 81.4 20.6 4.0 0.60 5.80 3 31.1 32.3 73.7 219.0 52.5 25.5 304.6 204.4 14.2 2.6 0.50 3.60 4 18.0 64.9 224.5 517.6 59.7 52.9 435.1 101.2 38.0 9.5 1.10 21.30 2 22.3 47.4 165.9 436.1 64.3 42.3 316.5 200.1 28.2 7.2 0.30 0.01 9 15.0 48.4 127.4 499.6 75.1 46.9 227.1 32.2 35.1 8.9 0.70 6.07 12 16.0 32.7 126.4 471.4 61.3 31.1 108.8 9.5 26.4 6.0 0.40 11.20 10 14.3 62.8 215.2 709.7 102.5 48.6 168.2 32.0 46.9 8.7 0.05 4.40 11 16.7 55.8 205.3 1169.7 126.3 35.9 253.6 96.4 25.1 8.2 0.05 7.60 21 21.0 26.5 104.4 484.8 74.4 22.2 35.8 5.9 27.5 5.3 0.20 56.00 Humdepth pH 18 2.2 2.7 15 2.2 2.8 24 2.0 3.0 27 2.9 2.8 23 3.0 2.7 19 3.8 2.7 22 2.8 2.8 16 2.0 2.8 28 3.0 2.8 13 2.2 2.8 14 2.7 2.7 20 2.5 2.9 25 2.6 2.9 7 1.7 3.1 5 1.0 3.1 6 1.9 3.0 3 1.8 3.3 4 1.8 2.9 2 1.5 2.9 9 2.2 3.0 12 2.2 2.9 10 1.2 3.2 11 1.1 3.6 21 2.5 3.0 > vare.cap <- capscale(varespec ~ N + P + K + Condition(Al), varechem, + dist="bray") > vare.cap Call: capscale(formula = varespec ~ N + P + K + Condition(Al), data = varechem, distance = "bray") Inertia Proportion Rank Total 4.5444 Real Total 4.8034 1.0000 Conditional 0.9772 0.2034 1 Constrained 0.9972 0.2076 3 Unconstrained 2.8290 0.5890 15 Imaginary -0.2590 8 Inertia is squared Bray distance Eigenvalues for constrained axes: CAP1 CAP2 CAP3 0.5413 0.3265 0.1293 Eigenvalues for unconstrained axes: MDS1 MDS2 MDS3 MDS4 MDS5 MDS6 MDS7 MDS8 0.906518 0.512743 0.337915 0.262598 0.203220 0.161762 0.124174 0.085570 MDS9 MDS10 MDS11 MDS12 MDS13 MDS14 MDS15 0.068881 0.058346 0.050083 0.027738 0.020839 0.007306 0.001345 > scores(vare.cap) $species CAP1 CAP2 Cal.vul -0.006448921 4.888236168 Emp.nig 0.153018771 -1.189027820 Led.pal -0.068044317 0.095189855 Vac.myr 0.742584615 2.240594072 Vac.vit 2.232417860 -3.344254859 Pin.syl 0.057974311 -0.136797057 Des.fle 0.258692462 0.189550043 Bet.pub -0.014708530 -0.007149292 Vac.uli -1.083660903 0.316176409 Dip.mon -0.077696481 -0.080392247 Dic.sp 2.169765674 -0.496350940 Dic.fus -1.942174460 2.577746250 Dic.pol 0.014376860 -0.141320923 Hyl.spl 1.367467444 1.393843571 Ple.sch 14.279011564 9.232122749 Pol.pil -0.007494301 -0.005199764 Pol.jun 0.098308187 -0.075702521 Pol.com -0.004479810 -0.002329448 Poh.nut 0.057001288 -0.052752334 Pti.cil -0.476069213 -0.296043379 Bar.lyc -0.165849157 -0.081109687 Cla.arb -7.990636632 0.325405396 Cla.ran -13.687786685 -0.116466288 Cla.ste 5.971375439 -18.377267493 Cla.unc 0.350216484 -0.449666555 Cla.coc -0.015908813 -0.023598158 Cla.cor 0.045461888 -0.043779328 Cla.gra -0.024915597 -0.015452367 Cla.fim -0.034091869 -0.033570867 Cla.cri 0.052580611 -0.019263438 Cla.chl 0.009916933 -0.043986029 Cla.bot -0.007370565 0.010425019 Cla.ama -0.007163512 -0.002097918 Cla.sp 0.009275709 -0.015009690 Cet.eri 0.045748279 -0.055495553 Cet.isl 0.014829071 -0.084444995 Cet.niv 0.734239267 -0.320701697 Nep.arc 0.036275693 -0.056054778 Ste.sp -1.318975160 0.126511869 Pel.aph 0.031333708 0.002324879 Ich.eri -0.021043973 0.003841619 Cla.cer 0.004201029 -0.001662251 Cla.def 0.044552541 0.042959813 Cla.phy 0.044365748 -0.048178336 $sites CAP1 CAP2 18 -1.22403840 -0.5852204 15 0.51838735 1.0389868 24 1.28697355 0.6925441 27 0.81120258 0.3862845 23 -0.04002145 -0.3228072 19 0.56088082 -0.3819465 22 0.21722477 0.7246445 16 -0.23336613 1.0351831 28 1.09852054 1.3769123 13 -0.34941139 1.6030718 14 -0.52943129 0.7824034 20 0.23176006 0.3562497 25 0.43174545 0.3127773 7 -1.23041415 1.1734626 5 -2.46471625 -0.0879167 6 -1.43866452 -0.1256552 3 -0.22563220 -0.6945824 4 0.25963382 0.8521804 2 0.38240215 -1.0544340 9 0.99411030 -1.9237862 12 0.14674394 -1.9475507 10 0.47442779 -2.2727283 11 0.28075996 0.1301925 21 0.04092272 -1.0682654 $centroids [1] NA attr(,"const") [1] 3.197437