#1

> scatterplotMatrix(env[,c(1:14)]) (#figura exploratoria para variables ambientales con paquete car)
> scatterplotMatrix(log10(env[,1:14]+1))
nMDS para datos biologicos

> esp.dist<-vegdist(spe[,c(1:44)],"bray")
> esp.dist
 18 15 24 27 23 19 22 16 28
15 0.5310021
24 0.6680661 0.3597783
27 0.5621247 0.4055610 0.4934947
23 0.3747078 0.3652097 0.5020306 0.4286111
19 0.5094738 0.4560757 0.5092318 0.4878190 0.3606242
22 0.6234419 0.3579517 0.5010050 0.4655224 0.4812706 0.4726483
16 0.5337610 0.3976674 0.5907623 0.5683930 0.4094312 0.4496731 0.2678031
28 0.8418209 0.5225414 0.5736665 0.3027802 0.6979519 0.6431734 0.5985666 0.7015360
13 0.3453347 0.6063846 0.7576747 0.7543736 0.6221471 0.5739244 0.6948736 0.5514941 0.8600122
14 0.5449810 0.4803756 0.6533606 0.7467915 0.5645808 0.6331942 0.5357609 0.4826350 0.8239667
20 0.3879069 0.3784188 0.4346892 0.4957833 0.2877014 0.3953776 0.4627020 0.3737797 0.6963560
25 0.6318891 0.3376115 0.3369098 0.5001593 0.4258617 0.4311299 0.3822981 0.4306058 0.6086150
7 0.3603697 0.6717391 0.7931069 0.7792917 0.6390838 0.6958570 0.7459886 0.6596144 0.8960202
5 0.4955699 0.7178612 0.8561753 0.8732190 0.7295255 0.7898205 0.8611451 0.7184789 0.9539592
6 0.3382309 0.6355122 0.7441373 0.7496935 0.6252483 0.5684030 0.7249162 0.6509879 0.9014440
3 0.5277480 0.7578503 0.8382119 0.8090236 0.7128798 0.5302756 0.8026152 0.6837953 0.9234485
4 0.4694018 0.6843974 0.8309875 0.8413800 0.7117919 0.5177604 0.8015314 0.6462648 0.9381169
2 0.5724092 0.8206269 0.8372551 0.7581924 0.7249869 0.5389222 0.8321464 0.7354202 0.9053213
9 0.6583569 0.7761039 0.7590517 0.7415898 0.6693889 0.5393143 0.7725082 0.8185866 0.8686670
12 0.4688038 0.6794199 0.6894538 0.6253616 0.5384762 0.4288556 0.7051751 0.6342166 0.8543167
10 0.6248996 0.7644564 0.7842829 0.7096540 0.6625476 0.5059910 0.7875328 0.7656598 0.9016604
11 0.4458523 0.4716274 0.5677373 0.6322919 0.4710280 0.3293493 0.5812219 0.5172825 0.7544064
21 0.5560864 0.7607281 0.7272727 0.5456001 0.4951221 0.5315894 0.6771167 0.7474559 0.7248773
13 14 20 25 7 5 6 3 4
15
24
27
23
19
22
16
28
13
14 0.5547565
20 0.5785542 0.5115258
25 0.7412605 0.5541517 0.4518556
7 0.4533054 0.6550830 0.5959162 0.7556726
5 0.5148988 0.7257681 0.7153827 0.8600858 0.3237446
6 0.3515673 0.6227473 0.5439118 0.7343872 0.1754713 0.3984538
3 0.4965478 0.7836661 0.6690479 0.8168684 0.5154487 0.5634432 0.4517627
4 0.3881748 0.6734743 0.6771854 0.8400134 0.5601721 0.5377506 0.4665100 0.3592689
2 0.5968691 0.8592489 0.6951539 0.8179089 0.6465777 0.7257597 0.5552754 0.2099203 0.4841145
9 0.7292530 0.8282497 0.6982486 0.7884243 0.8318435 0.9014583 0.7223126 0.3885811 0.6222340
12 0.5902386 0.7507074 0.5182426 0.7062564 0.6991666 0.7808641 0.5762462 0.2641851 0.4870742
10 0.7160439 0.8304088 0.6706349 0.7845955 0.7697453 0.8504191 0.6567926 0.3413378 0.5776062
11 0.4272808 0.6743277 0.4461712 0.6175930 0.5262233 0.5563798 0.4077948 0.3002597 0.3215966
21 0.7212772 0.8096450 0.6320431 0.7466232 0.7933350 0.8888316 0.6720141 0.7507773 0.7641304
2 9 12 10 11
15
24
27
23
19
22
16
28
13
14
20
25
7
5
6
3
4
2
9 0.2330286
12 0.1846147 0.2277228
10 0.1456729 0.1117280 0.1793368
11 0.4209596 0.5145260 0.3688102 0.5043578
21 0.6779661 0.5952563 0.5602137 0.6147874 0.6713363
> esp.mds <- metaMDS(spe[,c(1:44)], trace = FALSE)
> esp.mds

Call:
metaMDS(comm = spe[, c(1:44)], trace = FALSE)
global Multidimensional Scaling using monoMDS

Data: wisconsin(sqrt(spe[, c(1:44)]))

Distance: bray

Dimensions: 2
Stress: 0.1843196
Stress type 1, weak ties
Two convergent solutions found after 20 tries
Scaling: centring, PC rotation, halfchange scaling
Species: expanded scores based on ‘wisconsin(sqrt(spe[, c(1:44)]))’

> plot(esp.mds, type = "t",

+ ylab="Dim 2", xlab="Dim 1")
> abline(h=0,lty=2)
> abline(v=0,lty=2)
> x11()

nMDS para datos ambientales

> env.amb.mds <- metaMDS(env[,c(1:14)], trace = FALSE, "euclid")
> env.amb.mds

Call:
metaMDS(comm = env[, c(1:14)], distance = "euclid", trace = FALSE)
global Multidimensional Scaling using monoMDS

Data: wisconsin(sqrt(env[, c(1:14)]))

Distance: euclidean

Dimensions: 2
Stress: 0.094329
Stress type 1, weak ties
Two convergent solutions found after 20 tries
Scaling: centring, PC rotation
Species: expanded scores based on ‘wisconsin(sqrt(env[, c(1:14)]))’

> plot(env.amb.mds, type = "t", xlab="Dim 1", ylab="Dim 2")

> abline(h=0,lty=2)
> abline(v=0,lty=2)
>

#2
> spe.hel <- decostand(spe[,c(1:44)], "hellinger")
> env.amb <- env[,c(1:6)]
> env.amb <- env[,c(1:14)]
> datos.rda<-rda(spe.hel~.,env.amb)
> summary(datos.rda)

Call:
rda(formula = spe.hel ~ N + P + K + Ca + Mg + S + Al + Fe + Mn + Zn + Mo + Baresoil + Humdepth + pH,
data = env.amb)

Partitioning of variance:
Inertia Proportion
Total 0.3647 1.0000
Constrained 0.2551 0.6995
Unconstrained 0.1096 0.3005

Eigenvalues, and their contribution to the variance

Importance of components:
RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8 RDA9
Eigenvalue 0.1115 0.06171 0.02137 0.01843 0.01370 0.007873 0.006766 0.004602 0.002458
Proportion Explained 0.3056 0.16922 0.05859 0.05053 0.03758 0.021589 0.018554 0.012621 0.006740
Cumulative Proportion 0.3056 0.47484 0.53342 0.58395 0.62153 0.643116 0.661670 0.674291 0.681031
RDA10 RDA11 RDA12 RDA13 RDA14 PC1 PC2 PC3
Eigenvalue 0.002058 0.001542 0.001277 0.001237 0.0006376 0.0483 0.02129 0.01089
Proportion Explained 0.005643 0.004230 0.003502 0.003391 0.0017483 0.1324 0.05837 0.02985
Cumulative Proportion 0.686674 0.690904 0.694406 0.697797 0.6995457 0.8320 0.89036 0.92022
PC4 PC5 PC6 PC7 PC8 PC9
Eigenvalue 0.01025 0.007383 0.00559 0.003041 0.001937 0.0008977
Proportion Explained 0.02810 0.020246 0.01533 0.008338 0.005310 0.0024616
Cumulative Proportion 0.94832 0.968562 0.98389 0.992228 0.997538 1.0000000

Accumulated constrained eigenvalues

Importance of components:
RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8 RDA9
Eigenvalue 0.1115 0.06171 0.02137 0.01843 0.01370 0.007873 0.006766 0.004602 0.002458
Proportion Explained 0.4369 0.24189 0.08375 0.07223 0.05372 0.030862 0.026523 0.018041 0.009635
Cumulative Proportion 0.4369 0.67878 0.76253 0.83476 0.88847 0.919334 0.945857 0.963898 0.973533
RDA10 RDA11 RDA12 RDA13 RDA14
Eigenvalue 0.002058 0.001542 0.001277 0.001237 0.0006376
Proportion Explained 0.008067 0.006046 0.005006 0.004848 0.0024993
Cumulative Proportion 0.981600 0.987646 0.992653 0.997501 1.0000000

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: 1.701798

Species scores

RDA1 RDA2 RDA3 RDA4 RDA5 RDA6

Callvulg 0.0160159 0.0826907 0.2581366 1.009e-01 -6.217e-02 -0.0016558
Empenigr -0.0797945 -0.0318913 -0.0009659 -2.068e-01 3.972e-02 0.0171542
Rhodtome -0.0649940 -0.0036694 0.0099162 -5.521e-03 2.004e-02 -0.0369695
Vaccmyrt -0.1960368 -0.0587967 0.0376640 3.073e-02 1.042e-01 -0.1341711
Vaccviti -0.1030220 -0.0671526 -0.0359917 -1.917e-01 -7.543e-02 0.0266973
Pinusylv 0.0054482 -0.0216357 0.0219564 -5.092e-03 -3.067e-02 -0.0186065
Descflex -0.0585529 -0.0092884 -0.0093120 1.958e-02 3.876e-02 0.0137084
Betupube -0.0060662 0.0010395 -0.0007285 -9.983e-03 -5.652e-05 -0.0132610
Vacculig 0.0101729 0.0883246 -0.0453584 -3.014e-02 7.193e-02 0.0743936
Diphcomp 0.0150549 0.0340487 -0.0150175 -3.386e-02 1.075e-02 0.0399392
Dicrsp -0.1139536 -0.0125829 -0.1278945 5.131e-02 -1.597e-01 0.0302947
Dicrfusc -0.1841925 0.0864025 0.2259383 -9.122e-02 4.434e-02 0.0370906
Dicrpoly -0.0167640 -0.0150841 -0.0394492 -7.599e-03 -5.551e-02 -0.0654525
Hylosple -0.1293583 -0.0482427 -0.0402126 8.598e-02 7.241e-02 0.0201377
Pleuschr -0.5391269 -0.2127296 0.0127947 1.052e-01 -7.460e-04 0.0609398
Polypili -0.0002393 0.0079115 -0.0075790 -3.045e-03 -5.401e-03 -0.0087093
Polyjuni -0.0405160 -0.0135278 -0.0531760 -4.854e-02 2.640e-02 0.0082722
Polycomm -0.0163474 -0.0107698 -0.0084498 -1.321e-02 8.874e-03 -0.0142466
Pohlnuta -0.0070166 -0.0130415 0.0018057 -1.324e-02 -2.660e-02 -0.0070774
Ptilcili -0.0352700 -0.0091163 -0.0032319 -7.754e-02 -6.769e-03 -0.0897358
Barbhatc -0.0164054 0.0004019 -0.0018254 -2.776e-02 -3.280e-03 -0.0563063
Cladarbu 0.0847529 0.3321482 0.0601827 -3.323e-02 -1.974e-02 0.0434802
Cladrang 0.2703377 0.3334293 -0.0656048 5.668e-02 1.995e-02 -0.0229181
Cladstel 0.6095059 -0.4175626 0.0719799 6.319e-05 9.979e-03 0.0227190
Cladunci -0.0491593 -0.0007364 0.0510752 -1.500e-02 -1.827e-01 -0.0320825
Cladcocc 0.0100465 0.0105755 0.0129442 -6.232e-03 3.024e-03 0.0035279
Cladcorn -0.0135770 -0.0019280 -0.0129992 -2.494e-02 -7.449e-05 0.0156006
Cladgrac -0.0103700 0.0185140 -0.0032232 -1.195e-02 -1.991e-02 -0.0022603
Cladfimb -0.0029992 0.0086924 0.0151756 -2.275e-02 8.835e-03 -0.0002672
Cladcris -0.0069519 -0.0003240 0.0362857 -3.355e-02 -1.246e-02 -0.0081845
Cladchlo 0.0140180 -0.0136312 -0.0105742 -1.403e-02 -8.729e-03 -0.0067112
Cladbotr -0.0145513 -0.0015019 -0.0003707 -4.882e-03 -5.439e-03 -0.0152525
Cladamau 0.0010772 0.0103110 -0.0060380 -3.817e-03 1.095e-03 0.0018814
Cladsp 0.0028890 0.0012954 0.0110459 1.001e-03 -6.689e-03 0.0171827
Cetreric 0.0118467 0.0127120 -0.0006807 1.796e-02 -5.022e-02 0.0004990
Cetrisla 0.0094616 -0.0209747 0.0046985 -2.484e-03 -2.024e-02 -0.0282418
Flavniva 0.0728301 0.0333792 -0.0124718 6.192e-02 -1.384e-02 0.0510826
Nepharct -0.0132162 0.0069408 -0.0350123 -1.698e-02 3.911e-02 0.0352204
Stersp 0.0265283 0.0968733 -0.0623228 1.703e-02 1.913e-02 -0.0428120
Peltapht -0.0107622 -0.0019275 -0.0007184 -6.351e-03 5.430e-03 0.0097869
Icmaeric 0.0027110 0.0150911 -0.0014810 1.665e-03 2.981e-03 -0.0101809
Cladcerv 0.0045434 -0.0003724 -0.0006722 4.843e-03 1.054e-03 0.0055565
Claddefo -0.0379867 0.0083803 0.0220566 -4.589e-02 -3.476e-02 -0.0203269
Cladphyl 0.0171476 -0.0230933 0.0015490 -2.544e-03 -5.637e-03 -0.0003948
Site scores (weighted sums of species scores)

RDA1 RDA2 RDA3 RDA4 RDA5 RDA6

18 0.063547 0.376636 -0.104156 -0.47185 0.11742 0.446901
15 -0.411240 0.135628 0.273843 0.25414 -0.24911 0.295399
24 -0.411868 -0.085703 -0.658062 0.42715 -1.35085 0.163392
27 -0.467840 -0.285983 -0.152026 0.15129 0.71051 0.121111
23 -0.315381 0.141653 -0.186407 -0.64463 -0.04314 0.097545
19 -0.004261 -0.399878 -0.059006 -0.14275 0.28878 -0.002121
22 -0.462376 0.070743 0.822311 -0.09559 0.29920 0.106865
16 -0.362133 0.284168 0.654361 0.06059 0.08386 -0.023486
28 -0.681257 -0.394331 -0.296893 0.81467 0.68934 -0.396552
13 0.179225 0.295913 0.759287 0.43419 -0.19836 -0.087831
14 -0.268690 0.261510 0.758555 -0.24291 -0.78499 0.021648
20 -0.301031 0.197868 -0.234561 -0.20902 -0.41578 0.386947
25 -0.497264 -0.002898 -0.298710 -0.15410 -0.27959 0.822223
7 0.183035 0.776675 -0.444989 -0.16108 0.32012 0.237391
5 0.294006 0.765653 -0.533941 0.43349 0.20470 -0.572874
6 0.336722 0.459268 -0.026004 -0.17512 -0.15619 -0.073425
3 0.598903 -0.085259 -0.097912 0.05200 0.34220 0.106018
4 0.475554 0.104772 0.186388 0.61031 -0.02653 0.231377
2 0.559570 -0.440300 -0.138583 -0.02434 0.26990 -0.127091
9 0.416576 -0.714393 -0.017081 -0.15401 0.05445 0.012634
12 0.374595 -0.453514 -0.005886 -0.16715 -0.06860 0.123029
10 0.526130 -0.562440 0.009598 -0.20776 0.12627 -0.040189
11 0.224638 -0.119344 0.039537 0.36896 -0.20055 -0.073092
21 -0.049160 -0.326444 -0.249662 -0.75650 0.26694 -1.775819

Site constraints (linear combinations of constraining variables)

RDA1 RDA2 RDA3 RDA4 RDA5 RDA6

18 -0.21379 0.558461 -0.11727 -0.59446 -0.1030588 0.560664
15 -0.03060 -0.197524 0.16216 -0.09697 0.0046381 -0.184044
24 -0.24069 -0.048961 -0.65583 0.45567 -1.1760537 0.061603
27 -0.54468 -0.204033 -0.26284 0.31511 0.3497925 0.387774
23 -0.35644 0.026910 -0.01596 -0.49392 0.0689604 0.200855
19 -0.18585 -0.459134 -0.09984 -0.32297 0.1948144 -0.295013
22 -0.37857 0.186351 0.59820 -0.09808 0.0006994 0.391441
16 -0.08514 0.376485 0.42221 -0.01258 0.0435174 -0.373883
28 -0.67411 -0.328097 -0.10488 0.74028 0.6199817 -0.173171
13 0.05731 0.283086 0.89402 0.49623 -0.1044951 -0.007356
14 -0.09028 -0.110761 0.35629 -0.16882 -0.1965672 -0.317113
20 -0.28866 0.048365 -0.13748 -0.30326 -0.4317098 0.103730
25 -0.31881 -0.078802 -0.29691 -0.13108 0.3774984 0.389540
7 0.54824 0.649590 -0.38598 -0.16348 0.5457515 0.174917
5 0.07140 0.732257 -0.46679 0.32643 0.0365927 -0.522963
6 0.20025 0.204248 0.10080 0.01286 -0.0967437 0.121217
3 0.49206 0.006501 -0.33808 0.05614 0.3343959 -0.121481
4 0.35585 0.217950 0.08386 0.64441 -0.1829867 0.348402
2 0.57771 -0.328996 0.02187 0.01834 0.1253425 0.123114
9 0.46822 -0.575472 0.05032 -0.27148 -0.2660279 0.421621
12 0.12434 -0.158103 0.45698 -0.08925 -0.0469897 -0.044088
10 0.36368 -0.566018 -0.19959 -0.01007 0.1004688 -0.010500
11 0.30410 -0.267049 0.05138 0.20235 -0.0847382 -0.251980
21 -0.15554 0.032746 -0.11662 -0.51139 -0.1130826 -0.983286

Biplot scores for constraining variables

RDA1 RDA2 RDA3 RDA4 RDA5 RDA6

N -0.16243 0.540901 -0.13608 0.1950 0.35442 -0.15969
P -0.31687 -0.511904 -0.22625 0.4019 -0.18397 0.37035
K -0.36280 -0.365953 0.30169 0.4570 -0.11030 0.22278
Ca -0.46400 -0.458433 -0.05936 0.1576 -0.29432 0.14731
Mg -0.41675 -0.385411 -0.15504 0.1396 -0.40085 0.11282
S -0.07421 -0.430521 0.15893 0.3572 -0.42294 0.35883
Al 0.80087 -0.004068 0.11376 0.3396 -0.09083 0.15112
Fe 0.73577 0.073964 -0.03893 0.2036 0.12160 0.11746
Mn -0.72248 -0.196907 -0.03772 0.1501 0.25295 0.39429
Zn -0.35646 -0.333256 -0.20447 0.4652 -0.55826 0.11867
Mo 0.20086 0.099318 0.04045 0.2649 -0.50666 0.29539
Baresoil -0.57368 0.215740 0.08878 -0.4887 -0.19594 -0.17118
Humdepth -0.70654 -0.257932 0.16605 -0.2668 0.14390 0.08604
pH 0.57529 -0.075138 -0.33629 0.1969 -0.01625 -0.21160