Last data update: 2014.03.03

 R: Significant dimensions in principal coordinate analysis
pcoa.sigR Documentation

Significant dimensions in principal coordinate analysis

Description

Function for determine the number of significant dimensions in principal coordinate analysis (PCoA).

Usage

pcoa.sig(data, dist = "gower", correction = "none", squareroot = FALSE,
  n.start = NULL, axis = 6, iterations = 1000)

## S3 method for class 'pcoasig'
print(x, ...)

## S3 method for class 'pcoasig'
scores(x, choices = c(1, 2), ...)

## S3 method for class 'pcoasig'
summary(object, ...)

Arguments

data

Community data matrix.

dist

Dissimilarity index, as accepted by vegdist (Default dist="gower").

correction

Correction methods for negative eigenvalues, as accepted by pcoa: "lingoes" and "cailliez" (Default correction="none").

squareroot

Logical argument (TRUE or FALSE) to specify if use square root of dissimilarity index (Default squareroot = FALSE).

n.start

Initial sample size. One sampling unit is added at each sampling step. If n.start = NULL initial sample size is equal to total sample size (Default n.start=NULL).

axis

Maximum number of ordination principal axes to be monitored (Default axis=6).

iterations

Number of permutations to assess significance (Default iterations=1000).

x

An object of class pcoasig.

...

Other parameters for the respective functions.

choices

Axes for re-scaling. Choices must have length equal to two (Default choices = c(1,2)).

object

An object of class pcoasig.

Details

At each iteration step a bootstrap sample is subjected to PCoA ordination, the scores are submitted to a procrustean adjustment, and the correlation between observed and bootstrap ordination scores is computed. It compares such correlations to the same parameter generated in a parallel bootstrapped ordination of randomly permuted data. The number of axes in bootstrap or null PCoA with eigenvectors corresponding to positive eigenvalues may be smaller than the number of axes monitored, in this case, axes with values equal to 0 are created. The number of iterations with original values for each axis is shown in n.permut.bootstrap and n.permut.null.

The function scores.pcoasig re-scales the correlation values for biplot graphics.

Value

PCoA

PCoA result, exactly as returned for the pcoa function.

correlations

Correlations between axis and original data.

mean.cor.null

Mean correlations, for axis, between null and reference scores.

mean.cor.bootstrap

Mean correlations, for axis, between bootstrap and reference scores.

cumulative.frequency

Cumulative frequency in which the null correlations were greater than the bootstrap correlation.

n.permut.bootstrap

Number of iterations for each axis in bootstrap step.

n.permut.null

Number of iterations for each axis in null step.

probabilities

Probabilities for each axis.

Note

Principal Component Analysis (PCA)

You can use the same function to determine the number of significant dimensions in principal component analysis (PCA). For this, standardize each variable for zero mean and uni variance (function decostand and method standardize) and use euclidean distance as dissimilarity index.

Interpretation

If the higher dimension is significant, then all lower dimensions will also be significant.

Author(s)

Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

References

Pillar, V.D. (1999). The bootstrapped ordination reexamined. Journal of Vegetation Science 10, 895-902.

See Also

pcoa, procrustes

Examples


data(flona)
res<-pcoa.sig(flona$community, axis = 6, dist = "bray", iterations = 100)
res
summary(res)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PCPS)
Loading required package: SYNCSA
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
Loading required package: mice
Loading required package: Rcpp
mice 2.25 2015-11-09
Loading required package: FD
Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:vegan':

    cca

Loading required package: ape
Loading required package: geometry
Loading required package: magic
Loading required package: abind
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PCPS/pcoa.sig.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pcoa.sig
> ### Title: Significant dimensions in principal coordinate analysis
> ### Aliases: pcoa.sig print.pcoasig scores.pcoasig summary.pcoasig
> ### Keywords: PCPS
> 
> ### ** Examples
> 
> 
> data(flona)
> res<-pcoa.sig(flona$community, axis = 6, dist = "bray", iterations = 100)
> res
Call:
pcoa.sig(data = flona$community, dist = "bray", axis = 6, iterations = 100) 

PCoA values:
    Eigenvalues  Relative_eig Rel_corr_eig Broken_stick Cum_corr_eig
1   1.887197491  0.2155976279  0.121422908 0.1135563844    0.1214229
2   1.474472030  0.1684469556  0.097731440 0.0865293574    0.2191543
3   1.180263963  0.1348359734  0.080843165 0.0730158439    0.2999975
4   0.933750430  0.1066737205  0.066692676 0.0640068349    0.3666902
5   0.793114926  0.0906072086  0.058619848 0.0572500781    0.4253100
6   0.738461575  0.0843634885  0.055482610 0.0518446727    0.4807926
7   0.661048538  0.0755196515  0.051038909 0.0473401682    0.5318316
8   0.475947566  0.0543733057  0.040413653 0.0434791644    0.5722452
9   0.402954908  0.0460344626  0.036223693 0.0401007860    0.6084689
10  0.350001391  0.0399849353  0.033184029 0.0370977830    0.6416529
11  0.332171578  0.0379480180  0.032160554 0.0343950803    0.6738135
12  0.233892086  0.0267203508  0.026519067 0.0319380778    0.7003326
13  0.220316158  0.0251694066  0.025739775 0.0296858256    0.7260723
14  0.178218249  0.0203600481  0.023323250 0.0276068235    0.7493956
15  0.135085469  0.0154324637  0.020847321 0.0256763215    0.7702429
16  0.124180583  0.0141866653  0.020221353 0.0238745197    0.7904642
17  0.066406756  0.0075864551  0.016904992 0.0221853306    0.8073692
18  0.061085956  0.0069785951  0.016599565 0.0205955054    0.8239688
19  0.050988275  0.0058250136  0.016019933 0.0190940039    0.8399887
20  0.028140397  0.0032148213  0.014708408 0.0176715288    0.8546971
21  0.015362082  0.0017549983  0.013974901 0.0163201775    0.8686720
22  0.003584265  0.0004094744  0.013298825 0.0150331762    0.8819709
23  0.000000000  0.0000000000  0.012617773 0.0138046750    0.8945886
24 -0.008280234 -0.0009459523  0.011466143 0.0126295868    0.9060548
25 -0.028342617 -0.0032379234  0.011088532 0.0115034607    0.9171433
26 -0.034920916 -0.0039894429  0.010566364 0.0104223796    0.9277097
27 -0.044017530 -0.0050286603  0.009669135 0.0093828786    0.9373788
28 -0.059648014 -0.0068143214  0.009019903 0.0083818776    0.9463987
29 -0.070958184 -0.0081064203  0.008780538 0.0074166266    0.9551793
30 -0.075128129 -0.0085828041  0.008594375 0.0064846602    0.9637736
31 -0.078371244 -0.0089533048  0.007802472 0.0055837593    0.9715761
32 -0.092166866 -0.0105293473  0.007189413 0.0047119197    0.9787655
33 -0.102846869 -0.0117494544  0.006653531 0.0038673251    0.9854191
34 -0.112182389 -0.0128159650  0.004729051 0.0030483243    0.9901481
35 -0.145708466 -0.0166460584  0.004443663 0.0022534117    0.9945918
36 -0.150680174 -0.0172140374  0.004047965 0.0014812109    0.9986397
37 -0.157573564 -0.0180015536  0.001360269 0.0007304602    1.0000000
38 -0.204395504 -0.0233505958  0.000000000 0.0000000000    1.0000000
39 -0.228092546 -0.0260577985  0.000000000 0.0000000000    1.0000000
   Cumul_br_stick
1       0.1135564
2       0.2000857
3       0.2731016
4       0.3371084
5       0.3943585
6       0.4462032
7       0.4935433
8       0.5370225
9       0.5771233
10      0.6142211
11      0.6486162
12      0.6805542
13      0.7102401
14      0.7378469
15      0.7635232
16      0.7873977
17      0.8095831
18      0.8301786
19      0.8492726
20      0.8669441
21      0.8832643
22      0.8982974
23      0.9121021
24      0.9247317
25      0.9362352
26      0.9466575
27      0.9560404
28      0.9644223
29      0.9718389
30      0.9783236
31      0.9839073
32      0.9886193
33      0.9924866
34      0.9955349
35      0.9977883
36      0.9992695
37      1.0000000
38      1.0000000
39      1.0000000

Probabilities:
   Axis.1 Axis.2 Axis.3 Axis.4 Axis.5 Axis.6
39   0.37   0.45   0.33   0.53    0.5    0.5
> summary(res)
$call
pcoa.sig(data = flona$community, dist = "bray", axis = 6, iterations = 100)

$values
    Eigenvalues  Relative_eig Rel_corr_eig Broken_stick Cum_corr_eig
1   1.887197491  0.2155976279  0.121422908 0.1135563844    0.1214229
2   1.474472030  0.1684469556  0.097731440 0.0865293574    0.2191543
3   1.180263963  0.1348359734  0.080843165 0.0730158439    0.2999975
4   0.933750430  0.1066737205  0.066692676 0.0640068349    0.3666902
5   0.793114926  0.0906072086  0.058619848 0.0572500781    0.4253100
6   0.738461575  0.0843634885  0.055482610 0.0518446727    0.4807926
7   0.661048538  0.0755196515  0.051038909 0.0473401682    0.5318316
8   0.475947566  0.0543733057  0.040413653 0.0434791644    0.5722452
9   0.402954908  0.0460344626  0.036223693 0.0401007860    0.6084689
10  0.350001391  0.0399849353  0.033184029 0.0370977830    0.6416529
11  0.332171578  0.0379480180  0.032160554 0.0343950803    0.6738135
12  0.233892086  0.0267203508  0.026519067 0.0319380778    0.7003326
13  0.220316158  0.0251694066  0.025739775 0.0296858256    0.7260723
14  0.178218249  0.0203600481  0.023323250 0.0276068235    0.7493956
15  0.135085469  0.0154324637  0.020847321 0.0256763215    0.7702429
16  0.124180583  0.0141866653  0.020221353 0.0238745197    0.7904642
17  0.066406756  0.0075864551  0.016904992 0.0221853306    0.8073692
18  0.061085956  0.0069785951  0.016599565 0.0205955054    0.8239688
19  0.050988275  0.0058250136  0.016019933 0.0190940039    0.8399887
20  0.028140397  0.0032148213  0.014708408 0.0176715288    0.8546971
21  0.015362082  0.0017549983  0.013974901 0.0163201775    0.8686720
22  0.003584265  0.0004094744  0.013298825 0.0150331762    0.8819709
23  0.000000000  0.0000000000  0.012617773 0.0138046750    0.8945886
24 -0.008280234 -0.0009459523  0.011466143 0.0126295868    0.9060548
25 -0.028342617 -0.0032379234  0.011088532 0.0115034607    0.9171433
26 -0.034920916 -0.0039894429  0.010566364 0.0104223796    0.9277097
27 -0.044017530 -0.0050286603  0.009669135 0.0093828786    0.9373788
28 -0.059648014 -0.0068143214  0.009019903 0.0083818776    0.9463987
29 -0.070958184 -0.0081064203  0.008780538 0.0074166266    0.9551793
30 -0.075128129 -0.0085828041  0.008594375 0.0064846602    0.9637736
31 -0.078371244 -0.0089533048  0.007802472 0.0055837593    0.9715761
32 -0.092166866 -0.0105293473  0.007189413 0.0047119197    0.9787655
33 -0.102846869 -0.0117494544  0.006653531 0.0038673251    0.9854191
34 -0.112182389 -0.0128159650  0.004729051 0.0030483243    0.9901481
35 -0.145708466 -0.0166460584  0.004443663 0.0022534117    0.9945918
36 -0.150680174 -0.0172140374  0.004047965 0.0014812109    0.9986397
37 -0.157573564 -0.0180015536  0.001360269 0.0007304602    1.0000000
38 -0.204395504 -0.0233505958  0.000000000 0.0000000000    1.0000000
39 -0.228092546 -0.0260577985  0.000000000 0.0000000000    1.0000000
   Cumul_br_stick
1       0.1135564
2       0.2000857
3       0.2731016
4       0.3371084
5       0.3943585
6       0.4462032
7       0.4935433
8       0.5370225
9       0.5771233
10      0.6142211
11      0.6486162
12      0.6805542
13      0.7102401
14      0.7378469
15      0.7635232
16      0.7873977
17      0.8095831
18      0.8301786
19      0.8492726
20      0.8669441
21      0.8832643
22      0.8982974
23      0.9121021
24      0.9247317
25      0.9362352
26      0.9466575
27      0.9560404
28      0.9644223
29      0.9718389
30      0.9783236
31      0.9839073
32      0.9886193
33      0.9924866
34      0.9955349
35      0.9977883
36      0.9992695
37      1.0000000
38      1.0000000
39      1.0000000

$vectors
           Axis.1        Axis.2        Axis.3       Axis.4        Axis.5
uni1  -0.08399113  0.0810682902 -0.1146702680 -0.168417687  0.0838515635
uni2  -0.24149297 -0.3734304391 -0.1562829293  0.006536589 -0.0934351699
uni3  -0.28903489 -0.0590608494 -0.0679491208 -0.076384933  0.0008969974
uni4  -0.12932051 -0.1393932405 -0.1983597551 -0.046373671 -0.0942841245
uni5  -0.12260711  0.0008978571 -0.0681193883  0.116496360 -0.0175137572
uni6  -0.07904090 -0.1967585015 -0.0034285053  0.162679140  0.1747806777
uni7  -0.05942147 -0.0533302592 -0.1387691390 -0.198930666  0.0921938189
uni8   0.12933045 -0.1257430629 -0.1825020031 -0.261223904  0.0616225451
uni9   0.11266750  0.0903573616 -0.2412449758 -0.224049725  0.0561294011
uni10  0.13402921 -0.1474335968 -0.0665136115 -0.119316713 -0.0189029031
uni11  0.12720922 -0.3360975046  0.0503527766  0.300217329  0.0642788135
uni12  0.06100683 -0.1339309130 -0.1278878228  0.028798112  0.1433475702
uni13  0.07004786 -0.0748517739 -0.0543642267 -0.170220076  0.1484401930
uni14 -0.01063172 -0.1970021515 -0.1286381823  0.033832004  0.0397697311
uni15 -0.17698137 -0.1535613539  0.0806789094 -0.041531126 -0.0045885166
uni16 -0.35454726 -0.1312659471 -0.0095194837 -0.128668705 -0.0502590449
uni17 -0.18704754 -0.1763097302 -0.0203569912  0.112070423  0.0245020364
uni18 -0.22740249 -0.5083206798  0.3568221581 -0.101436039  0.0017113359
uni19 -0.22651930  0.1416829787  0.3900488427  0.006998402  0.2481089428
uni20 -0.28372948  0.1132618777  0.2131709638  0.114528212  0.1451388594
uni21 -0.18129409  0.3449486300  0.2030846377  0.023006943  0.1164687055
uni22 -0.24249683  0.3082208094  0.0864475537 -0.048689733 -0.0578583203
uni23 -0.14187089  0.2766316474 -0.0631012542 -0.044077085 -0.0741107497
uni24 -0.12207496  0.1830315339 -0.0227394470  0.277342314 -0.2365843272
uni25 -0.23906638  0.2236839449 -0.0828378193 -0.026122953 -0.1866047638
uni26 -0.03873378  0.2216972329 -0.1439676387 -0.117439464 -0.0643325409
uni27 -0.24556116  0.2211759341 -0.0006711014 -0.014058957 -0.1295485324
uni28  0.08185383  0.1092961888 -0.1543457676  0.058215707  0.0070942896
uni29  0.17995581 -0.0170381201 -0.1990020126  0.214407321 -0.0839042933
uni30  0.02217864  0.1200596847 -0.1616123204  0.233377016 -0.1617527023
uni31  0.51212604 -0.0931112278  0.1917619413 -0.058641367 -0.0923747060
uni32  0.22665494 -0.1156990248  0.5531389662 -0.182270343 -0.4994903973
uni33  0.43057458 -0.1234575172 -0.1190713689 -0.062909278 -0.0601082556
uni34  0.32673280  0.1327411896  0.1817281071  0.095421146  0.2987768197
uni35  0.38433395  0.1362953333 -0.0992088680  0.082618776 -0.1336206612
uni36  0.29396737  0.2150557831  0.1297099258 -0.326047187  0.1922485560
uni37  0.12579824 -0.0316701382  0.1171644083  0.356574749  0.1080320019
uni38  0.23886039  0.2443673657  0.0873565687  0.078357671 -0.0025577669
uni39  0.22553857  0.0229923882 -0.0163017587  0.115331399  0.0544386747
            Axis.6        Axis.7       Axis.8       Axis.9      Axis.10
uni1   0.041069505  0.0441179273 -0.032835155  0.007580892 -0.026759958
uni2  -0.147222046  0.0007107137 -0.123074939  0.112084896 -0.168011935
uni3   0.021027093  0.0335897375 -0.023391399  0.016021371  0.067162908
uni4   0.097540789 -0.1565234537  0.069531255 -0.092047159 -0.065124124
uni5   0.017343050  0.1532570057  0.107323242 -0.071762727 -0.082190988
uni6  -0.031672728 -0.0200984061 -0.104997281  0.031887107  0.046798558
uni7   0.018437454 -0.0631005520 -0.058517578  0.049082697  0.029234620
uni8   0.301809291 -0.1676725597 -0.086908243  0.064976388 -0.076620127
uni9  -0.160411506  0.0438573962 -0.102956389 -0.066760502 -0.124334751
uni10  0.001385166 -0.0716841990 -0.083010276 -0.036690057  0.084823819
uni11  0.229914446 -0.0127066269  0.026276603 -0.076150273  0.060081748
uni12 -0.012350042 -0.1025226194 -0.054265256  0.042431150 -0.018260059
uni13 -0.027782569 -0.1074839074  0.047365742  0.074884450  0.035249980
uni14 -0.005779455  0.0079382970  0.043282203 -0.094064732  0.098528102
uni15  0.162903627  0.2549607163 -0.117192193 -0.095906409 -0.002979473
uni16 -0.132205992  0.1138292955  0.020559485 -0.059582811  0.162163625
uni17 -0.006791132  0.0133622105  0.141495520 -0.150113757 -0.020237912
uni18 -0.114002627  0.2156463371  0.231141749  0.187660839 -0.029954461
uni19  0.071592666 -0.1343158214  0.073146787  0.032417640 -0.011890690
uni20  0.061477779 -0.1726877450 -0.095549417  0.091968227 -0.149985996
uni21  0.162150105 -0.0480361737 -0.013448756 -0.070591378 -0.002083436
uni22 -0.235739526 -0.2220212964 -0.058625115  0.160495496 -0.015239500
uni23  0.123197182 -0.0444709442  0.092647381 -0.052561135 -0.006016068
uni24  0.045382563 -0.1536587251  0.118272870  0.035731217 -0.025409556
uni25 -0.137597176  0.0329388621  0.006901450 -0.143160170  0.208640471
uni26  0.076228383  0.0095837234  0.050009579 -0.060114749  0.030490823
uni27  0.094248969  0.0402163052  0.087745965  0.113028059  0.091260026
uni28  0.014080005  0.1715181981 -0.170798518  0.028664558  0.149853041
uni29  0.091028444  0.1095741500 -0.104911079  0.144296766 -0.015513842
uni30  0.034591056  0.0925668717  0.034729191  0.010571819 -0.169803204
uni31  0.243654704 -0.1508219319  0.062782491  0.084977487  0.113362598
uni32 -0.002216088 -0.0354843112 -0.213714938 -0.131589089 -0.056347743
uni33 -0.285390168 -0.2562868685  0.164171687  0.034170296  0.111542946
uni34  0.060690131  0.1190773384 -0.005474214 -0.063298877  0.117348214
uni35  0.024111709  0.1455166924  0.268298612  0.095149508 -0.097278763
uni36 -0.161289165  0.1856997901  0.147950037 -0.114288922 -0.161776627
uni37 -0.370393826 -0.1406163666 -0.059953696 -0.123036342  0.003633397
uni38 -0.119632889  0.2571462068 -0.167250729  0.262112835  0.063072128
uni39 -0.043387183  0.0150847334 -0.116756677 -0.178474607 -0.147427790
           Axis.11     Axis.12       Axis.13      Axis.14      Axis.15
uni1   0.165561007 -0.01922107  2.818242e-02 -0.012141932 -0.019325305
uni2   0.017798273  0.03105176 -3.589491e-02 -0.097100395  0.019757421
uni3   0.140512964  0.07391147  1.417749e-01  0.071090111 -0.036703176
uni4  -0.083664514  0.04814819 -3.963111e-02 -0.027635707  0.052795315
uni5   0.012291563  0.16524468  1.311921e-01  0.004529843  0.057215705
uni6   0.021236528  0.03325963 -3.991213e-02  0.067366437 -0.063600244
uni7   0.186701351 -0.01334501 -6.396417e-05 -0.013787124 -0.025550915
uni8  -0.048438226 -0.04611188 -2.531148e-02 -0.082502247 -0.002070782
uni9  -0.067353252 -0.02244173 -8.863282e-03 -0.007644103 -0.053020648
uni10 -0.001710635  0.05227920  9.441605e-02  0.056920044  0.039814304
uni11 -0.092943444 -0.14238431 -4.333644e-02 -0.137562284 -0.029649151
uni12  0.063855271  0.07573200 -6.727150e-03 -0.036247676  0.049849790
uni13 -0.114342168 -0.18850218  4.836093e-03  0.222698234 -0.018403869
uni14 -0.157667739  0.06874997  5.959149e-02  0.033175096 -0.005143942
uni15 -0.043550638  0.01597599  6.570740e-02 -0.005719406  0.067617796
uni16 -0.111911761  0.07157676 -5.546466e-02  0.034320356 -0.009530383
uni17  0.005269053 -0.12920613 -3.147789e-02  0.101993082  0.003061839
uni18 -0.025369813 -0.04515480  2.155503e-03 -0.050823541 -0.056178823
uni19  0.173731760  0.04602633 -7.797309e-02  0.009947257 -0.059547245
uni20 -0.013851151  0.02321395 -3.072554e-02  0.014757762  0.089030444
uni21 -0.164187244 -0.01163925 -3.864260e-02 -0.069358601 -0.017795290
uni22 -0.132506429 -0.08526639  8.250629e-02  0.021581893  0.025624361
uni23 -0.031246099 -0.05384262  1.187434e-01 -0.085014850 -0.101749869
uni24 -0.028063488  0.02885683  1.610486e-01 -0.020537986 -0.054007190
uni25  0.061526864 -0.08319822 -1.500021e-01 -0.082835999  0.038752699
uni26 -0.094739435  0.12619123 -1.064497e-01  0.080193381 -0.004746539
uni27  0.097638181  0.03790790 -1.381225e-01 -0.011307075  0.044524742
uni28  0.150870960 -0.12412884  6.368174e-02 -0.037094727 -0.015118258
uni29 -0.038090717 -0.02369377 -1.150750e-01  0.057706863  0.079891260
uni30  0.085686891 -0.13217231  5.175477e-02  0.045579605  0.051928431
uni31  0.022442339  0.11193614 -3.340247e-03  0.034725214  0.052969955
uni32  0.050000373 -0.04237929  8.309540e-03  0.046229392 -0.006590734
uni33  0.029297068  0.01245390  2.544578e-02 -0.113434682 -0.017887438
uni34  0.013126979 -0.03028636  9.954531e-02 -0.004767411  0.048512349
uni35  0.069957676  0.01159565 -8.052489e-02  0.071651109 -0.041842202
uni36 -0.017465304 -0.02366297  3.247861e-03 -0.070232448  0.108468913
uni37  0.049149379  0.02778733 -2.621889e-02  0.008634745  0.070671307
uni38 -0.164994338  0.07063434  1.991028e-03 -0.046564038 -0.062581043
uni39  0.015441911  0.08410390 -9.037263e-02  0.029211809 -0.199443584
           Axis.16      Axis.17       Axis.18      Axis.19      Axis.20
uni1  -0.008969306 -0.027685723  0.0570594592  0.099289299  0.063042733
uni2  -0.038957645 -0.012244288 -0.0395377494  0.012546676 -0.021886948
uni3  -0.079975518 -0.018947204  0.0383460219 -0.028185273 -0.027238184
uni4  -0.031236699 -0.016054906 -0.0126292683  0.086226914  0.023742307
uni5  -0.054229530 -0.045936241 -0.0238849063 -0.031176711  0.020769675
uni6   0.049649358 -0.067036652  0.0183967147 -0.054225159  0.002880995
uni7   0.103169593  0.061377382 -0.0156200826 -0.021434110 -0.044644370
uni8  -0.037319641 -0.016115255  0.0268803658 -0.059994436 -0.005604973
uni9  -0.018224235 -0.024805176 -0.0056786485 -0.013649210 -0.065620087
uni10 -0.085119076  0.029553497 -0.0833011870  0.006720802 -0.001169319
uni11 -0.020962660  0.006728028  0.0254484771 -0.039113026  0.001200030
uni12  0.024780242  0.046522269  0.0042416953 -0.022168063  0.017517676
uni13  0.095366048 -0.020639469 -0.0165653980  0.026415234  0.004790241
uni14  0.070349544  0.007532825 -0.0207436421 -0.018549621  0.031231457
uni15  0.122367010  0.052478653 -0.0103878641  0.053628089 -0.024795581
uni16  0.024726985 -0.062380550  0.0486278600 -0.052714173  0.032030710
uni17 -0.129801507  0.093735300 -0.0444243799 -0.010424650  0.007156450
uni18 -0.006445977  0.009944084  0.0244313304  0.041814768 -0.016911494
uni19 -0.041898674 -0.028333848 -0.0352495187  0.003698881  0.001783004
uni20  0.021358801  0.039935432  0.0585986902 -0.003085033  0.014297652
uni21 -0.001942671 -0.098128463 -0.0381581790  0.042550544 -0.023988548
uni22 -0.082502041  0.034104541  0.0043982815 -0.010992116  0.018305200
uni23  0.034651704  0.014958808 -0.0796704931 -0.025248396  0.023106430
uni24  0.089902336  0.016367362  0.0372522272  0.025900617 -0.049292869
uni25 -0.017553373  0.051399636  0.0428606137  0.011411168 -0.012442750
uni26 -0.039100353  0.023002670  0.0799830524  0.014799979 -0.039006693
uni27  0.061237834  0.009182963 -0.0775387827 -0.053882135  0.011081109
uni28 -0.007881505 -0.047252222 -0.0232434127  0.039256237  0.017914707
uni29 -0.036396228 -0.048614802 -0.0323110138  0.025961909 -0.010229294
uni30  0.036305219 -0.014554336  0.0709567731 -0.047392770  0.031147871
uni31  0.020509386  0.034125308  0.0094554630  0.019322211  0.011216626
uni32 -0.006959778 -0.037241495 -0.0004112998 -0.025349979  0.002532950
uni33  0.001705167 -0.036965648  0.0268126955  0.010709664  0.012097007
uni34 -0.090478563  0.003928300  0.0442207137 -0.003363238 -0.037921137
uni35 -0.020240710 -0.024112119 -0.0213531161  0.001106579 -0.023899236
uni36  0.052384584  0.004928436 -0.0051455223 -0.034632228  0.017997680
uni37  0.061350220 -0.018378881 -0.0351480508  0.017521654 -0.022438160
uni38 -0.020083235  0.065881297 -0.0067897407 -0.001645372  0.025254884
uni39  0.006464895  0.059740487  0.0098218209  0.018344474  0.035992252
           Axis.21       Axis.22
uni1   0.033895514 -0.0014104454
uni2   0.000594869  0.0016369952
uni3  -0.034842697  0.0191178671
uni4  -0.014860405  0.0010803711
uni5  -0.014936578  0.0106601572
uni6   0.005134989 -0.0090530850
uni7  -0.015507340  0.0079829267
uni8  -0.015691377 -0.0083089237
uni9   0.029557864 -0.0086502136
uni10  0.011469755 -0.0134253285
uni11  0.004907137  0.0048196272
uni12  0.030538383  0.0043824062
uni13 -0.008593088  0.0155503304
uni14 -0.046365144 -0.0085511670
uni15  0.030809694 -0.0017842944
uni16  0.042707629 -0.0061035225
uni17  0.013084100 -0.0081488700
uni18 -0.013591551 -0.0021248582
uni19  0.011007821  0.0020669225
uni20 -0.020841336 -0.0060048740
uni21 -0.011701506 -0.0007640885
uni22  0.003445059 -0.0070454224
uni23  0.025600175  0.0188885657
uni24  0.006628610 -0.0110740722
uni25 -0.022757309  0.0101926813
uni26 -0.002291340 -0.0012105942
uni27  0.006617599 -0.0092986894
uni28 -0.037223270 -0.0236812162
uni29  0.006159793  0.0235992444
uni30  0.009128143 -0.0003498630
uni31  0.004884957 -0.0020300120
uni32 -0.001306883  0.0038582536
uni33  0.009575513  0.0059551240
uni34  0.018902597  0.0023023538
uni35 -0.001028089 -0.0131732167
uni36 -0.022307733  0.0003757563
uni37 -0.001361135  0.0011856942
uni38 -0.003175829  0.0064881602
uni39 -0.016267589  0.0020493194

$correlations
                                Axis.1      Axis.2        Axis.3        Axis.4
araucaria_angustifolia     0.011330361  0.13432156 -0.0371636553  0.5393508903
podocarpus_lamberti        0.060363002  0.09118581 -0.1439281213  0.0610330782
calyptranthes_grandifolia  0.060363002  0.09118581 -0.1439281213  0.0610330782
eugenia_handroi            0.245413815  0.15984322  0.0474810542  0.1455144595
eugenia_subterminalis      0.166323132  0.01918255 -0.0152014631  0.1209129060
eugenia_uruguayensis      -0.090024022  0.15270321 -0.0212046364  0.2907644002
myrceugenia_miersiana      0.119061579  0.01394074 -0.2295390137  0.1726110378
myrceugenia_myrcioides     0.447797581 -0.01183796 -0.4114624064 -0.5178281472
myrceugenia_ovata          0.238963788 -0.05542542  0.3587314713 -0.0502897980
myrceugenia_oxysepala     -0.070410687 -0.11724256 -0.1314795841  0.1129384871
myrceugenia_sp             0.060363002  0.09118581 -0.1439281213  0.0610330782
myrcia_guianensis         -0.334743153  0.28660176 -0.2450703198 -0.0002232899
myrcia_hartwegiana        -0.259562195  0.17451621 -0.1078087573  0.1493187358
myrcia_retorta            -0.438378777  0.14328717 -0.5105724207 -0.1096078609
myrciaria_delicatula      -0.130514686 -0.12811624  0.0752334452 -0.0435410403
genx_sp                   -0.043820289 -0.04449343 -0.1294028452 -0.2085579907
psidium_cattleianum       -0.220487190  0.26799988  0.0763360073  0.1860754584
siphoneugena_reitzii      -0.317598177 -0.23649709 -0.6710811583 -0.0288277995
leandra_dasytricha        -0.146448053 -0.35642783 -0.1943098164  0.6758805539
leandra_laevigata         -0.261460425 -0.10951518 -0.0088769613 -0.1348956757
leandra_sublanata         -0.431508036  0.61810018  0.0691296757  0.0675038661
miconia_cinerascens       -0.326315780  0.39798142 -0.0042464733 -0.1442070447
miconia_hyemalis          -0.679098809  0.46389450 -0.0183245651  0.0719559558
miconia_sellowiana         0.051656703 -0.06244883 -0.0506948855 -0.1784579406
daphnopsis_fasciculata     0.268489346  0.49490090 -0.1754212179  0.0325867996
matayba_elaeagnoides       0.222019898  0.20529384 -0.0967909753  0.0581403975
zanthoxylum_rhoifoliu     -0.001129469  0.11381096 -0.1797649583 -0.0827923929
casearia_decandra          0.188641347  0.28305158 -0.2798647878  0.1686412030
xylosma_pseudosalzmanii    0.092769751 -0.02642240  0.1092563368  0.3738313194
sapium_glandulosum        -0.102805650  0.43998552  0.0427347162  0.1436144869
lamanonia_ternata         -0.337294225  0.23266984 -0.1151382985 -0.1563720673
weinmannia_paulliniifolia -0.261460425 -0.10951518 -0.0088769613 -0.1348956757
inga_lentiscifolia        -0.280888804 -0.17028633  0.0475509616 -0.1278674959
prunus_myrtifolia          0.025580487  0.26080470  0.0862277925 -0.2555144787
clethra_uleana            -0.181088766  0.18452708 -0.0006258051 -0.0147393457
laplacea_acutifolia       -0.085717557  0.14128045  0.1052815223  0.1735954251
symplocos_tetrandra       -0.061939154  0.06763527 -0.1069305398 -0.1765683250
myrsine_coriacea          -0.090024022  0.15270321 -0.0212046364  0.2907644002
myrsine_lorentziana       -0.031994501  0.05924213 -0.2363816986  0.2425747844
ilex_brevicuspis          -0.456587506  0.24933811 -0.1422157551  0.0119333506
ilex_dumosa               -0.197009322  0.08093024 -0.1548976920 -0.0480885860
ilex_microdonta           -0.575963464 -0.29416751  0.1105043389 -0.1031349296
ilex_paraguariensis       -0.135444367  0.14417215  0.3691925777  0.3578392792
ilex_sp                   -0.063251935  0.23716516 -0.1501606634  0.1422169928
piptocarpha_notata         0.128346177  0.35663221 -0.2344106086  0.2706562866
piptocarpha_tomentosa     -0.305534882  0.42789667  0.2571761891 -0.0153650283
vernonia_discolor         -0.438460485  0.54601074  0.3096586150  0.1360418420
rudgea_parquioides        -0.125337344  0.26177061 -0.1673845175  0.3298031708
solanum_variabile         -0.178828979  0.25714862  0.0806127320 -0.0510460909
cinnamomum_glaziovii       0.298201577  0.07129890 -0.1992738700  0.2231493592
cryptocaria_aschersoniana  0.267338817 -0.22159210  0.3687723651 -0.2194416630
nectandra_grandiflora      0.591386540 -0.08691293 -0.1600651816  0.6392210100
nectandra_megapotamica    -0.428459308 -0.56924441 -0.0939205852 -0.0928937289
ocotea_corymbosa          -0.191675611  0.04013661 -0.7202520756  0.1266052326
ocotea_sp                  0.333074817  0.26073920 -0.0668869423  0.0850801804
mollinedia_elegans         0.245413815  0.15984322  0.0474810542  0.1455144595
rollinia_rugulosa          0.283426581  0.11371119 -0.0925127148  0.0866171427
drimys_angustifolia       -0.281717940 -0.25387965 -0.1017972144 -0.0046659232
dicksonia_sellowiana      -0.242017097 -0.57940581  0.0991199392  0.0685108163
                                Axis.5        Axis.6       Axis.7      Axis.8
araucaria_angustifolia    -0.195887589 -0.2030875524 -0.149082734  0.08104937
podocarpus_lamberti        0.008070145  0.0165989023  0.213714523 -0.25081012
calyptranthes_grandifolia  0.008070145  0.0165989023  0.213714523 -0.25081012
eugenia_handroi            0.042291778 -0.1377189087  0.243073297 -0.29885915
eugenia_subterminalis      0.061926992 -0.0511491009  0.018795828 -0.17145205
eugenia_uruguayensis      -0.269127709  0.0535014521 -0.191461323  0.17367851
myrceugenia_miersiana     -0.065598468  0.0684162545  0.069961162 -0.01987390
myrceugenia_myrcioides     0.122204514  0.0875264507 -0.267773449  0.19384209
myrceugenia_ovata         -0.362792975 -0.0385255175 -0.018214655 -0.34775313
myrceugenia_oxysepala      0.018142410  0.0097688931  0.143930274  0.15848113
myrceugenia_sp             0.008070145  0.0165989023  0.213714523 -0.25081012
myrcia_guianensis         -0.250836987  0.1780982514  0.184330971 -0.03318965
myrcia_hartwegiana        -0.193982224  0.1271070179 -0.007324422  0.22557603
myrcia_retorta            -0.007589689  0.1941257807  0.001214080 -0.35759362
myrciaria_delicatula      -0.005219691  0.1920469033  0.317685287 -0.17209158
genx_sp                    0.104875549  0.0217358940 -0.078624336 -0.08593049
psidium_cattleianum       -0.050251188 -0.0976701280 -0.223313560 -0.10404233
siphoneugena_reitzii      -0.065169083  0.2479597627  0.201733771 -0.23812252
leandra_dasytricha         0.022997530  0.0469521680 -0.045080700 -0.11249319
leandra_laevigata         -0.057172433 -0.1558574955  0.141833193  0.03019070
leandra_sublanata         -0.217046179  0.0873783564 -0.272226136  0.10803846
miconia_cinerascens        0.517333765 -0.2096197823  0.157519343 -0.22459203
miconia_hyemalis          -0.165914010  0.1263456294 -0.159459327  0.27298694
miconia_sellowiana         0.168858899 -0.0327528397 -0.133926734  0.06955451
daphnopsis_fasciculata     0.098541043  0.1235887657  0.611060421 -0.06233945
matayba_elaeagnoides      -0.071496764 -0.0523558047  0.374591399  0.42712717
zanthoxylum_rhoifoliu      0.074136364  0.0465901551  0.192540142 -0.21428239
casearia_decandra         -0.242058067 -0.0121290258  0.083490004  0.16185493
xylosma_pseudosalzmanii    0.122892355 -0.4366568655 -0.175210328 -0.08803937
sapium_glandulosum        -0.219940011 -0.1147266114 -0.105816135 -0.01144175
lamanonia_ternata         -0.255282092 -0.0610051469  0.127604162  0.12639855
weinmannia_paulliniifolia -0.057172433 -0.1558574955  0.141833193  0.03019070
inga_lentiscifolia        -0.044710107  0.0259332780  0.329290286 -0.10168597
prunus_myrtifolia          0.051111201 -0.0566353735  0.201719063  0.24802137
clethra_uleana            -0.147368594  0.1111100035  0.050110184  0.12885109
laplacea_acutifolia        0.071954729  0.3603166778 -0.077763577  0.09187373
symplocos_tetrandra        0.095385774  0.0484167939  0.054971670 -0.04821698
myrsine_coriacea          -0.269127709  0.0535014521 -0.191461323  0.17367851
myrsine_lorentziana        0.236620153  0.7727306560 -0.085528084  0.07987163
ilex_brevicuspis          -0.280330910  0.2084570543  0.091924601  0.24017105
ilex_dumosa               -0.054621732  0.0801374473  0.145181941  0.11666908
ilex_microdonta            0.226825924  0.0200198693  0.151909387 -0.04426730
ilex_paraguariensis        0.422083697 -0.0775892645 -0.273296715 -0.20428884
ilex_sp                   -0.192268896  0.1332990701  0.042944552  0.13403754
piptocarpha_notata        -0.323706876


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO