Last data update: 2014.03.03

 R: Principal Coordinates of Phylogenetic Structure
pcpsR Documentation

Principal Coordinates of Phylogenetic Structure

Description

Function to generate Principal Coordinates of Phylogenetic Structure (PCPS).

Usage

pcps(comm, dist.spp, method = "bray", squareroot = TRUE)

## S3 method for class 'pcps'
plot(x, display = c("text", "points"), groups,
  showlabel = TRUE, choices = c(1, 2), ...)

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

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

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

Arguments

comm

Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.

dist.spp

Matrix containing phylogenetic distances between species.

method

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

squareroot

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

x

An object of class pcps.

display

Display text or points for the sampling units.

groups

Factor giving the groups (Clades) for each species.

showlabel

Label the groups by their names in the centroid of the object.

choices

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

...

Other parameters for the respective functions.

object

An object of class pcps.

Details

The function obtains a matrix containing phylogeny-weighted species composition (matrix.p) and is submitted to principal coordinates analysis (PCoA). This method generates the principal coordinates of phylogenetic structure (PCPS) (Duarte, 2011).

The function scores.pcps re-scales the correlation values for biplot graphics. The function plot.pcps draws a simple biplot and represent clades as "spider" graphs (see ordispider).

Value

P

Phylogeny-weighted species composition matrix.

values

The eigenvalues, relative eigenvalues and cumulative relative eigenvalues.

vectors

The principal coordinates of phylogenetic structure (PCPS).

correlations

Correlations between a PCPS axis and phylogenetically weighted species abundances or frequencies.

Note

IMPORTANT: The sequence species show up in the community data matrix MUST be the same as they show up in the phylogenetic distance matrix. See organize.syncsa.

Author(s)

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

References

Duarte, L.S. (2011). Phylogenetic habitat filtering influences forest nucleation in grasslands. Oikos, 120, 208:215.

See Also

matrix.p, wcmdscale

Examples

data(flona)
res<-pcps(flona$community, flona$phylo)
res
summary(res)
scores(res)
plot(res, display = "text", groups = c(rep("Clade-A", 30), rep("Clade-B", 29)))

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/pcps.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pcps
> ### Title: Principal Coordinates of Phylogenetic Structure
> ### Aliases: pcps plot.pcps print.pcps scores.pcps summary.pcps
> ### Keywords: PCPS
> 
> ### ** Examples
> 
> data(flona)
> res<-pcps(flona$community, flona$phylo)
> res
Call:
pcps(comm = flona$community, dist.spp = flona$phylo) 

PCPS values:
   Eigenvalues Relative_eig Cumul_eig
1  0.560852249 0.2557465289 0.2557465
2  0.344645836 0.1571572129 0.4129037
3  0.206592424 0.0942053728 0.5071091
4  0.178392779 0.0813464403 0.5884556
5  0.155583901 0.0709456774 0.6594012
6  0.076457508 0.0348643379 0.6942656
7  0.072603997 0.0331071510 0.7273727
8  0.069090308 0.0315049221 0.7588776
9  0.051620567 0.0235387857 0.7824164
10 0.043883641 0.0200107761 0.8024272
11 0.039880674 0.0181854382 0.8206126
12 0.033718368 0.0153754499 0.8359881
13 0.029859072 0.0136156252 0.8496037
14 0.028842028 0.0131518569 0.8627556
15 0.026033786 0.0118713092 0.8746269
16 0.023436206 0.0106868221 0.8853137
17 0.020348270 0.0092787351 0.8945924
18 0.019763788 0.0090122134 0.9036047
19 0.018926739 0.0086305223 0.9122352
20 0.018173139 0.0082868836 0.9205221
21 0.016477590 0.0075137192 0.9280358
22 0.014745718 0.0067239922 0.9347598
23 0.014265282 0.0065049153 0.9412647
24 0.014017766 0.0063920487 0.9476567
25 0.012949122 0.0059047513 0.9535615
26 0.011807660 0.0053842486 0.9589457
27 0.011080675 0.0050527465 0.9639985
28 0.009839186 0.0044866320 0.9684851
29 0.009667217 0.0044082150 0.9728933
30 0.009045708 0.0041248092 0.9770181
31 0.008646208 0.0039426383 0.9809608
32 0.008087399 0.0036878237 0.9846486
33 0.007227021 0.0032954944 0.9879441
34 0.006939706 0.0031644801 0.9911086
35 0.006554201 0.0029886910 0.9940973
36 0.006160182 0.0028090199 0.9969063
37 0.005570498 0.0025401264 0.9994464
38 0.001214017 0.0005535871 1.0000000
> summary(res)
$values
   Eigenvalues Relative_eig Cumul_eig
1  0.560852249 0.2557465289 0.2557465
2  0.344645836 0.1571572129 0.4129037
3  0.206592424 0.0942053728 0.5071091
4  0.178392779 0.0813464403 0.5884556
5  0.155583901 0.0709456774 0.6594012
6  0.076457508 0.0348643379 0.6942656
7  0.072603997 0.0331071510 0.7273727
8  0.069090308 0.0315049221 0.7588776
9  0.051620567 0.0235387857 0.7824164
10 0.043883641 0.0200107761 0.8024272
11 0.039880674 0.0181854382 0.8206126
12 0.033718368 0.0153754499 0.8359881
13 0.029859072 0.0136156252 0.8496037
14 0.028842028 0.0131518569 0.8627556
15 0.026033786 0.0118713092 0.8746269
16 0.023436206 0.0106868221 0.8853137
17 0.020348270 0.0092787351 0.8945924
18 0.019763788 0.0090122134 0.9036047
19 0.018926739 0.0086305223 0.9122352
20 0.018173139 0.0082868836 0.9205221
21 0.016477590 0.0075137192 0.9280358
22 0.014745718 0.0067239922 0.9347598
23 0.014265282 0.0065049153 0.9412647
24 0.014017766 0.0063920487 0.9476567
25 0.012949122 0.0059047513 0.9535615
26 0.011807660 0.0053842486 0.9589457
27 0.011080675 0.0050527465 0.9639985
28 0.009839186 0.0044866320 0.9684851
29 0.009667217 0.0044082150 0.9728933
30 0.009045708 0.0041248092 0.9770181
31 0.008646208 0.0039426383 0.9809608
32 0.008087399 0.0036878237 0.9846486
33 0.007227021 0.0032954944 0.9879441
34 0.006939706 0.0031644801 0.9911086
35 0.006554201 0.0029886910 0.9940973
36 0.006160182 0.0028090199 0.9969063
37 0.005570498 0.0025401264 0.9994464
38 0.001214017 0.0005535871 1.0000000

$vectors
            pcps.1       pcps.2       pcps.3        pcps.4       pcps.5
uni1   0.120053383  0.048930968 -0.028682384 -0.0338116901 -0.013502082
uni2  -0.008122345 -0.098849498 -0.006192660 -0.0083032243  0.065960407
uni3   0.045928019 -0.019981595  0.015159415  0.0113950184  0.072848965
uni4   0.051735943 -0.023581433 -0.023723760 -0.0072924987  0.069613647
uni5   0.064382307  0.001098834  0.037914239  0.0109814449  0.064888726
uni6  -0.169639928  0.058773023  0.010043597  0.1151525070  0.025719115
uni7   0.108882067  0.041416868 -0.058321864 -0.0375872099 -0.005329399
uni8   0.130077192  0.060764080 -0.059671911 -0.0593576631 -0.116014196
uni9   0.098512389  0.026036238 -0.139710582 -0.0667566976 -0.041350615
uni10 -0.054214352 -0.159810854 -0.032752176  0.0002449094 -0.022380358
uni11 -0.232587433  0.146115321 -0.001146381  0.0478094749 -0.094282568
uni12  0.051862941 -0.023486617 -0.024001261 -0.0074076254  0.069575624
uni13 -0.106801952  0.146283840 -0.125300584  0.0677195319 -0.066418381
uni14 -0.147711288  0.015707855 -0.065233777  0.1025765256  0.016045470
uni15 -0.054991548  0.088855699 -0.038515017  0.0973142626  0.034648839
uni16 -0.091075647  0.066753298 -0.030748277  0.1045102613  0.036793911
uni17 -0.179455747  0.083555679 -0.043543376  0.1137794478 -0.013301450
uni18 -0.403539751  0.176980289  0.072455028 -0.2949083887  0.081654674
uni19  0.050925541  0.061051809  0.212228927  0.0384944118 -0.120727954
uni20  0.140557073  0.076430314  0.070425624 -0.0306477601 -0.056564890
uni21  0.104755334  0.067204229  0.153625008  0.0151216536 -0.080798896
uni22  0.111707044  0.040043128 -0.018282539 -0.0224985379  0.030250333
uni23  0.120834559  0.057826800  0.075860707 -0.0069921651 -0.010300321
uni24  0.078200326  0.016447599  0.046896227  0.0151010182  0.051764687
uni25  0.110007922  0.044123331 -0.006125204 -0.0226285388  0.035479640
uni26  0.089130190  0.019750403 -0.004913491 -0.0055485053  0.061564305
uni27  0.060809311  0.031896301  0.127378186  0.0376936851 -0.004668441
uni28  0.074672658 -0.001105875 -0.056615033 -0.0122888611  0.043582021
uni29 -0.026719429 -0.128956213  0.008061230  0.0078788918  0.035642889
uni30  0.093326736  0.019729094  0.006761019 -0.0015582429  0.060877809
uni31 -0.133490417 -0.198955634  0.052243897 -0.0193352683 -0.104214261
uni32 -0.059796779 -0.172707004 -0.085953493 -0.0395563133 -0.063005792
uni33 -0.131214593 -0.212997173 -0.028649585 -0.0283492531 -0.118679118
uni34  0.005775592 -0.057519399  0.032863001  0.0142233756  0.023302111
uni35 -0.062804108 -0.142563073  0.098752292 -0.0060929659 -0.001036468
uni36  0.130938955  0.061782859 -0.125054622 -0.0855656653 -0.116491162
uni37 -0.042149887 -0.097341434  0.054140128  0.0154170020  0.061349412
uni38 -0.002675537 -0.102842609 -0.009972800 -0.0012604116  0.055676067
uni39  0.063915263 -0.016859448 -0.061697748 -0.0176659354  0.051827704
             pcps.6       pcps.7        pcps.8        pcps.9       pcps.10
uni1  -0.0306254815 -0.042710842  0.0079182254 -0.0068275485 -0.0281386526
uni2  -0.0170190769  0.056002344  0.0236635146  0.0139989153  0.0140474879
uni3  -0.0604984573  0.002767737 -0.0023446199 -0.0331965304  0.0262557684
uni4  -0.0734343981 -0.011581546  0.0202261366 -0.0293428590  0.0279099648
uni5  -0.0432098838  0.005197170 -0.0226264434 -0.0035339769  0.0147521295
uni6  -0.0003185880 -0.023611270  0.0198331867 -0.0808849359  0.0237338856
uni7  -0.0355051112 -0.036462812  0.0138242081 -0.0295720926 -0.0198579719
uni8  -0.0380156162 -0.034046266  0.1018797672 -0.0122171716 -0.0492173727
uni9   0.0745486407 -0.016019807 -0.0055971412  0.0131136762  0.0218508089
uni10 -0.0353499888  0.055636603  0.0022879127  0.0466414753 -0.0162185135
uni11 -0.0380952598 -0.115241093 -0.0298527247  0.0991900412 -0.0107763241
uni12 -0.0739467661 -0.011633760  0.0203378937 -0.0291953068  0.0276248068
uni13 -0.0450165599  0.063269152 -0.0634078544  0.0553122496  0.0433681023
uni14 -0.0002164004  0.056172479  0.0446651006 -0.0324387328 -0.0307142235
uni15  0.0163911564  0.042578330 -0.0064807709 -0.0238828977 -0.0862034809
uni16  0.1017443420  0.023102766  0.0103093099 -0.0458951719 -0.0578402167
uni17 -0.0076005404 -0.026603699  0.0237904523 -0.0057042682  0.0670041016
uni18  0.0042792283  0.034251605  0.0096483401 -0.0129682628 -0.0078446792
uni19  0.0118982857  0.035017443  0.0492634305 -0.0165850867  0.0695428530
uni20 -0.0294706293  0.039518488 -0.0165068575 -0.0371577770  0.0005457552
uni21 -0.0158254740  0.063969344  0.0209976800  0.0198166871 -0.0127486826
uni22  0.0388669824 -0.007113160 -0.0620056783 -0.0121170918  0.0004936073
uni23 -0.0212241793  0.018063366 -0.0484903657  0.0055809354 -0.0138334563
uni24  0.0269260954 -0.029063660 -0.0588284818  0.0356393395 -0.0138901595
uni25  0.0352466248  0.004237814 -0.0670527170 -0.0237909514  0.0058494155
uni26  0.0173389920 -0.019558275 -0.0406242960 -0.0007921919  0.0008947927
uni27  0.0292181999  0.023938220 -0.0374511456  0.0312725828 -0.0301851671
uni28 -0.0214080403 -0.047257100  0.0111918978  0.0130813102  0.0182204126
uni29 -0.0275934679  0.034079667  0.0381616960  0.0462715718 -0.0307462087
uni30  0.0119514963 -0.036339776 -0.0560547513  0.0213473273 -0.0011696461
uni31 -0.0221819581 -0.086307995 -0.0305434705 -0.0554538276 -0.0395820182
uni32 -0.0235380045  0.080734889 -0.0357438509  0.0248592153  0.0122736856
uni33  0.0124567458  0.008045384 -0.0806602119 -0.0623479565  0.0204752908
uni34 -0.0081846072 -0.029719554  0.0902871769  0.0462368840 -0.0194510160
uni35  0.0471736653 -0.062122134 -0.0005421192  0.0093868336 -0.0292944234
uni36  0.0980346648  0.017481042  0.0487688494 -0.0093760740  0.0210168034
uni37  0.1087610826 -0.038591964  0.0466457046  0.0220247147  0.0794183472
uni38  0.0479954021  0.035504548  0.0356957973  0.0601652291 -0.0115022489
uni39 -0.0145531154 -0.025583679  0.0254172199 -0.0006582765  0.0139364430
            pcps.11      pcps.12      pcps.13       pcps.14       pcps.15
uni1   0.0001542589  0.013418180  0.018679958 -0.0537473712 -0.0318779363
uni2  -0.0359243564  0.018517358  0.014377228 -0.0207701658  0.0478834699
uni3   0.0079391792 -0.016803591  0.006100130  0.0390816958  0.0212545996
uni4   0.0037010305 -0.018725491  0.017794338 -0.0127678928  0.0231067649
uni5   0.0190479761 -0.019258163 -0.010878412  0.0524797698 -0.0101501832
uni6  -0.0340179670 -0.004476962  0.019831193  0.0397108682 -0.0199309307
uni7   0.0048318931  0.049786960  0.057068873 -0.0275368295 -0.0116420739
uni8  -0.0201919600  0.057308058 -0.031637427  0.0328672298 -0.0053790608
uni9   0.0582259718 -0.023623370  0.046689934  0.0128252628 -0.0201480435
uni10 -0.0137270039  0.006929714  0.017953929  0.0248149710  0.0098349913
uni11 -0.0150606521 -0.028369547  0.037345727  0.0076526756  0.0692009935
uni12  0.0036847854 -0.017851450  0.018605604 -0.0144816388  0.0224621624
uni13 -0.0170984742  0.029713235 -0.029656847 -0.0423136849 -0.0447400783
uni14  0.0083702472 -0.025083307 -0.022729876  0.0027518869  0.0091017507
uni15  0.0072157294  0.042534527  0.004392166 -0.0181605236  0.0222228121
uni16  0.0320899193  0.005881934  0.015989346  0.0019771502  0.0098958846
uni17 -0.0134360302 -0.016790664 -0.023392531  0.0076588024 -0.0441129157
uni18  0.0133012528  0.006907294 -0.007380989  0.0009645773 -0.0090229907
uni19  0.0465055608  0.037195144  0.048802595 -0.0164691849  0.0097075690
uni20 -0.0759303959 -0.026901925 -0.035045423  0.0018327720  0.0124188604
uni21  0.0174461033 -0.014816798 -0.020656089 -0.0059906689  0.0004334780
uni22 -0.0369898564 -0.021107293  0.012949847 -0.0453241358  0.0015484380
uni23 -0.0215033986 -0.007167601 -0.019502357  0.0065557365 -0.0263919331
uni24  0.0152460281  0.035152977 -0.036995587  0.0378470124  0.0190356360
uni25 -0.0352919136 -0.021093660  0.018496939 -0.0372487995  0.0110087212
uni26  0.0140882848 -0.017193447  0.004477877  0.0127108646  0.0038938901
uni27  0.0513988080 -0.023680313  0.018466147  0.0176317139 -0.0089659374
uni28  0.0491148814  0.040303330 -0.039734311  0.0102874453  0.0008241725
uni29 -0.0318493652  0.001668359  0.012321174 -0.0037222774 -0.0021071681
uni30  0.0103125974  0.040715761 -0.035782603  0.0254045543 -0.0056131830
uni31  0.0056170391 -0.002586717 -0.031051147 -0.0223370277  0.0144546358
uni32  0.0117310281  0.024021576  0.045048538  0.0398708790 -0.0178235694
uni33  0.0464091907 -0.006745465 -0.036353734 -0.0238350541  0.0115273869
uni34  0.0493326095 -0.067994607 -0.031821245 -0.0453121139 -0.0301963169
uni35 -0.0717561896 -0.005655268  0.039014618  0.0256794297 -0.0739183395
uni36 -0.0347546149 -0.047928681 -0.016056316  0.0377730775  0.0340707111
uni37 -0.0307492973  0.063120568 -0.022301846 -0.0237058829  0.0228778180
uni38 -0.0148316546 -0.017538091 -0.019370038 -0.0244677006  0.0021995252
uni39  0.0273487551 -0.021782564 -0.004059383 -0.0001874228 -0.0169436105
            pcps.16       pcps.17       pcps.18      pcps.19       pcps.20
uni1   0.0098396531 -0.0622841297 -0.0011947282  0.002251835  0.0049706512
uni2  -0.0290964486 -0.0153984826  0.0161543355  0.008005480 -0.0257722619
uni3  -0.0187591743 -0.0092656737  0.0150340690  0.011457129 -0.0081186521
uni4  -0.0074591543  0.0032468592  0.0138937975 -0.021886456  0.0279069998
uni5   0.0060927380 -0.0056444659  0.0234612915  0.013420188 -0.0266626731
uni6  -0.0118173459 -0.0281958485 -0.0142273269  0.010807957 -0.0255647517
uni7  -0.0214677884 -0.0045854100 -0.0112012373  0.033344008 -0.0153659720
uni8  -0.0478941517  0.0502748467  0.0001014800 -0.018841282 -0.0133871413
uni9  -0.0260344632  0.0004677953 -0.0136515209  0.015489135 -0.0256602775
uni10  0.0216698785  0.0183229035 -0.0235527655  0.034511519  0.0387503416
uni11  0.0083906710 -0.0072727817 -0.0039980520 -0.021786096 -0.0220334602
uni12 -0.0082089880  0.0016636793  0.0142897321 -0.021261537  0.0275995398
uni13 -0.0170004235 -0.0056293321  0.0354970471 -0.005079899  0.0136844411
uni14  0.0016380145 -0.0026257549 -0.0371797448 -0.010394978 -0.0094759917
uni15  0.0235154129 -0.0076910613  0.0218452734  0.016921417  0.0006166996
uni16  0.0086422016  0.0031932536  0.0174514083 -0.040723043  0.0227615252
uni17 -0.0048893559  0.0390815580 -0.0140283176  0.036478463  0.0162957782
uni18  0.0016569975  0.0029197399 -0.0014944297  0.004777094  0.0050510288
uni19  0.0406776259  0.0257039591  0.0209593999  0.004843764  0.0093133039
uni20  0.0152309378 -0.0143608304 -0.0420534836 -0.012270166  0.0050438479
uni21  0.0021857301 -0.0079052358  0.0109614645 -0.001426428 -0.0226249744
uni22  0.0151214536  0.0415514711 -0.0264034270  0.009654531  0.0063417306
uni23 -0.0136609346 -0.0183857731 -0.0008981013 -0.038905897 -0.0149673506
uni24 -0.0309508858  0.0037710588  0.0099969449  0.017105078  0.0295200484
uni25  0.0002719619  0.0294434926 -0.0181638901  0.005619418 -0.0016443567
uni26 -0.0114991175  0.0201340682  0.0446356403  0.001943129  0.0075309073
uni27 -0.0493142953 -0.0027570156 -0.0529941203  0.011577594  0.0103137777
uni28  0.0788502689 -0.0214131112 -0.0419381779  0.003729119 -0.0152881432
uni29  0.0184165128  0.0043242155  0.0029555479  0.045468318 -0.0168291903
uni30  0.0243630636 -0.0039792065  0.0101966345  0.006408771  0.0077692845
uni31 -0.0031986216  0.0155829473  0.0008475330  0.008792895  0.0339283695
uni32 -0.0001806068 -0.0163014106 -0.0222724595 -0.050114548  0.0264169363
uni33 -0.0087452914 -0.0078373999  0.0162914774  0.005525189 -0.0477128571
uni34 -0.0203178972 -0.0270322068  0.0055844581  0.006204909  0.0275085135
uni35  0.0230483658 -0.0059861855  0.0313137127 -0.013360578 -0.0036554477
uni36  0.0231032816 -0.0334290815  0.0312687009  0.023786278  0.0266800703
uni37 -0.0332926158 -0.0261276008 -0.0245192565 -0.021232503  0.0062185469
uni38  0.0059217281  0.0329084181  0.0110653452 -0.012771370 -0.0447175113
uni39  0.0351510623  0.0415177320 -0.0040342547 -0.048068434 -0.0147413292
            pcps.21       pcps.22       pcps.23       pcps.24       pcps.25
uni1   0.0024796851 -1.673954e-02  0.0151704238  5.987544e-03  2.326711e-02
uni2   0.0145089354 -6.336613e-03 -0.0050287803  1.313981e-02 -1.708742e-02
uni3   0.0023488361 -1.688184e-02 -0.0207899930  3.219499e-02  8.645574e-05
uni4  -0.0016193869  3.469466e-02  0.0131143738 -9.982409e-03 -7.172018e-03
uni5   0.0141243919 -7.336952e-03 -0.0399102808  8.471678e-03 -7.896338e-03
uni6  -0.0168364519 -3.917918e-02  0.0248729413 -2.410714e-02 -3.605199e-03
uni7   0.0089286129  8.314819e-03  0.0113765870  2.612854e-03 -4.489062e-03
uni8  -0.0109812922 -1.426042e-04 -0.0220706680  2.518336e-03  8.380689e-03
uni9  -0.0081175504  7.818989e-03 -0.0084016496 -1.044938e-02 -1.151468e-02
uni10  0.0116403686 -1.812183e-04 -0.0020090554 -3.434768e-03  5.913899e-02
uni11 -0.0049020324  3.521638e-03 -0.0090014925 -1.161172e-03  6.339743e-03
uni12 -0.0014890527  3.425753e-02  0.0135006285 -9.239694e-03 -7.557146e-03
uni13  0.0057669069 -4.940881e-03  0.0011233252  1.485161e-02 -2.122466e-02
uni14 -0.0594147046  8.162803e-03  0.0271464998  2.143485e-02  1.085537e-02
uni15  0.0138315617  1.758489e-02 -0.0095590217 -2.123639e-02 -4.014845e-03
uni16  0.0275918351  1.407355e-03 -0.0322234794  1.428016e-02  1.784178e-03
uni17  0.0316569614  1.580186e-02 -0.0059498954 -7.229704e-03  6.827116e-03
uni18 -0.0002583058  1.961333e-04  0.0014517099  1.697093e-04  2.122539e-03
uni19 -0.0273449081 -8.424677e-03  0.0004943955  3.006234e-02 -4.840047e-04
uni20  0.0058621697  1.743394e-02 -0.0305379610 -9.224778e-03 -2.000199e-02
uni21  0.0103307518 -2.270793e-03  0.0153645027 -7.103736e-02 -1.727747e-03
uni22 -0.0289123525  9.755344e-05 -0.0084340045 -3.738070e-03 -8.756937e-03
uni23  0.0156746517 -5.673595e-03  0.0195900444  4.058601e-02  4.404573e-02
uni24 -0.0384821023  9.319447e-03  0.0228967675 -2.195127e-06 -1.800666e-02
uni25 -0.0120371689 -2.863934e-02 -0.0245778876 -5.083365e-05  1.241948e-02
uni26  0.0048289275 -3.406144e-02  0.0024007859 -3.146927e-02  3.206061e-02
uni27  0.0392473858  2.081431e-02  0.0208192734  1.904738e-02 -1.669902e-02
uni28  0.0158189129 -5.658147e-03 -0.0146991700  5.602229e-03 -1.586242e-02
uni29  0.0011472120  5.602222e-03  0.0059171857  3.627984e-03 -5.154337e-03
uni30 -0.0343572352  8.453131e-03  0.0112287449 -4.753798e-03  3.317598e-03
uni31  0.0257694685 -4.249708e-02  0.0181472877  7.918247e-03 -3.076675e-02
uni32 -0.0155207532 -2.708036e-02 -0.0123942318 -2.196749e-02 -2.034837e-02
uni33 -0.0091440919  4.086531e-02 -0.0097436568 -2.259824e-03  2.427007e-02
uni34 -0.0313529577 -1.227270e-02 -0.0391733428 -2.841970e-03  1.499054e-03
uni35 -0.0102001424  3.839967e-02 -0.0072341399  4.288438e-03 -1.201529e-02
uni36  0.0128910740  1.903305e-03  0.0259567415  1.485073e-02 -4.261014e-03
uni37  0.0150054035  3.878898e-03 -0.0084662957 -1.533468e-02  1.965338e-02
uni38  0.0041783656 -2.182107e-02  0.0235896965  1.470598e-02 -2.259720e-02
uni39  0.0273380710  1.609566e-03  0.0360430911 -6.829950e-03  5.175006e-03
            pcps.26       pcps.27       pcps.28       pcps.29       pcps.30
uni1  -1.919816e-02  0.0162955406  0.0037983584 -1.797728e-02 -0.0243184065
uni2  -3.606325e-02 -0.0027755838  0.0408935798 -4.256290e-02  0.0109136266
uni3   1.593592e-02 -0.0025593835 -0.0075368983  2.730341e-02 -0.0379962866
uni4   7.767753e-03  0.0010120691 -0.0126081006 -7.150873e-03 -0.0042927686
uni5  -2.338298e-02 -0.0145307180  0.0137427553  2.568129e-02  0.0151047233
uni6   1.668078e-02  0.0245185225 -0.0024854352 -9.693638e-03  0.0048116426
uni7   2.790754e-03 -0.0043289657  0.0053907149  3.636274e-02  0.0017985289
uni8   1.065782e-02  0.0138073020  0.0056666745 -9.764308e-03  0.0003444861
uni9  -1.473264e-02 -0.0445746938 -0.0248199858 -2.279303e-02 -0.0032935239
uni10  1.116767e-03 -0.0124455441  0.0088856955 -1.511831e-03 -0.0213791490
uni11 -8.612733e-04  0.0037377769 -0.0003481847  3.861087e-03  0.0009669961
uni12  7.811551e-03  0.0008724946 -0.0108069546 -6.330565e-03 -0.0044316778
uni13  3.399548e-02 -0.0178844059  0.0112815202  4.367342e-03  0.0002085869
uni14 -1.330797e-03 -0.0415463335  0.0148391509  5.598911e-03  0.0036210855
uni15 -2.604736e-02  0.0020312507 -0.0256169482  2.146599e-02  0.0202988829
uni16  1.385107e-02  0.0055677221  0.0074532072 -1.579893e-02 -0.0208982568
uni17 -4.141367e-02  0.0174064829 -0.0085800149 -1.078634e-02 -0.0075917649
uni18  4.897517e-04  0.0007803703 -0.0007909831  3.561477e-05 -0.0008560661
uni19 -4.395508e-03  0.0009852086 -0.0072381112 -6.742196e-03  0.0094911413
uni20  1.652358e-03 -0.0108816566 -0.0222894293 -1.466813e-02  0.0066848341
uni21 -3.274799e-05 -0.0155380558  0.0192033657  9.934426e-03 -0.0291472967
uni22 -6.776932e-03  0.0113560224  0.0029505093  1.322738e-02 -0.0080319493
uni23 -2.162964e-02 -0.0073439735 -0.0287577792  1.222689e-04  0.0136576595
uni24 -1.535086e-02  0.0074446272  0.0004592330 -4.030236e-03 -0.0171841190
uni25  1.104574e-02  0.0086313590  0.0238880370  4.096556e-03  0.0035781106
uni26  2.695095e-02 -0.0148981223 -0.0137644900 -2.493350e-02  0.0199429123
uni27  2.418104e-02  0.0202679576  0.0135924389 -4.314598e-03  0.0120650032
uni28  2.312313e-02 -0.0038681224  0.0029758339 -1.868842e-02 -0.0095488645
uni29  3.646583e-02  0.0075001837 -0.0219976392 -8.677215e-03  0.0283294002
uni30 -9.350945e-03  0.0120603136  0.0074407723 -7.251946e-03  0.0126830618
uni31 -9.522882e-03 -0.0310645956 -0.0042136452  1.606801e-03  0.0044754116
uni32 -1.694259e-02  0.0244753486 -0.0091031792  1.127117e-02  0.0082401362
uni33  1.016481e-02  0.0273562961  0.0017839891 -1.238095e-03 -0.0007132535
uni34 -2.928768e-03  0.0155869202  0.0024817891  9.092915e-03  0.0168401011
uni35  6.871829e-03 -0.0165785401  0.0166755084 -2.066150e-03 -0.0099678417
uni36  2.758243e-03  0.0145918699  0.0097450985  1.584975e-02  0.0072813453
uni37  8.409066e-03 -0.0176648989 -0.0069760620  2.559199e-02  0.0076069835
uni38 -5.467702e-03  0.0185946559 -0.0337757746  4.821575e-03 -0.0315057014
uni39 -7.291923e-03  0.0036032987  0.0285613832  1.668898e-02  0.0222122667
            pcps.31       pcps.32       pcps.33       pcps.34       pcps.35
uni1   0.0119778848  0.0022851975  0.0364681841 -1.118795e-02 -0.0022863900
uni2  -0.0007044102 -0.0033940057 -0.0094460282  3.973477e-03 -0.0005676009
uni3   0.0071190843 -0.0177780220  0.0098593000  2.182639e-02 -0.0253376333
uni4  -0.0132653089 -0.0071963100 -0.0042434672 -4.644767e-03  0.0084087616
uni5  -0.0008343508  0.0140299768  0.0120760600 -2.591995e-02  0.0276477209
uni6   0.0177287769 -0.0123498083 -0.0221987652 -1.727877e-03  0.0170159406
uni7  -0.0045311152  0.0424267281 -0.0237029102 -4.564884e-03 -0.0094875459
uni8  -0.0052282146 -0.0139469093  0.0062542817 -5.245608e-03  0.0062154298
uni9   0.0115755562 -0.0144579859 -0.0075351519  1.411851e-02  0.0008547748
uni10  0.0224633677 -0.0074143916 -0.0229257891 -1.172808e-02  0.0082806424
uni11 -0.0003489875  0.0047088889  0.0006673552 -6.549052e-05 -0.0013803121
uni12 -0.0121547440 -0.0050881905 -0.0053816629 -5.407799e-03  0.0079313287
uni13  0.0113092280 -0.0075074443 -0.0056900709 -3.263544e-03  0.0044048033
uni14 -0.0165057667  0.0100993239  0.0182616144 -1.135175e-02 -0.0087680206
uni15  0.0064802239 -0.0395805232  0.0042140047 -5.774641e-03 -0.0084827493
uni16  0.0014380002  0.0322164350 -0.0085548243  1.579957e-02  0.0094212046
uni17 -0.0203076264  0.0117999348  0.0124347686  7.060530e-03 -0.0131474447
uni18  0.0003826370 -0.0003585969  0.0004268764  2.060032e-04  0.0005481126
uni19  0.0085954123 -0.0018269341  0.0019282684 -4.877552e-03 -0.0016458450
uni20  0.0348268495  0.0207794900 -0.0042780379 -8.293489e-03 -0.0192803372
uni21 -0.0193600580  0.0028588582 -0.0018440973  1.757169e-02  0.0035259496
uni22 -0.0028726677 -0.0034618745  0.0039986483 -5.631173e-04  0.0395573870
uni23 -0.0195752457 -0.0037930929 -0.0172762736  2.138734e-02  0.0166774079
uni24  0.0280521823  0.0105855940  0.0150436757  1.391793e-02  0.0108853474
uni25 -0.0193143599 -0.0182794980  0.0033680071  1.140029e-02 -0.0206616478
uni26 -0.0051009310  0.0149156198  0.0155820793 -2.597733e-02 -0.0118409331
uni27 -0.0055458091 -0.0145882941  0.0054440887 -1.946028e-02 -0.0054453171
uni28 -0.0193228023 -0.0114017313 -0.0028468437 -2.760862e-03  0.0093229825
uni29 -0.0040073197  0.0174153122  0.0236647550  3.665509e-02  0.0091061242
uni30 -0.0150767261  0.0073009957 -0.0308165548  2.830517e-03 -0.0268000938
uni31 -0.0059982559 -0.0024537199 -0.0031492385  3.871683e-03  0.0015894890
uni32 -0.0151828835  0.0072268659  0.0114761284  2.103524e-03 -0.0059775760
uni33  0.0069245665  0.0034181462  0.0023800231 -2.661215e-03  0.0002521718
uni34  0.0084761014 -0.0024667366 -0.0203968599  4.633863e-03 -0.0013153895
uni35 -0.0050487856 -0.0135353541  0.0019073864 -6.092280e-03 -0.0075246992
uni36 -0.0111871424 -0.0019173260 -0.0002503510 -2.610171e-03  0.0023623250
uni37  0.0013016738 -0.0026069984  0.0100782321 -1.853161e-03  0.0029659644
uni38 -0.0001215717  0.0056420073 -0.0120081616 -2.784488e-02 -0.0084730528
uni39  0.0429435381 -0.0023056267  0.0070113505  1.652027e-02 -0.0085512800
            pcps.36       pcps.37       pcps.38
uni1   1.578895e-02  1.163702e-02 -1.053203e-04
uni2  -1.867719e-03 -1.673658e-02 -2.874617e-04
uni3   1.426105e-02 -2.099525e-02  5.102220e-05
uni4  -7.518772e-04  1.160050e-02 -2.443307e-02
uni5   7.553164e-03  2.464932e-02 -2.216601e-05
uni6  -1.096186e-03  5.185166e-03 -2.579079e-05
uni7  -1.725851e-02 -9.266635e-03 -7.480603e-04
uni8   5.957944e-03  2.071318e-03  2.420688e-04
uni9   7.856789e-03  9.483005e-03  2.450569e-04
uni10  4.405176e-04  6.122205e-03 -4.309730e-05
uni11  1.132829e-03 -4.792192e-04  1.704277e-05
uni12 -1.381866e-03  1.084859e-02  2.481756e-02
uni13  2.738729e-03  2.013113e-03 -2.311297e-04
uni14 -5.689070e-04 -2.553303e-03 -5.198561e-05
uni15 -5.528154e-03 -5.184787e-03  2.389997e-04
uni16  7.099472e-03  6.316595e-03 -1.008909e-04
uni17 -4.265456e-03 -4.906483e-03  1.714571e-04
uni18  6.482552e-05 -1.561393e-05  1.060144e-05
uni19 -1.358085e-03  8.476039e-04  1.455097e-06
uni20 -5.182671e-04 -9.913348e-04 -9.558618e-05
uni21  2.838239e-03 -4.726273e-04  3.548914e-05
uni22  2.265565e-02 -3.037667e-02  8.879862e-05
uni23 -1.279445e-02 -6.056030e-03  1.363342e-04
uni24 -3.225913e-02  4.356208e-03 -6.969809e-05
uni25 -2.419009e-02  3.429405e-02  1.554753e-04
uni26 -7.764115e-03 -2.573229e-02 -2.215215e-05
uni27  9.077420e-03 -2.665749e-03  1.243806e-06
uni28 -2.230817e-02 -1.233415e-02  8.204793e-05
uni29  1.063770e-02  1.094039e-02  2.390324e-04
uni30  4.136162e-02  8.888875e-03  1.778946e-05
uni31  8.020258e-03  5.069232e-03  2.947619e-05
uni32 -3.148105e-03 -6.401819e-03  7.731686e-05
uni33 -4.177530e-03 -2.059496e-03 -3.803196e-05
uni34 -9.020991e-03 -8.221095e-03 -2.144883e-04
uni35 -1.026567e-02 -7.930864e-03 -5.624880e-05
uni36 -3.238662e-03 -2.091363e-03 -2.342869e-05
uni37  8.012620e-03  3.262819e-03  3.673126e-05
uni38 -2.851422e-03  1.043075e-02 -3.190430e-05
uni39  1.115582e-03 -2.545426e-03 -9.449478e-05

$correlations
                               pcps.1       pcps.2      pcps.3      pcps.4
araucaria_angustifolia     0.06012119 -0.224388726  0.13602160  0.05232872
podocarpus_lamberti        0.09632973 -0.244630241  0.06103214  0.03797044
calyptranthes_grandifolia  0.86226968 -0.021135551 -0.45403083  0.13580692
eugenia_handroi            0.85941307 -0.031490629 -0.45356519  0.13431293
eugenia_subterminalis      0.86080403 -0.026805552 -0.45365561  0.13459585
eugenia_uruguayensis       0.86282516 -0.025966601 -0.45087286  0.13615074
myrceugenia_miersiana      0.77626091 -0.103067842 -0.53966531  0.09242456
myrceugenia_myrcioides     0.73634551 -0.144870739 -0.55599687  0.04241117
myrceugenia_ovata          0.74003257 -0.151903470 -0.54252421  0.06569120
myrceugenia_oxysepala      0.78138915 -0.107318689 -0.53359367  0.09244352
myrceugenia_sp             0.78527305 -0.107808244 -0.53329859  0.08458209
myrcia_guianensis          0.86057954  0.030286517 -0.42144802  0.12936300
myrcia_hartwegiana         0.86047822  0.017968113 -0.42201722  0.13382316
myrcia_retorta             0.83725558  0.029308012 -0.43428732  0.12814508
myrciaria_delicatula       0.85817633 -0.007694548 -0.45283451  0.15252415
genx_sp                    0.85772249 -0.009750498 -0.45030767  0.13010671
psidium_cattleianum        0.87238097  0.001160496 -0.42847803  0.12678575
siphoneugena_reitzii       0.78720296  0.028422451 -0.48772324  0.15230082
leandra_dasytricha         0.83264506  0.132478774 -0.24598299  0.31266189
leandra_laevigata          0.86651761  0.132428540 -0.24963393  0.28750071
leandra_sublanata          0.87328965  0.143042811 -0.21626944  0.26879819
miconia_cinerascens        0.83697761  0.173768528 -0.23478283  0.26514135
miconia_hyemalis           0.86423647  0.184007785 -0.19093564  0.26934982
miconia_sellowiana         0.85606362  0.170952818 -0.24753015  0.27117258
daphnopsis_fasciculata     0.73981650 -0.056502700 -0.23800045  0.02440602
matayba_elaeagnoides       0.78061889 -0.037916236 -0.25890065  0.03022586
zanthoxylum_rhoifoliu      0.81084554 -0.037899702 -0.26397256  0.04755342
casearia_decandra          0.72805088 -0.126807700 -0.07747477  0.10687668
xylosma_pseudosalzmanii    0.72907382 -0.137375005 -0.05820068  0.12491651
sapium_glandulosum         0.75603593 -0.116271923 -0.05304093  0.12882220
lamanonia_ternata          0.74457946 -0.058095824 -0.05234437  0.18754544
weinmannia_paulliniifolia  0.75416725 -0.071314116 -0.06494557  0.19719796
inga_lentiscifolia         0.74746882


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