HW #10 Computer Intensive Statistics in Ecology
蘇主弦 Eric Su
2017/5/4
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Load packages
library(ggbiplot)
library(vegan)
library(cluster)Q. Use the “dominant” copepod species data (from HW1). Apply PCA or MDS using matrix algebra to extract major gradients of the dominant species. Make a bi-plot to show the relationships among species and sites. Then, check your results with those from build-in functions of PCA, MDS, and NMDS.
Import data
Import copepod data and extract dominant species data. Also extract group from the result of hierarchical clustering in previous homework.
#import copepod data
copdata = read.table("copepod_composition.txt", header = T)
#import species name
species_name <- read.table("copepodSPlist.txt", sep = "\t")
#assign copepod species name
rownames(copdata) <- as.character(unlist(species_name))
#convert species frequency into percentage
copdata = copdata / 100
#find dominant species
dom = apply(copdata >= 0.02, 2, which)
dom = sort(unique(unlist(dom)))
dom = t(copdata[dom, ])
#calculate distance matrix
dist_dom = vegdist(dom, method = "jaccard")
#perform hierarchical clustring
hc_dom = agnes(dist_dom, method = "ward")
group = cutree(hc_dom, 3)
group = factor(group, labels = c("Spring", "Summer", "Winter"))Conduct eigen analysis on dominant copepod data
#eigen analysis on correlation matrix
dom_eigen <- eigen(cor(dom))
#extract pc loadings
loading = dom_eigen$vectors
rownames(loading) <- colnames(dom)
#calculate pc scores
score = scale(dom) %*% loadingDetermine number of PCs to keep
var_expla = dom_eigen$values / sum(dom_eigen$values)
plot(var_expla, type = "b")
plot(cumsum(var_expla), type = "b")
It seems that the first 4 PCs explains most of the variance.
Create bi-plot to visualize result
biplot(cbind(score[,1], score[,2]), loading[, 1:34], ylabs = colnames(dom), xlab = paste("PC1(", 100 * round(var_expla[1], 2), "%)", sep = "" ), ylab = paste("PC2(", 100 * round(var_expla[2], 2), "%)", sep = "" ))
Loading plots
Create loading plots to inspect copepods’ effect on each PC.
for(i in 1:4){
cat("\n")
cat("#### ", "PC", i, "\n")
pc_load = loading[, i]
dotchart(pc_load[order(pc_load, decreasing = FALSE)], main = paste("Loading Plot for PC", i, sep = ""), xlab = "Variable Loadings", col = "blue")
cat("\n")
}PC 1
PC 2
PC 3
PC 4
PCA
Conduct PCA using build-in function prcomp
dom_pca <- prcomp(dom, scale. = T)Visulize PCA results using bi-plot
PCA bi-plot
biplot(dom_pca)
Compare with matrix algebra result
Since the +/- sign of the PCs is arbitrary, we can reverse them without distorting the results. This graph is made after reversing the +/- of eigen vectors.
biplot(cbind(-score[, 1], -score[, 2]), -loading[, 1:34], ylabs = colnames(dom), xlab = paste("PC1(", 100 * round(var_expla[1], 2), "%)", sep = "" ), ylab = paste("PC2(", 100 * round(var_expla[2], 2), "%)", sep = "" ))
The two bi-plots are very similar, indicating that we have done the eigen analysis correctly.
Add group to graph
In this bi-plot, groups from hierarchical clustering are added and also a prettier graph is used
ggbiplot(dom_pca, obs.scale = 1, var.scale = 1, ellipse = TRUE, groups = group,
circle = TRUE) +
scale_color_discrete(name = '') +
theme(legend.direction = 'horizontal', legend.position = 'top') +
theme_bw()
We can see that the first two principle components seperates summer from the other seasons but does not seperates spring and winter too well.
Other unconstrained ordination methods
MDS
Conduct MDS using build-in function cmdscale
dom_mds <- cmdscale(dist(dom), k = 4, eig = T)
dom_mds$points## [,1] [,2] [,3] [,4]
## p1 -0.225743926 -0.08223870 0.414066249 0.199761132
## p3 -0.378408680 -0.10068738 0.025754148 0.032332619
## p4 -0.421018376 -0.12521990 0.067765953 0.087615375
## p6 -0.425597458 -0.09730906 -0.095352956 -0.033027565
## p13 -0.218293394 -0.03988159 -0.038170701 -0.061805568
## p16 -0.421751602 -0.06767344 -0.197555818 -0.041912982
## p19 -0.161956306 -0.01592267 -0.075094116 -0.055641912
## p21 -0.206374281 -0.02901280 0.156306585 0.030269302
## p23 -0.022878320 0.03890064 -0.014739602 -0.073275057
## p25 -0.174645655 -0.02316880 -0.058332224 -0.057207184
## s18 -0.021393710 -0.01614660 -0.050675247 -0.047487841
## s19 0.046360116 -0.04147406 -0.036943815 -0.024672598
## s20 0.093256721 -0.07633705 -0.035638166 0.021469180
## s22 0.163907597 -0.04419809 -0.006166941 0.018622706
## s23 0.142959251 0.01335315 0.006617901 -0.028362943
## s25 0.107057739 -0.04672766 -0.006647783 -0.036380685
## s27 0.228783131 -0.14355914 -0.017841758 0.018939710
## s29 0.310935531 -0.22996587 -0.052206634 0.115628701
## sA 0.124620686 -0.04288379 0.012405192 -0.078749475
## sB 0.129731279 0.02470909 0.053275031 -0.157139704
## sC 0.166592555 -0.09258834 -0.013977067 -0.014840541
## sD 0.144967854 -0.10320786 -0.022165296 -0.029041783
## sE 0.075421345 -0.01724177 0.016144804 -0.115024043
## sF 0.193106709 0.02054493 0.072836131 -0.136516574
## sG 0.366576273 -0.33227864 -0.101191417 0.201551483
## w22 0.001834991 0.26908433 -0.091014269 0.137172631
## w23 0.096122399 0.33298358 -0.104373805 0.276395187
## w25 -0.115236721 0.19426390 -0.131688355 0.058039177
## w27 0.046823737 0.20118324 -0.021194355 0.014033010
## w29 -0.089958918 0.08131234 -0.046824983 -0.008428319
## wA 0.078422500 0.18630906 0.096867055 -0.015851203
## wB 0.131657197 0.14333238 0.150200189 -0.076604644
## wC 0.128455343 0.08412393 0.091194586 -0.097416170
## wD 0.105664392 0.17762263 0.054361486 -0.022443422#visulize result
ordiplot(dom_mds)
CA
Conduct CA using build-in function cca
dom_ca <- cca(dom)
summary(dom_ca)##
## Call:
## cca(X = dom)
##
## Partitioning of mean squared contingency coefficient:
## Inertia Proportion
## Total 2.619 1
## Unconstrained 2.619 1
##
## Eigenvalues, and their contribution to the mean squared contingency coefficient
##
## Importance of components:
## CA1 CA2 CA3 CA4 CA5 CA6 CA7
## Eigenvalue 0.5553 0.4294 0.2967 0.21667 0.1901 0.17901 0.12140
## Proportion Explained 0.2120 0.1640 0.1133 0.08274 0.0726 0.06835 0.04636
## Cumulative Proportion 0.2120 0.3760 0.4893 0.57202 0.6446 0.71298 0.75934
## CA8 CA9 CA10 CA11 CA12 CA13
## Eigenvalue 0.09672 0.07107 0.06851 0.05735 0.04814 0.04377
## Proportion Explained 0.03693 0.02714 0.02616 0.02190 0.01838 0.01671
## Cumulative Proportion 0.79627 0.82341 0.84957 0.87147 0.88985 0.90657
## CA14 CA15 CA16 CA17 CA18 CA19
## Eigenvalue 0.03777 0.03543 0.03172 0.02427 0.02075 0.01895
## Proportion Explained 0.01442 0.01353 0.01211 0.00927 0.00792 0.00723
## Cumulative Proportion 0.92099 0.93452 0.94663 0.95590 0.96382 0.97105
## CA20 CA21 CA22 CA23 CA24 CA25
## Eigenvalue 0.01807 0.01216 0.009732 0.009026 0.007034 0.006217
## Proportion Explained 0.00690 0.00464 0.003720 0.003450 0.002690 0.002370
## Cumulative Proportion 0.97796 0.98260 0.986320 0.989760 0.992450 0.994820
## CA26 CA27 CA28 CA29 CA30
## Eigenvalue 0.004542 0.003037 0.002635 0.001955 0.000703
## Proportion Explained 0.001730 0.001160 0.001010 0.000750 0.000270
## Cumulative Proportion 0.996560 0.997720 0.998720 0.999470 0.999740
## CA31 CA32 CA33
## Eigenvalue 0.0004339 0.0002092 4.532e-05
## Proportion Explained 0.0001700 0.0000800 2.000e-05
## Cumulative Proportion 0.9999000 0.9999800 1.000e+00
##
## Scaling 2 for species and site scores
## * Species are scaled proportional to eigenvalues
## * Sites are unscaled: weighted dispersion equal on all dimensions
##
##
## Species scores
##
## CA1 CA2 CA3
## Acartia negligence -0.43019 0.09351 0.744306
## Acartia pacifica 0.19399 -1.99844 -1.438317
## Calanus sinicus 0.77394 -0.10538 0.419189
## Canthocalanus pauper -0.64950 0.08516 0.387195
## Cosmocalanus darwinii -0.15254 -0.21767 1.064380
## Undinula vulgaris -0.73823 0.13638 0.536169
## Clausocalanus furcatus -0.38640 -0.01428 0.932989
## Clausocalanus minor -0.01159 -0.25861 0.793473
## Subeucalanus pileatus -0.13107 -0.59529 0.214090
## Subeucalanus subcrassus 0.15447 -1.05664 0.400449
## Subeucalanus copepodid -0.35117 0.01713 0.346669
## Euchaeta concinna 0.37897 -0.98905 0.667179
## Euchaeta copepodid 0.32394 -1.18182 -0.020221
## Acrocalanus gibber -0.72135 0.16986 0.241793
## Acrocalanus gracilis -0.71284 0.15047 0.525504
## Calocalanus gracilis -0.13150 -0.00390 0.983935
## Calocalanus pavoninus -0.65192 0.22427 0.976567
## Calocalanus plumulosus -0.17132 0.18675 0.870530
## Calocalanus styliremis -0.66833 0.22284 0.845657
## Paracalanus aculeatus 0.36486 -0.75610 0.364187
## Paracalanus pavus 0.51165 0.19650 0.008427
## Paracalanus serrulus -0.97170 0.25408 -0.177618
## Parvocalanus crassirostris -1.23674 0.61910 -0.547916
## Scolecithricella longispinosa 0.07680 -1.06064 -0.252935
## Temora stylifera 0.27407 0.13426 0.772266
## Temora turbinata -0.75822 0.19732 0.046414
## Oithona attenuata -1.33143 0.63817 -0.578974
## Oithona brevicornis -0.98568 0.22542 -1.562021
## Oithona fallax -0.21878 -0.60597 0.061148
## Oithona plumifera -0.21900 -0.13492 0.714987
## Oithona similis 1.05811 0.73080 -0.161895
## Euterpina acutifrons -0.78185 0.18977 -0.905639
## Corycaeus (Ditrichocorycaeus) affinis 1.76638 1.41646 -0.772465
## Corycaeus (Ditrichocorycaeus) dahli -0.76147 0.03294 0.818118
## Corycaeus (Ditrichocorycaeus) lubbocki -0.57579 -0.18029 -1.088170
## Corycaeus (Ditrichocorycaeus) subtilis -0.56648 0.04396 0.613623
## Corycaeus (Onychocorycaeus) giesbrechti -0.78542 0.15513 0.158593
## Farranula gibbula -0.67880 0.25180 0.784909
## Corycaeidae copepodid 0.65131 0.28872 0.600560
## Oncaea conifera -0.64905 -0.01431 0.567199
## Oncaea media -0.20723 -0.21954 0.681058
## Oncaea mediterranea 0.07479 -0.34654 0.815194
## Oncaea venusta -0.45279 0.03707 0.494862
## CA4 CA5 CA6
## Acartia negligence 0.135514 -0.076031 -0.115817
## Acartia pacifica 0.147562 -0.817406 -0.871610
## Calanus sinicus 0.361205 0.152520 0.766025
## Canthocalanus pauper 0.009638 -0.354035 -0.015872
## Cosmocalanus darwinii 0.172974 0.109806 0.130877
## Undinula vulgaris 0.141466 -0.557618 -0.153716
## Clausocalanus furcatus -0.037131 -0.285167 0.021401
## Clausocalanus minor -0.059510 0.169563 0.326945
## Subeucalanus pileatus -0.088787 0.056621 0.828682
## Subeucalanus subcrassus 0.312624 -0.063436 0.592669
## Subeucalanus copepodid -0.294087 -0.058239 -0.235898
## Euchaeta concinna 0.595914 0.473127 1.279366
## Euchaeta copepodid 0.311812 0.224831 0.343385
## Acrocalanus gibber 0.259858 -0.195098 -0.091653
## Acrocalanus gracilis -0.170943 -0.598894 -0.066356
## Calocalanus gracilis -0.337548 0.084262 -0.528066
## Calocalanus pavoninus -0.287572 -0.714039 -0.585163
## Calocalanus plumulosus -0.338476 0.001279 -0.729650
## Calocalanus styliremis -0.162421 -0.581950 -0.463046
## Paracalanus aculeatus 0.287201 0.273547 0.246342
## Paracalanus pavus -0.132607 0.260726 -0.316823
## Paracalanus serrulus -0.733579 -0.558606 0.244743
## Parvocalanus crassirostris 0.772132 0.327749 -0.066462
## Scolecithricella longispinosa -0.018014 0.167988 0.706710
## Temora stylifera -0.396383 0.646723 -0.725227
## Temora turbinata 0.440927 -0.098334 0.007937
## Oithona attenuata 0.713312 0.192372 0.002277
## Oithona brevicornis -1.754451 0.615534 1.202605
## Oithona fallax 0.013554 -0.100980 0.222532
## Oithona plumifera -0.296873 -0.084809 -0.049911
## Oithona similis -0.286594 0.413742 -0.564944
## Euterpina acutifrons -1.260914 0.319419 0.621072
## Corycaeus (Ditrichocorycaeus) affinis 0.396664 -1.100845 0.593805
## Corycaeus (Ditrichocorycaeus) dahli -0.882176 -1.747292 0.030620
## Corycaeus (Ditrichocorycaeus) lubbocki -1.310881 0.351361 0.622828
## Corycaeus (Ditrichocorycaeus) subtilis -0.398836 -0.641961 -0.243820
## Corycaeus (Onychocorycaeus) giesbrechti -0.038611 -0.461819 -0.201293
## Farranula gibbula 0.031129 -0.402036 -0.427138
## Corycaeidae copepodid -0.536983 1.075919 -1.153201
## Oncaea conifera -0.414652 -0.838903 -0.146970
## Oncaea media -0.183451 -0.073150 0.488349
## Oncaea mediterranea 0.040627 0.267297 0.580612
## Oncaea venusta -0.389072 -0.387766 -0.073520
##
##
## Site scores (weighted averages of species scores)
##
## CA1 CA2 CA3 CA4 CA5 CA6
## p1 2.21690 1.89768 -1.19899 1.02442 -2.579290 1.83827
## p3 1.50293 1.08597 -0.40774 -0.16395 0.253662 -0.70221
## p4 1.65293 1.32013 -0.73540 0.09983 -0.617388 -0.25414
## p6 1.19816 0.70994 -0.02166 -0.45154 1.110697 -1.22085
## p13 0.84657 0.49512 0.50146 -0.67787 1.236915 -1.43853
## p16 0.74962 0.14018 0.30345 -0.34916 1.308578 -1.26790
## p19 0.32794 0.05731 0.61053 -0.39210 0.729869 -0.63629
## p21 1.58170 0.95474 -0.22326 0.18115 0.243942 0.04030
## p23 0.06942 -0.17799 1.31073 -0.36943 0.359753 -0.50101
## p25 0.41032 0.10647 0.74869 -0.35054 1.008980 -0.66416
## s18 -0.19103 -0.09991 0.04173 -0.52457 0.008991 -0.42727
## s19 -0.45272 0.06720 -0.12610 -0.77267 0.233358 0.10380
## s20 -0.80964 0.26291 -1.78250 -2.08204 1.134383 1.50010
## s22 -1.15145 0.16441 -2.12925 -2.32884 0.675417 1.68801
## s23 -0.56165 -0.19199 -0.79654 -1.40391 -0.216240 -0.05202
## s25 -0.78279 0.25533 0.06524 -0.56615 -0.469098 0.05662
## s27 -1.29542 0.68434 0.06038 1.01688 -0.134733 -0.37945
## s29 -1.75295 0.98767 -0.90097 2.10878 0.538567 -0.17266
## sA -0.83922 0.26576 0.67351 -0.15178 -0.753916 -0.35818
## sB -0.65375 0.04639 1.54940 -0.81834 -1.388453 -0.50677
## sC -1.10081 0.48932 0.24534 0.83941 -0.426168 -0.34281
## sD -1.00087 0.47299 0.32063 0.56613 -0.300748 -0.38096
## sE -0.64661 0.28033 1.05645 -0.42845 -0.884905 -0.77849
## sF -1.08269 0.13103 1.04496 -1.36174 -2.855341 -0.08361
## sG -1.88104 1.14413 -1.26354 2.51522 1.050035 -0.25066
## w22 0.49268 -2.05927 -0.92055 0.39346 -0.016402 -0.06982
## w23 0.42983 -3.16032 -2.45178 0.62329 -1.797023 -2.08820
## w25 0.49772 -1.23566 0.07092 0.41545 0.866189 0.30523
## w27 0.32567 -1.41634 0.37158 0.65030 0.386109 0.96336
## w29 0.33645 -0.66562 0.24070 0.54049 0.316904 -0.05730
## wA 0.53676 -0.99285 0.83426 0.98910 0.661945 2.02973
## wB 0.35682 -0.79562 1.27112 0.48131 0.278242 2.09120
## wC -0.16081 -0.41936 1.65444 0.25772 -0.295797 0.84893
## wD 0.23149 -1.08444 0.88821 0.52798 0.344771 1.58702#Visulize CA result
ordiplot(dom_ca) 
DCA
Conduct DCA using build-in function decorana
dom_dca = decorana(dom)
summary(dom_dca)##
## Call:
## decorana(veg = dom)
##
## Detrended correspondence analysis with 26 segments.
## Rescaling of axes with 4 iterations.
##
## DCA1 DCA2 DCA3 DCA4
## Eigenvalues 0.5518 0.2723 0.2270 0.13601
## Decorana values 0.5553 0.2874 0.1344 0.06853
## Axis lengths 3.9772 2.3414 1.7222 1.41754## Species scores:
##
## DCA1 DCA2 DCA3
## Acartia negligence -0.81937 -2.41835 0.98851
## Acartia pacifica 0.17665 2.27437 -0.56384
## Calanus sinicus 1.57049 -1.30552 -1.80339
## Canthocalanus pauper -1.12782 -0.81543 -0.51614
## Cosmocalanus darwinii -0.45733 -1.98573 0.65868
## Undinula vulgaris -1.26168 -1.50172 -0.54342
## Clausocalanus furcatus -0.76104 -1.83348 -0.60034
## Clausocalanus minor -0.25008 -1.54271 -0.53082
## Subeucalanus pileatus -0.42884 0.66940 -1.98943
## Subeucalanus subcrassus 0.08278 0.46828 -2.01826
## Subeucalanus copepodid -0.71467 -1.08583 1.17748
## Euchaeta concinna 0.66895 -1.52415 -2.89978
## Euchaeta copepodid 0.51881 1.24135 -1.33795
## Acrocalanus gibber -1.23574 -0.73191 -0.25690
## Acrocalanus gracilis -1.22265 -1.16094 -0.75388
## Calocalanus gracilis -0.42945 -2.16179 2.84759
## Calocalanus pavoninus -1.13142 -2.53064 0.90979
## Calocalanus plumulosus -0.48203 -2.94935 2.44759
## Calocalanus styliremis -1.15588 -2.17848 0.90565
## Paracalanus aculeatus 0.63041 -0.08617 -0.93436
## Paracalanus pavus 1.01157 0.14679 1.00013
## Paracalanus serrulus -1.67962 0.78626 -0.32761
## Parvocalanus crassirostris -2.25924 0.48252 0.53815
## Scolecithricella longispinosa -0.08674 1.43152 -1.55581
## Temora stylifera 0.38457 -2.89658 3.52937
## Temora turbinata -1.29327 -0.42600 -0.51538
## Oithona attenuata -2.46632 0.53317 0.21194
## Oithona brevicornis -1.71017 1.84483 1.03378
## Oithona fallax -0.54399 0.94100 -0.85714
## Oithona plumifera -0.54427 -1.45971 1.01968
## Oithona similis 2.01144 0.50569 -0.18896
## Euterpina acutifrons -1.33160 1.60108 0.88622
## Corycaeus (Ditrichocorycaeus) affinis 2.83477 0.45456 0.38005
## Corycaeus (Ditrichocorycaeus) dahli -1.29856 -1.29594 -2.13766
## Corycaeus (Ditrichocorycaeus) lubbocki -1.02055 1.80321 0.43606
## Corycaeus (Ditrichocorycaeus) subtilis -1.00744 -0.61285 0.08215
## Corycaeus (Onychocorycaeus) giesbrechti -1.33743 -0.21993 -0.29242
## Farranula gibbula -1.17147 -2.00696 0.83132
## Corycaeidae copepodid 1.32625 -1.07334 2.10760
## Oncaea conifera -1.12714 -0.78155 -0.78880
## Oncaea media -0.52899 -0.93488 -0.97008
## Oncaea mediterranea -0.09072 -2.07076 -0.88011
## Oncaea venusta -0.84973 -0.81738 -0.29797
## DCA4 Totals
## Acartia negligence -0.21660 0.24
## Acartia pacifica 0.86607 1.09
## Calanus sinicus -1.64517 1.58
## Canthocalanus pauper -0.16819 1.02
## Cosmocalanus darwinii -2.11614 0.09
## Undinula vulgaris 1.23113 0.22
## Clausocalanus furcatus -1.45029 0.58
## Clausocalanus minor -1.77373 0.40
## Subeucalanus pileatus 1.27390 0.24
## Subeucalanus subcrassus -1.16850 0.16
## Subeucalanus copepodid -1.20996 0.18
## Euchaeta concinna -0.66718 0.10
## Euchaeta copepodid 1.17693 1.99
## Acrocalanus gibber -0.05824 0.89
## Acrocalanus gracilis -0.58187 0.13
## Calocalanus gracilis 2.21634 0.06
## Calocalanus pavoninus 1.44814 0.11
## Calocalanus plumulosus -0.31928 0.06
## Calocalanus styliremis 1.22486 0.08
## Paracalanus aculeatus -0.46079 1.43
## Paracalanus pavus 0.35250 7.96
## Paracalanus serrulus 0.40792 0.38
## Parvocalanus crassirostris -0.47850 2.36
## Scolecithricella longispinosa -0.87341 0.41
## Temora stylifera -1.99975 0.10
## Temora turbinata -0.41440 1.26
## Oithona attenuata -0.46118 0.63
## Oithona brevicornis -2.42249 0.26
## Oithona fallax 0.00366 0.23
## Oithona plumifera 0.87745 0.74
## Oithona similis -0.74201 1.07
## Euterpina acutifrons -1.66721 0.87
## Corycaeus (Ditrichocorycaeus) affinis 0.18455 1.26
## Corycaeus (Ditrichocorycaeus) dahli 2.74955 0.25
## Corycaeus (Ditrichocorycaeus) lubbocki -1.17151 0.41
## Corycaeus (Ditrichocorycaeus) subtilis 2.02990 0.09
## Corycaeus (Onychocorycaeus) giesbrechti -0.42186 0.17
## Farranula gibbula 1.56047 0.11
## Corycaeidae copepodid -0.21898 0.16
## Oncaea conifera 1.91921 0.53
## Oncaea media -2.19826 0.09
## Oncaea mediterranea -0.43842 0.10
## Oncaea venusta 1.02622 1.87
##
## Site scores:
##
## DCA1 DCA2 DCA3 DCA4 Totals
## p1 2.08274 0.11225 0.23177 -0.03468 1.00
## p3 1.52650 0.16407 0.44063 -0.01742 0.99
## p4 1.62066 0.23928 0.63728 0.17563 0.99
## p6 1.27821 0.07890 0.45600 -0.02106 0.99
## p13 0.90576 -0.21996 0.43713 -0.10635 0.97
## p16 0.81246 0.01231 0.64461 0.22009 0.96
## p19 0.34288 -0.27485 0.45792 0.13843 0.92
## p21 1.60762 0.01290 -0.04224 -0.35508 1.00
## p23 0.05314 -0.69917 0.42860 0.20815 0.89
## p25 0.44116 -0.47252 0.51274 -0.28264 0.94
## s18 -0.18597 0.05842 0.10317 0.24192 0.92
## s19 -0.46014 0.12736 0.17322 -0.00596 0.91
## s20 -0.79086 0.86083 0.44972 -0.65652 0.93
## s22 -1.14241 0.98563 0.31733 -0.65078 0.97
## s23 -0.56276 0.40972 0.05196 -0.09215 0.96
## s25 -0.76651 -0.10081 0.05916 -0.17821 0.94
## s27 -1.29031 -0.30688 0.13840 -0.14939 0.92
## s29 -1.75029 0.10470 0.17274 -0.35927 0.94
## sA -0.83899 -0.41898 0.03439 0.18106 0.91
## sB -0.66905 -0.86193 -0.02206 0.58362 0.91
## sC -1.07596 -0.31100 -0.02090 0.00869 0.92
## sD -0.99484 -0.33839 0.07514 0.07955 0.93
## sE -0.63164 -0.74819 0.22801 0.21435 0.92
## sF -1.05771 -0.53808 -0.54886 0.76101 0.93
## sG -1.89449 0.26124 0.36898 -0.37310 0.95
## w22 0.44456 0.95213 -0.59303 0.43757 0.98
## w23 0.32268 1.47944 -0.59211 0.61846 0.98
## w25 0.48771 0.50986 -0.33456 0.46321 0.99
## w27 0.29736 0.28881 -0.77984 0.18942 0.94
## w29 0.36697 0.01066 -0.27983 -0.02764 0.94
## wA 0.56564 -0.24699 -1.07757 -0.30686 0.89
## wB 0.34646 -0.64438 -0.93041 -0.43683 0.87
## wC -0.18742 -0.85685 -0.56305 -0.62698 0.86
## wD 0.20064 -0.09022 -0.88268 0.09341 0.88#Visulize DCA result
ordiplot(dom_dca, color = group) ## Warning in plot.window(...): "color" 不是一個繪圖參數## Warning in plot.xy(xy, type, ...): "color" 不是一個繪圖參數## Warning in axis(side = side, at = at, labels = labels, ...): "color" 不是一
## 個繪圖參數
## Warning in axis(side = side, at = at, labels = labels, ...): "color" 不是一
## 個繪圖參數## Warning in box(...): "color" 不是一個繪圖參數## Warning in title(...): "color" 不是一個繪圖參數
NMDS
Conduct NMDS using build-in function metaMDS
dom_nmds = metaMDS(dom, trace = F, k = 4)
stressplot(dom_nmds)
dom_nmds$points## MDS1 MDS2 MDS3 MDS4
## p1 -0.92105394 0.50712442 -0.130173072 -0.541694523
## p3 -0.96754255 0.55490924 0.013595575 0.024281857
## p4 -0.97829692 0.65032045 -0.125309256 0.057098569
## p6 -0.93016082 0.49320199 0.072520667 0.151523975
## p13 -0.57354546 0.33563191 0.266242285 0.114323178
## p16 -0.73107199 0.22048564 0.037836387 0.309729707
## p19 -0.32723531 0.11048263 0.188475434 0.168926400
## p21 -0.95252709 0.23652202 0.104701292 -0.282815896
## p23 -0.22337281 -0.13728722 0.417275805 0.223590359
## p25 -0.43053279 0.15848212 0.285138214 0.002057276
## s18 0.04986085 0.13243401 -0.063172379 0.197420213
## s19 0.20143247 0.09946819 -0.195513352 0.310990610
## s20 0.28394686 0.19464458 -0.653776499 0.204431634
## s22 0.64581130 0.05889992 -0.760405465 0.203216499
## s23 0.51648571 -0.08651063 -0.234565831 0.514237783
## s25 0.53059973 0.22740444 -0.165336843 0.097480030
## s27 0.87095058 0.27713267 0.179628509 -0.180391383
## s29 1.12611802 0.43695241 -0.135364442 -0.441951204
## sA 0.60975472 0.02952813 0.227452927 0.253880945
## sB 0.46584826 -0.14864873 0.581235903 0.423921385
## sC 0.70210234 0.17158760 -0.008891518 -0.208025062
## sD 0.63967351 0.11767002 0.110864516 -0.037732710
## sE 0.43220040 0.22440757 0.362157227 0.164546585
## sF 1.03620418 -0.14741851 0.348215887 0.240693401
## sG 1.05619655 0.50309858 -0.326913490 -0.608529558
## w22 -0.52172126 -0.65831823 -0.405034468 0.091747532
## w23 -0.34962407 -0.98027742 -0.586869306 0.106889836
## w25 -0.55607528 -0.35668954 -0.249555905 0.089465305
## w27 -0.14887484 -0.60175716 -0.217770117 -0.140172161
## w29 -0.34989245 -0.11392470 -0.089587495 -0.259095198
## wA -0.22915767 -0.65272414 -0.024463035 -0.530411274
## wB -0.07724960 -0.75550148 0.465318371 -0.257504879
## wC 0.17385943 -0.40588855 0.555306567 -0.347661169
## wD -0.07311005 -0.69544225 0.156736904 -0.114468061
## attr(,"centre")
## [1] TRUE
## attr(,"pc")
## [1] TRUE
## attr(,"halfchange")
## [1] TRUE
## attr(,"internalscaling")
## [1] 1.151142dom_nmds$species## MDS1 MDS2
## Acartia negligence 0.366339382 -0.039305723
## Acartia pacifica -0.268627952 -0.998293160
## Calanus sinicus -0.583302086 -0.290658054
## Canthocalanus pauper 0.607676822 0.025198719
## Cosmocalanus darwinii 0.083452766 -0.304671804
## Undinula vulgaris 0.713763810 0.008667430
## Clausocalanus furcatus 0.388115979 -0.167658550
## Clausocalanus minor 0.002051775 -0.300448149
## Subeucalanus pileatus 0.159927754 -0.529317848
## Subeucalanus subcrassus -0.119061613 -0.795129219
## Subeucalanus copepodid 0.273721606 0.126149572
## Euchaeta concinna -0.275876580 -0.873192418
## Euchaeta copepodid -0.377425111 -0.730903423
## Acrocalanus gibber 0.653418367 0.071531218
## Acrocalanus gracilis 0.724928784 0.044620778
## Calocalanus gracilis -0.018745116 -0.050928661
## Calocalanus pavoninus 0.575918538 0.149786312
## Calocalanus plumulosus 0.053442701 0.236357135
## Calocalanus styliremis 0.608337623 0.093827850
## Paracalanus aculeatus -0.372766592 -0.519504397
## Paracalanus pavus -0.518260942 0.230791762
## Paracalanus serrulus 0.921695165 0.117444566
## Parvocalanus crassirostris 1.021279348 0.432112358
## Scolecithricella longispinosa -0.115324787 -0.727821765
## Temora stylifera -0.389409080 0.206075026
## Temora turbinata 0.677091585 0.135116133
## Oithona attenuata 1.141829195 0.412406023
## Oithona brevicornis 0.728231106 0.172623287
## Oithona fallax 0.194640292 -0.454894529
## Oithona plumifera 0.161027062 -0.176712798
## Oithona similis -0.935515833 0.561617384
## Euterpina acutifrons 0.604551793 0.190999702
## Corycaeus (Ditrichocorycaeus) affinis -1.231708161 0.786260924
## Corycaeus (Ditrichocorycaeus) dahli 0.969114313 -0.184440587
## Corycaeus (Ditrichocorycaeus) lubbocki 0.407911465 -0.032327542
## Corycaeus (Ditrichocorycaeus) subtilis 0.530724582 0.008542541
## Corycaeus (Onychocorycaeus) giesbrechti 0.752892240 0.075136877
## Farranula gibbula 0.584636026 0.078314149
## Corycaeidae copepodid -0.704748608 0.358579568
## Oncaea conifera 0.662331740 -0.130632941
## Oncaea media 0.234050899 -0.275352707
## Oncaea mediterranea -0.034032457 -0.476736896
## Oncaea venusta 0.452378585 -0.052972382
## MDS3 MDS4
## Acartia negligence 0.50557048 0.02996109
## Acartia pacifica -0.80222444 0.25800940
## Calanus sinicus 0.25695815 -0.49813093
## Canthocalanus pauper 0.19053685 0.01567589
## Cosmocalanus darwinii 0.63530248 -0.20491162
## Undinula vulgaris 0.32360147 0.03582609
## Clausocalanus furcatus 0.61600404 -0.01520655
## Clausocalanus minor 0.40733919 -0.04657081
## Subeucalanus pileatus -0.08930566 -0.03271155
## Subeucalanus subcrassus 0.04674054 -0.22529696
## Subeucalanus copepodid 0.10419376 0.20723824
## Euchaeta concinna 0.04721062 -0.52594916
## Euchaeta copepodid -0.25845321 -0.03326148
## Acrocalanus gibber 0.16218508 -0.09959613
## Acrocalanus gracilis 0.32593965 0.05705482
## Calocalanus gracilis 0.62767568 0.49808001
## Calocalanus pavoninus 0.63057917 0.39636336
## Calocalanus plumulosus 0.59433169 0.32194140
## Calocalanus styliremis 0.57149168 0.35068072
## Paracalanus aculeatus 0.04855619 -0.19418187
## Paracalanus pavus 0.01980830 0.11807627
## Paracalanus serrulus -0.16874770 0.27368964
## Parvocalanus crassirostris -0.26138509 -0.39143436
## Scolecithricella longispinosa -0.33387387 -0.06778868
## Temora stylifera 0.53341979 0.18403677
## Temora turbinata -0.05827843 -0.28069200
## Oithona attenuata -0.25488403 -0.38885493
## Oithona brevicornis -1.04566703 0.42833037
## Oithona fallax -0.02930439 0.15279385
## Oithona plumifera 0.41624592 0.31965388
## Oithona similis 0.09795863 0.07377576
## Euterpina acutifrons -0.65579317 0.42648183
## Corycaeus (Ditrichocorycaeus) affinis -0.12481679 -0.54817782
## Corycaeus (Ditrichocorycaeus) dahli 0.42562770 0.34432411
## Corycaeus (Ditrichocorycaeus) lubbocki -0.78566498 0.58740217
## Corycaeus (Ditrichocorycaeus) subtilis 0.28692436 0.36046277
## Corycaeus (Onychocorycaeus) giesbrechti 0.07242181 0.17513843
## Farranula gibbula 0.55408507 0.17771899
## Corycaeidae copepodid 0.47239632 0.33375290
## Oncaea conifera 0.34045666 0.41723992
## Oncaea media 0.29303594 -0.01065384
## Oncaea mediterranea 0.47719547 -0.03119279
## Oncaea venusta 0.30046428 0.30912930
## attr(,"shrinkage")
## MDS1 MDS2 MDS3 MDS4
## 0.5325255 0.3913007 0.2786114 0.1941436
## attr(,"centre")
## MDS1 MDS2 MDS3 MDS4
## -0.0117619450 0.0068393239 -0.0070081491 0.0006378526#Visulize NMDS result
ordiplot(dom_nmds) 