Dear all,
I want to assign phytoplankton species to different functional groups
based on the similarity of their traits. According to Weithoff (2003,
Freshw.Biol) a principal coordination analysis(PCoA) is the most
suitable technique to calculate functional groups, since those where
mainly binary coded. What I did then was using cmdscale after
calculating the Euclidean Distance.
fg<-read.csv2("functional.groups.csv",header=T,row.names=1)
'data.frame': 169 obs. of 16 variables:
$ size.class : num 1 1 1 1 1 1 1 1 1 1 ...
$ cell.shape : num 7 7 7 7 7 7 7 7 7 7 ...
$ organization : num 1 1 1 1 1 1 1 1 1 1 ...
$ cell.protection : num 0 0 0 0 0 0 0 0 0 0 ...
$ nitrogen.fixation: num 1 1 1 1 0 0 0 0.5 0.5 0.5 ...
$ silica.demand : num 0 0 0 0 0 0 0 0 0 0 ...
$ nutritional.mode : num 0 0 0 0 0 0 0 0 0 0 ...
$ motility : num 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0 0.5 0.5 ...
$ edibility : num 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 ...
$ resting.stages : num 1 1 1 1 0 0 0 0 0 0 ...
$ reproduction : num 0 0 0 0 0 0 0 0 0 0 ...
$ pigments : num 1 1 1 1 1 1 1 1 1 1 ...
$ chl : num 0 0 0 0 0 0 0 0 0 0 ...
$ tox : num 1 1 1 1 0 0 0 1 1 1 ...
$ trichome : num 1 1 1 1 1 1 1 1 1 1 ...
$ pyr : num 0 0 0 0 0 0 0 0 0 0 ...
fgdist<-dist(fg, method = "eucl")
fgPCoA<-cmdscale (fgdist,k=2, eig=T, add=T)
summary(fgPCoA)
Length Class Mode
points 338 -none- numeric
eig 169 -none- numeric
x 0 -none- NULL
ac 1 -none- numeric
GOF 2 -none- numeric
$points
[,1]
[,2] Aphanizomenon spec. 2.2851600
-6.31635652 Aphanizomenon flosaquae
2.2851600 -6.31635652 Aphanizomenon
issatschenkoi 2.2851600 -6.31635652
Aphanizomenon gracile 2.2851600
-6.31635652 Limnothrix redekei
2.2995711 -6.19662677 Limnothrix
planctonica 2.2995711 -6.19662677
Limnothrix spec. 2.2995711
-6.19662677 Planktolyngbya spec.
2.2966344 -6.26669801 Pseudanabaena
mucicola 2.2870117 -6.26602878
Pseudanabaena spec. 2.2870117
-6.26602878 Planktothrix agardhii
2.2918600 -6.24483947 Anabaena
flosaquae -6.4111960 -4.08280414
Anabaena circinalis -6.4111960
-4.08280414 Anabaena compacta
-6.4034848 -4.03459144 Anabaena
crassa -6.4111960 -4.08280414
Anabaena lemmermannii -6.4111960
-4.08280414 Anabaena smithii
-6.4034848 -4.03459144 Anabaena
solitaria -6.4034848 -4.03459144
Anabaena spiroides -6.4034848
-4.03459144 Anabaena spec.
-6.4034848 -4.03459144 Anabaenopsis
elenkinii 2.2851600 -6.31635652
Microcystis aeruginosa -6.3824790
-3.96358158 Microcystis novacekii
-6.3824790 -3.96358158 Microcystis
viridis -6.3824790 -3.96358158
Microcystis wesenbergii -6.3824790
-3.96358158 Microcystis spec.
-6.3824790 -3.96358158 Chroococcus limneticus
(Kol.) -6.3681419 -3.88689965 Woronichinia
naegeliana -6.3777646 -3.88623041
Aulacoseira granulata (3 ?m) 3.0906988
-3.19885281 Aulacoseira granulata (5 ?m)
3.0906988 -3.19885281 Aulacoseira granulata (8
?m) 3.0906988 -3.19885281 Aulacoseira
granulata (10 ?m) 3.0906988 -3.19885281
Aulacoseira granulata (12 ?m) 3.0906988
-3.19885281 Aulacoseira granulata (15 ?m)
3.0906988 -3.19885281 Aulacoseira granulata var. angustissima f.
spiralis 3.0906988 -3.19885281 Aulacoseira
ambigua 3.3002089 -2.52734333
Melosira varians 3.3792753
-2.42890560 Skeletonema spec.
1.1442515 -2.72990782 Asterionella
formosa 6.2611582 -3.42020772
Fragilaria ulna var. acus -1.2773374
-1.36239412 Fragilaria ulna angustissima Sippen
-1.3703275 -1.48823186 Fragilaria
spec. -1.2773374 -1.36239412
Fragilaria ulna -1.2773374
-1.36239412 Diatoma tenuis
-1.2538693 -0.92062577 Diatoma
vulgaris -1.3468595 -1.04646350
Fragilaria crotonensis -1.3946955
-1.51971574 Fragilaria capucina
-1.3946955 -1.51971574 Nitzschia
acicularis -3.2977136 -0.95501912
Nitzschia fruticosa -3.5766841
-1.33253232 Nitzschia fonticola
-3.6696742 -1.45837005 Nitzschia
spec. -3.4836940 -1.20669459
Tabellaria spec. 7.5111705
-3.08175857 Dinobryon divergens
-4.9180730 -2.71413364 Dinobryon
spec. -4.9180730 -2.71413364
Dinobryon sociale -4.9180730
-2.71413364 Synura uvella
-3.5064068 3.22048514 Synura
spec. -3.5064068 3.22048514
Uroglena spec. 4.5130348
-5.62769660 Chrysococcus spp.
-5.0972055 -2.97809447 Chrysochromulina
parva -4.3484434 4.23073661
Chrysoflagellaten spp. -6.0924187
-2.72698317 Pseudokephyrion spec.
-0.1623710 -4.05015856 Kephyrion
spec. -5.0866701 -2.93513385
Mallomonas spec. -3.3960334
3.37699809 Tribonema angustissima
2.9469931 -3.97580168 Ceratium
hirundinella 0.8468201 3.07523447
Ceratium rhomvoides 0.8468201
3.07523447 Ceratium furcoides
0.8328964 3.04783447 Peridinium
aciculiferum 1.5124766 2.37393612
Peridinium spec. 1.5201877
2.42214883 Peridinium (15 ?m)
1.3342074 2.17047335 Peridinium (20
?m) 1.7991581 2.79966200
Peridinium (2530 ?m) 1.4271976
2.29631110 Peridinium (3040 ?m)
1.4271976 2.29631110 Peridinium (4050
?m) 1.4194864 2.24809839 Peridinium
(5060 ?m) 1.5201877 2.42214883
Kolkwitziella acuta 40/30 9.6402670
-1.66539938 Kolkwitziella acuta 50/40
9.7332571 -1.53956164 Gymnodinium
spec. 0.9233072 0.12306010
Gymnodinium helveticum 0.7020322
-0.75836620 Gymnodinium spp. (1020 ?m)
1.1651861 1.44957919 Gymnodinium spp. (2030
?m) 1.0907417 0.84923851 Cryptomonas spec.
(10 ?m) -4.1150888 1.10857495 Cryptomonas
ovata (1315 ?m) -4.2825233 0.38239656
Cryptomonas spec. (15 ?m) -4.1150888
1.10857495 Cryptomonas spec. (20 ?m)
-4.2825233 0.38239656 Cryptomonas spec. (25
?m) -4.0220986 1.23441269 Cryptomonas
spec. (30 ?m) -4.0220986 1.23441269
Cryptomonas spec. (35 ?m) -4.0220986
1.23441269 Cryptomonas spec. (40 ?m)
-4.0220986 1.23441269 Cryptomonas spec. (45
?m) -3.9291085 1.36025041 Cryptomonas
spec. (50 ?m) -3.9291085 1.36025041
Cryptomonas spec. (55 ?m) -3.9291085
1.36025041 Cryptomonas spec. (60 ?m)
-3.9291085 1.36025041 Rhodomonas minuta
lacustris 5.2425899 -2.60644072 Rhodomonas
lens 5.2425899 -2.60644072
Chroomonas spec. 5.2410031
-2.60115649 Actinastrum hantzschii
3.7213776 3.42576902 Ankyra
judayi 9.9886054 -0.75157632
Ankyra lanceolata 10.1745856
-0.49990084 Ankyra spec.
10.1745856 -0.49990084 Carteria
spec. -4.4751663 3.81860069
Chlamydomonas spec. (5 ?m) -4.4751663
3.81860069 Chlamydomonas spec. (10 ?m)
-4.4751663 3.81860069 Chlamydomonas spec. (15
?m) -4.4751663 3.81860069 Coenochloris
polycocca -4.7344374 2.72564927
Crucigeniella spec. 5.5609110
2.80358630 Crucigeniella apiculata
5.5609110 2.80358630 Dactylosphaerium
spp. -4.7273908 2.70452346 Coelastrum
astroideum -4.7395748 2.68878152
Coelastrum microporum -4.7395748
2.68878152 Dictyosphaerium spp.
-4.0947220 5.28611979 Didymocystis
spec. 1.6191314 3.43399571
Elakatothrix spec. 1.2399025
1.70360676 Gonatozygon kinahanii
5.9681452 7.30952552 Gonium
pectorale -3.7774396 2.45048546
Lagerheimia genevensis 1.7166956
3.84237395 Lagerheimia wratislawiensis
1.7166956 3.84237395 Koliella
spec. -3.7675401 5.71612141
Kirchneriella spp. 9.9985188
0.05465312 Monoraphidium contortum
9.7909895 -1.26871187 Monoraphidium
arcuatum 9.8839796 -1.14287413
Monoraphidium spec. 9.7909895
-1.26871187 Oocystis spp.
-3.0620296 5.17768146 Pandorina
morum -3.7820231 2.48490814
Pediastrum boryanum -0.8424821
1.70114825 Pediastrum biradiatum
-0.8424821 1.70114825 Pediastrum
duplex -0.7494919 1.82698598
Pediastrum simplex -0.7494919
1.82698598 Phacotus lenticularis
0.9835536 0.84551912 Planctonema
lauterbornii 4.5043122 2.65845760
Planktosphaeria gelatinosa -4.7244559
2.69731944 Pteromonas spec.
1.0782373 1.24110680 Raphidocelis
spp. 9.6758338 -1.38196171
Scenedesmus abundans -3.7593894
2.46800908 Scenedesmus acutus
-3.7593894 2.46800908 Scenedesmus
acuminatus -3.7593894 2.46800908
Scenedesmus armatus -3.7593894
2.46800908 Scenedesmus denticulatus
-3.6663992 2.59384680 Scenedesmus
falcatus -3.6663992 2.59384680
Scenedesmus intermedius -3.7593894
2.46800908 Scenedesmus linearis
-3.7593894 2.46800908 Scenedesmus
maximus -3.6663992 2.59384680
Scenedesmus opoliensis -3.6663992
2.59384680 Scenedesmus quadricauda
-3.6663992 2.59384680 Scenedesmus
serratus -3.7593894 2.46800908
Scenedesmus subspicatus -3.7593894
2.46800908 Scenedesmus spp.
-3.7593894 2.46800908 Schroederia
spec. 10.2675757 -0.37406310
Pseudoschroederia antillarum 9.8026251
-1.00325179 Pseudoschroederia robusta
9.8026251 -1.00325179 Siderocelis
ornata -3.7348920 2.44394972
Tetrastrum staurogeniaeforme -4.7430343
2.68550625 Tetrastrum spec.
-4.7186663 2.71699014 Tetrastrum
glabrum -4.7186663 2.71699014
Tetraedron caudatum 7.8504974
-0.47790781 Tetraedron spec.
7.8504974 -0.47790781 Tetraselmis
cordiformis -4.7384403 2.69165678 Volvox
spec. -4.7397133 2.72860498
Closterium limneticum 11.5825720
5.08103705 Closterium aciculare
11.6873270 5.41679170 Closterium acutum var.
variabile 11.3965917 4.82936159 Closterium
spec. 11.6349495 5.24891438
Mougeotia spec. 5.7579955
6.54006589 Staurastrum gracile
9.9343773 3.43165755 Staurastrum
spec. 9.9343773 3.43165755
Colacium spec. 1.4977078
2.79515454 Euglena spp.
-1.0185197 4.06404902 Trachelomonas
spp. 1.5098918 2.81089648
$eig
[1] 4.413995e+03 1.828408e+03 8.916502e+02 3.137676e+02
2.580554e+02 5.419609e+01 4.460909e+01
[8] 2.755899e+01 2.526947e+01 1.840100e+01 1.183275e+01
8.566003e+00 8.315184e+00 5.094462e+00
[15] 3.632828e+00 1.362971e+00 8.852134e-05 5.479116e-05
3.086643e-05 2.884336e-05 2.557268e-05
[22] 2.042089e-05 1.944959e-05 1.743079e-05 1.628349e-05
1.485782e-05 1.318177e-05 1.238003e-05
[29] 1.162161e-05 1.112619e-05 1.043634e-05 9.727099e-06
8.749476e-06 8.294379e-06 7.930409e-06
[36] 7.199765e-06 6.909239e-06 6.810420e-06 6.487319e-06
6.024823e-06 5.892755e-06 5.691160e-06
[43] 5.411011e-06 5.212191e-06 4.932932e-06 4.914962e-06
4.789790e-06 4.734317e-06 4.541929e-06
[50] 4.408631e-06 4.388594e-06 4.255247e-06 4.177571e-06
3.898428e-06 3.789852e-06 3.563687e-06
[57] 3.509621e-06 3.408577e-06 3.359202e-06 3.230766e-06
3.201829e-06 3.116792e-06 3.077027e-06
[64] 2.997358e-06 2.974724e-06 2.933465e-06 2.841115e-06
2.704219e-06 2.636667e-06 2.597003e-06
[71] 2.539601e-06 2.445140e-06 2.415113e-06 2.310817e-06
2.219788e-06 2.030041e-06 1.961819e-06
[78] 1.923939e-06 1.904338e-06 1.878695e-06 1.804515e-06
1.731039e-06 1.688142e-06 1.518596e-06
[85] 1.474661e-06 1.471060e-06 1.441984e-06 1.376906e-06
1.349053e-06 1.332413e-06 1.272975e-06
[92] 1.259647e-06 1.035801e-06 1.020958e-06 9.880309e-07
9.536912e-07 9.192215e-07 8.495361e-07
[99] 7.417919e-07 7.297226e-07 1.415812e-12 1.184466e-12
1.125331e-12 1.100901e-12 1.093639e-12
[106] 1.091167e-12 1.073224e-12 1.073089e-12 1.066129e-12
1.065699e-12 1.062614e-12 1.062197e-12
[113] 1.062128e-12 1.061720e-12 1.060507e-12 1.058105e-12
1.057531e-12 1.056834e-12 1.056167e-12
[120] 1.056055e-12 1.055751e-12 1.055655e-12 1.055461e-12
1.055432e-12 1.055237e-12 1.055160e-12
[127] 1.055079e-12 1.055047e-12 1.054878e-12 1.054680e-12
1.054347e-12 1.054320e-12 1.054305e-12
[134] 1.054140e-12 1.054075e-12 1.053989e-12 1.053959e-12
1.053709e-12 1.053598e-12 1.053376e-12
[141] 1.052990e-12 1.052987e-12 1.052957e-12 1.052783e-12
1.052694e-12 1.052648e-12 1.052260e-12
[148] 1.051812e-12 1.051738e-12 1.051657e-12 1.051648e-12
1.051647e-12 1.051612e-12 1.051581e-12
[155] 1.051580e-12 1.051557e-12 1.051426e-12 1.049198e-12
1.048493e-12 1.048301e-12 1.048282e-12
[162] 1.043455e-12 1.031637e-12 1.025863e-12 1.015731e-12
9.931268e-13 9.908391e-13 7.647115e-13
[169] -2.338367e-14
$x
NULL
$ac
[1] 1.451867e-06
$GOF
[1] 0.7887084 0.7887084
plot(fgPCoA$points[,1],
fgPCoA$points[,2],asp=1,xlab="axis1",ylab="axis2") #####I attached
the plot as pdf.file
Since I?m new in this field (especially R, but also this kind of
stats) I was wondering, if this is the right way to go, when creating
functional groups and if so, is my R analysis sufficient to get the
information I need or is there a better way? My first thought was to
run a PCA, but its sensitivity to binominal data convinced me not to
use this technique.
I would be glad to get some feedback on that!
Best,
Joanna