[R-sig-eco] calculating functional diversity
Joanna Filip
joanna.filip at igb-berlin.de
Wed Oct 17 16:28:20 CEST 2012
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)
> str(fg)
'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
> fgPCoA
$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 µm) 3.0906988 -3.19885281
Aulacoseira granulata (5 µm) 3.0906988 -3.19885281
Aulacoseira granulata (8 µm) 3.0906988 -3.19885281
Aulacoseira granulata (10 µm) 3.0906988 -3.19885281
Aulacoseira granulata (12 µm) 3.0906988 -3.19885281
Aulacoseira granulata (15 µm) 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 µm) 1.3342074 2.17047335
Peridinium (20 µm) 1.7991581 2.79966200
Peridinium (2530 µm) 1.4271976 2.29631110
Peridinium (3040 µm) 1.4271976 2.29631110
Peridinium (4050 µm) 1.4194864 2.24809839
Peridinium (5060 µm) 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 µm) 1.1651861 1.44957919
Gymnodinium spp. (2030 µm) 1.0907417 0.84923851
Cryptomonas spec. (10 µm) -4.1150888 1.10857495
Cryptomonas ovata (1315 µm) -4.2825233 0.38239656
Cryptomonas spec. (15 µm) -4.1150888 1.10857495
Cryptomonas spec. (20 µm) -4.2825233 0.38239656
Cryptomonas spec. (25 µm) -4.0220986 1.23441269
Cryptomonas spec. (30 µm) -4.0220986 1.23441269
Cryptomonas spec. (35 µm) -4.0220986 1.23441269
Cryptomonas spec. (40 µm) -4.0220986 1.23441269
Cryptomonas spec. (45 µm) -3.9291085 1.36025041
Cryptomonas spec. (50 µm) -3.9291085 1.36025041
Cryptomonas spec. (55 µm) -3.9291085 1.36025041
Cryptomonas spec. (60 µm) -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 µm) -4.4751663 3.81860069
Chlamydomonas spec. (10 µm) -4.4751663 3.81860069
Chlamydomonas spec. (15 µm) -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
_________________________________________________________________
Dr. Joanna Filip
Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Müggelseedamm 310
12587 Berlin
Germany
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