[R-sig-eco] calculating functional diversity
Olmo
ulmusnigra at yahoo.es
Wed Oct 17 21:07:30 CEST 2012
Hi Joanna,
You can try with FD package: http://cran.r-project.org/web/packages/FD/
Or the vegan approach:
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/treedive.html
Bye and hope this helps.
El Wed, 17 Oct 2012 16:28:20 +0200
"Joanna Filip" <joanna.filip at igb-berlin.de> escribió:
> 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
>
--
Olmo Hernández Cuba
Instituto Universitario de Investigación CIBIO
Universidad de Alicante
Campus Universitario San Vicente del Raspeig
03690 Alicante
España
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