library (vegan)
## Carregando pacotes exigidos: permute
## Carregando pacotes exigidos: lattice
## This is vegan 2.6-4
library(BiodiversityR)
## Carregando pacotes exigidos: tcltk
## BiodiversityR 2.15-1: Use command BiodiversityRGUI() to launch the Graphical User Interface;
## to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)
data (BCI)
dim(BCI) # Foram plotas 50 linhas com 225colunas. que representa respectivamente 1h e as éspecies de arvorés
## [1] 50 225
specnumber(BCI) # foi usado o pacote "vegan"
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 93 84 90 94 101 85 82 88 90 94 87 84 93 98 93 93 93 89 109 100
## 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
## 99 91 99 95 105 91 99 85 86 97 77 88 86 92 83 92 88 82 84 80
## 41 42 43 44 45 46 47 48 49 50
## 102 87 86 81 81 86 102 91 91 93
rowSums(BCI)
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 448 435 463 508 505 412 416 431 409 483 401 366 409 438 462 437 381 347 433 429
## 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
## 408 418 340 392 442 407 417 387 364 475 421 459 436 447 601 430 435 447 424 489
## 41 42 43 44 45 46 47 48 49 50
## 402 414 407 409 444 430 425 415 427 432
(colSums(BCI)) # é visto a tabela inteira das éspecies
## Abarema.macradenia Vachellia.melanoceras
## 1 3
## Acalypha.diversifolia Acalypha.macrostachya
## 2 1
## Adelia.triloba Aegiphila.panamensis
## 92 23
## Alchornea.costaricensis Alchornea.latifolia
## 156 1
## Alibertia.edulis Allophylus.psilospermus
## 1 27
## Alseis.blackiana Amaioua.corymbosa
## 983 3
## Anacardium.excelsum Andira.inermis
## 22 28
## Annona.spraguei Apeiba.glabra
## 27 236
## Apeiba.tibourbou Aspidosperma.desmanthum
## 21 52
## Astrocaryum.standleyanum Astronium.graveolens
## 201 39
## Attalea.butyracea Banara.guianensis
## 33 1
## Beilschmiedia.pendula Brosimum.alicastrum
## 294 188
## Brosimum.guianense Calophyllum.longifolium
## 1 55
## Casearia.aculeata Casearia.arborea
## 23 100
## Casearia.commersoniana Casearia.guianensis
## 3 2
## Casearia.sylvestris Cassipourea.guianensis
## 54 87
## Cavanillesia.platanifolia Cecropia.insignis
## 19 264
## Cecropia.obtusifolia Cedrela.odorata
## 25 2
## Ceiba.pentandra Celtis.schippii
## 39 38
## Cespedesia.spathulata Chamguava.schippii
## 2 3
## Chimarrhis.parviflora Maclura.tinctoria
## 1 1
## Chrysochlamys.eclipes Chrysophyllum.argenteum
## 2 85
## Chrysophyllum.cainito Coccoloba.coronata
## 25 22
## Coccoloba.manzinellensis Colubrina.glandulosa
## 13 1
## Cordia.alliodora Cordia.bicolor
## 63 325
## Cordia.lasiocalyx Coussarea.curvigemma
## 364 55
## Croton.billbergianus Cupania.cinerea
## 98 1
## Cupania.latifolia Cupania.rufescens
## 12 4
## Cupania.seemannii Dendropanax.arboreus
## 47 88
## Desmopsis.panamensis Diospyros.artanthifolia
## 13 16
## Dipteryx.oleifera Drypetes.standleyi
## 33 285
## Elaeis.oleifera Enterolobium.schomburgkii
## 21 2
## Erythrina.costaricensis Erythroxylum.macrophyllum
## 26 18
## Eugenia.florida Eugenia.galalonensis
## 81 12
## Eugenia.nesiotica Eugenia.oerstediana
## 55 177
## Faramea.occidentalis Ficus.colubrinae
## 1717 1
## Ficus.costaricana Ficus.insipida
## 7 3
## Ficus.maxima Ficus.obtusifolia
## 4 7
## Ficus.popenoei Ficus.tonduzii
## 3 23
## Ficus.trigonata Ficus.yoponensis
## 5 6
## Garcinia.intermedia Garcinia.madruno
## 92 12
## Genipa.americana Guapira.myrtiflora
## 23 99
## Guarea.fuzzy Guarea.grandifolia
## 68 10
## Guarea.guidonia Guatteria.dumetorum
## 376 244
## Guazuma.ulmifolia Guettarda.foliacea
## 38 85
## Gustavia.superba Hampea.appendiculata
## 644 13
## Hasseltia.floribunda Heisteria.acuminata
## 229 7
## Heisteria.concinna Hirtella.americana
## 288 5
## Hirtella.triandra Hura.crepitans
## 681 101
## Hieronyma.alchorneoides Inga.acuminata
## 41 26
## Inga.cocleensis Inga.goldmanii
## 52 49
## Inga.laurina Inga.semialata
## 10 98
## Inga.nobilis Inga.oerstediana
## 67 2
## Inga.pezizifera Inga.punctata
## 20 10
## Inga.ruiziana Inga.sapindoides
## 5 76
## Inga.spectabilis Inga.umbellifera
## 14 14
## Jacaranda.copaia Lacistema.aggregatum
## 236 33
## Lacmellea.panamensis Laetia.procera
## 51 12
## Laetia.thamnia Lafoensia.punicifolia
## 27 5
## Licania.hypoleuca Licania.platypus
## 14 10
## Lindackeria.laurina Lonchocarpus.heptaphyllus
## 64 121
## Luehea.seemannii Macrocnemum.roseum
## 93 25
## Maquira.guianensis.costaricana Margaritaria.nobilis
## 167 2
## Marila.laxiflora Maytenus.schippii
## 10 21
## Miconia.affinis Miconia.argentea
## 8 70
## Miconia.elata Miconia.hondurensis
## 1 7
## Mosannona.garwoodii Myrcia.gatunensis
## 15 5
## Myrospermum.frutescens Nectandra.cissiflora
## 7 33
## Nectandra.lineata Nectandra.purpurea
## 10 4
## Ochroma.pyramidale Ocotea.cernua
## 5 29
## Ocotea.oblonga Ocotea.puberula
## 36 22
## Ocotea.whitei Oenocarpus.mapora
## 184 788
## Ormosia.amazonica Ormosia.coccinea
## 1 5
## Ormosia.macrocalyx Pachira.quinata
## 3 1
## Pachira.sessilis Perebea.xanthochyma
## 9 21
## Cinnamomum.triplinerve Picramnia.latifolia
## 16 45
## Piper.reticulatum Platymiscium.pinnatum
## 9 61
## Platypodium.elegans Posoqueria.latifolia
## 43 15
## Poulsenia.armata Pourouma.bicolor
## 755 13
## Pouteria.fossicola Pouteria.reticulata
## 2 203
## Pouteria.stipitata Prioria.copaifera
## 31 345
## Protium.costaricense Protium.panamense
## 111 50
## Protium.tenuifolium Pseudobombax.septenatum
## 381 8
## Psidium.friedrichsthalianum Psychotria.grandis
## 4 2
## Pterocarpus.rohrii Quararibea.asterolepis
## 80 724
## Quassia.amara Randia.armata
## 4 248
## Sapium.broadleaf Sapium.glandulosum
## 3 17
## Schizolobium.parahyba Senna.dariensis
## 2 1
## Simarouba.amara Siparuna.guianensis
## 289 13
## Siparuna.pauciflora Sloanea.terniflora
## 16 78
## Socratea.exorrhiza Solanum.hayesii
## 346 12
## Sorocea.affinis Spachea.membranacea
## 28 8
## Spondias.mombin Spondias.radlkoferi
## 29 63
## Sterculia.apetala Swartzia.simplex.var.grandiflora
## 26 218
## Swartzia.simplex.continentalis Symphonia.globulifera
## 118 26
## Handroanthus.guayacan Tabebuia.rosea
## 30 68
## Tabernaemontana.arborea Tachigali.versicolor
## 322 98
## Talisia.nervosa Talisia.princeps
## 1 3
## Terminalia.amazonia Terminalia.oblonga
## 28 43
## Tetragastris.panamensis Tetrathylacium.johansenii
## 379 7
## Theobroma.cacao Thevetia.ahouai
## 12 2
## Tocoyena.pittieri Trattinnickia.aspera
## 5 40
## Trema.micrantha Trichanthera.gigantea
## 15 2
## Trichilia.pallida Trichilia.tuberculata
## 82 1681
## Trichospermum.galeottii Triplaris.cumingiana
## 1 147
## Trophis.caucana Trophis.racemosa
## 33 32
## Turpinia.occidentalis Unonopsis.pittieri
## 58 163
## Virola.multiflora Virola.sebifera
## 25 617
## Virola.surinamensis Vismia.baccifera
## 164 1
## Vochysia.ferruginea Xylopia.macrantha
## 12 143
## Zanthoxylum.ekmanii Zanthoxylum.juniperinum
## 149 45
## Zanthoxylum.panamense Zanthoxylum.setulosum
## 67 1
## Zuelania.guidonia
## 10
sp1<-specaccum(BCI, "random")
sp1
## Species Accumulation Curve
## Accumulation method: random, with 100 permutations
## Call: specaccum(comm = BCI, method = "random")
##
##
## Sites 1.00000 2.00000 3.0000 4.00000 5.00000 6.00000 7.00000
## Richness 91.08000 121.13000 139.7100 151.32000 159.61000 165.86000 171.23000
## sd 7.30806 7.09767 6.5417 6.49146 5.98296 5.22237 5.26443
##
## Sites 8.00000 9.0000 10.00000 11.00000 12.00000 13.00000 14.00000
## Richness 175.71000 179.2700 182.75000 185.50000 188.31000 190.34000 192.16000
## sd 5.06382 5.1323 4.91622 4.69795 4.66167 4.54877 4.58086
##
## Sites 15.00000 16.00000 17.00000 18.00000 19.00000 20.00000 21.00000
## Richness 194.27000 196.10000 198.01000 199.69000 201.18000 202.41000 203.80000
## sd 4.40352 4.46875 4.52935 4.42147 4.12526 4.16356 4.26401
##
## Sites 22.00000 23.00000 24.00000 25.0000 26.00000 27.0000 28.00000
## Richness 205.12000 206.32000 207.43000 208.6600 209.69000 210.4300 211.35000
## sd 4.02085 4.27792 4.00064 3.9086 3.84733 3.7234 3.41232
##
## Sites 29.00000 30.00000 31.00000 32.00000 33.00000 34.00000 35.00000
## Richness 212.20000 213.15000 213.90000 214.76000 215.45000 216.12000 216.84000
## sd 3.14627 2.99284 3.02348 2.84665 2.77206 2.64491 2.61588
##
## Sites 36.00000 37.00000 38.00000 39.00000 40.00000 41.00000 42.00000
## Richness 217.46000 218.22000 218.82000 219.49000 220.27000 220.95000 221.56000
## sd 2.40547 2.47239 2.31106 2.29402 2.13605 2.12429 1.92967
##
## Sites 43.00000 44.0000 45.00000 46.00000 47.0000 48.00000 49.00000
## Richness 222.02000 222.6800 223.13000 223.57000 223.9600 224.36000 224.71000
## sd 1.79213 1.6629 1.49514 1.32005 1.1885 0.91585 0.53739
##
## Sites 50
## Richness 225
## sd 0
plot(sp1, ci.type="poly", col="green", lwd=2, ci.lty=0, ci.col="lightblue")
boxplot(sp1, col="yellow", add=TRUE, pch="+")
mod <- rad.lognormal(BCI[5,])
mod
##
## RAD model: Log-Normal
## Family: poisson
## No. of species: 101
## Total abundance: 505
##
## log.mu log.sigma Deviance AIC BIC
## 0.951926 1.165929 17.077549 317.656487 322.886728
plot(mod)
mod2 <- radfit(BCI[1,])
mod2
##
## RAD models, family poisson
## No. of species 93, total abundance 448
##
## par1 par2 par3 Deviance AIC BIC
## Null 39.5261 315.4362 315.4362
## Preemption 0.042797 21.8939 299.8041 302.3367
## Lognormal 1.0687 1.0186 25.1528 305.0629 310.1281
## Zipf 0.11033 -0.74705 61.0465 340.9567 346.0219
## Mandelbrot 100.52 -2.312 24.084 4.2271 286.1372 293.7350
plot(mod2)
data(dune)
data("dune.env")
bio<-rankabuncomp(dune, dune.env, factor='Management', return.data=TRUE, specnames=c(1:2), legend=FALSE)
bio
## Grouping species labelit rank abundance proportion plower pupper accumfreq
## 1 BF Lolipere TRUE 1 18 15.4 3.6 27.2 15.4
## 2 BF Trifrepe TRUE 2 14 12.0 6.6 17.3 27.4
## 3 BF Scorautu FALSE 3 13 11.1 0.7 21.5 38.5
## 4 BF Poaprat FALSE 4 12 10.3 6.3 14.2 48.7
## 5 BF Poatriv FALSE 5 11 9.4 -9.9 28.7 58.1
## 6 BF Bromhord FALSE 6 8 6.8 -5.2 18.9 65.0
## 7 BF Achimill FALSE 7 7 6.0 -5.0 17.0 70.9
## 8 BF Planlanc FALSE 8 6 5.1 -6.9 17.1 76.1
## 9 BF Bracruta FALSE 9 6 5.1 -9.3 19.5 81.2
## 10 BF Bellpere FALSE 10 5 4.3 -4.0 12.5 85.5
## 11 BF Anthodor FALSE 11 4 3.4 -10.6 17.4 88.9
## 12 BF Elymrepe FALSE 12 4 3.4 -10.8 17.6 92.3
## 13 BF Vicilath FALSE 13 3 2.6 -4.6 9.8 94.9
## 14 BF Alopgeni FALSE 14 2 1.7 -5.4 8.8 96.6
## 15 BF Hyporadi FALSE 15 2 1.7 -6.3 9.7 98.3
## 16 BF Sagiproc FALSE 16 2 1.7 -6.3 9.7 100.0
## 17 HF Poatriv TRUE 1 24 11.3 8.4 14.1 11.3
## 18 HF Lolipere TRUE 2 20 9.4 3.7 15.1 20.7
## 19 HF Poaprat FALSE 3 17 8.0 4.9 11.1 28.6
## 20 HF Rumeacet FALSE 4 16 7.5 1.1 13.9 36.2
## 21 HF Planlanc FALSE 5 15 7.0 -0.7 14.7 43.2
## 22 HF Scorautu FALSE 6 14 6.6 5.2 8.0 49.8
## 23 HF Trifrepe FALSE 7 14 6.6 3.3 9.8 56.3
## 24 HF Bracruta FALSE 8 14 6.6 1.9 11.2 62.9
## 25 HF Elymrepe FALSE 9 10 4.7 -3.6 13.0 67.6
## 26 HF Anthodor FALSE 10 9 4.2 -0.8 9.2 71.8
## 27 HF Trifprat FALSE 11 9 4.2 -1.4 9.9 76.1
## 28 HF Alopgeni FALSE 12 8 3.8 -3.1 10.6 79.8
## 29 HF Juncarti FALSE 13 8 3.8 -2.8 10.3 83.6
## 30 HF Agrostol FALSE 14 7 3.3 -2.6 9.1 86.9
## 31 HF Achimill FALSE 15 6 2.8 -0.3 5.9 89.7
## 32 HF Juncbufo FALSE 16 6 2.8 -2.5 8.1 92.5
## 33 HF Eleopalu FALSE 17 4 1.9 -3.4 7.2 94.4
## 34 HF Sagiproc FALSE 18 4 1.9 -1.4 5.2 96.2
## 35 HF Bromhord FALSE 19 4 1.9 -1.4 5.1 98.1
## 36 HF Bellpere FALSE 20 2 0.9 -1.7 3.5 99.1
## 37 HF Ranuflam FALSE 21 2 0.9 -1.7 3.6 100.0
## 38 NM Scorautu TRUE 1 19 12.6 6.0 19.2 12.6
## 39 NM Bracruta TRUE 2 17 11.3 2.6 19.9 23.8
## 40 NM Agrostol FALSE 3 13 8.6 -1.2 18.4 32.5
## 41 NM Eleopalu FALSE 4 13 8.6 -1.4 18.6 41.1
## 42 NM Salirepe FALSE 5 11 7.3 -0.2 14.8 48.3
## 43 NM Trifrepe FALSE 6 11 7.3 -2.0 16.6 55.6
## 44 NM Anthodor FALSE 7 8 5.3 -3.8 14.4 60.9
## 45 NM Ranuflam FALSE 8 8 5.3 -1.2 11.8 66.2
## 46 NM Hyporadi FALSE 9 7 4.6 -3.8 13.1 70.9
## 47 NM Juncarti FALSE 10 7 4.6 -2.7 12.0 75.5
## 48 NM Callcusp FALSE 11 7 4.6 -2.8 12.1 80.1
## 49 NM Airaprae FALSE 12 5 3.3 -2.4 9.0 83.4
## 50 NM Planlanc FALSE 13 5 3.3 -2.6 9.2 86.8
## 51 NM Poaprat FALSE 14 4 2.6 -2.5 7.8 89.4
## 52 NM Comapalu FALSE 15 4 2.6 -1.8 7.1 92.1
## 53 NM Sagiproc FALSE 16 3 2.0 -2.9 6.9 94.0
## 54 NM Achimill FALSE 17 2 1.3 -2.4 5.0 95.4
## 55 NM Bellpere FALSE 18 2 1.3 -2.0 4.7 96.7
## 56 NM Empenigr FALSE 19 2 1.3 -1.9 4.6 98.0
## 57 NM Lolipere FALSE 20 2 1.3 -2.0 4.7 99.3
## 58 NM Vicilath FALSE 21 1 0.7 -1.0 2.3 100.0
## 59 SF Agrostol TRUE 1 28 13.7 7.8 19.7 13.7
## 60 SF Poatriv TRUE 2 28 13.7 6.3 21.1 27.5
## 61 SF Alopgeni FALSE 3 26 12.7 4.5 21.0 40.2
## 62 SF Lolipere FALSE 4 18 8.8 -2.1 19.8 49.0
## 63 SF Poaprat FALSE 5 15 7.4 0.5 14.2 56.4
## 64 SF Elymrepe FALSE 6 12 5.9 -1.0 12.8 62.3
## 65 SF Bracruta FALSE 7 12 5.9 0.8 10.9 68.1
## 66 SF Sagiproc FALSE 8 11 5.4 -0.8 11.5 73.5
## 67 SF Eleopalu FALSE 9 8 3.9 -6.3 14.1 77.5
## 68 SF Scorautu FALSE 10 8 3.9 1.4 6.4 81.4
## 69 SF Trifrepe FALSE 11 8 3.9 0.5 7.3 85.3
## 70 SF Juncbufo FALSE 12 7 3.4 -2.3 9.2 88.7
## 71 SF Bellpere FALSE 13 4 2.0 -0.9 4.8 90.7
## 72 SF Ranuflam FALSE 14 4 2.0 -1.3 5.2 92.6
## 73 SF Juncarti FALSE 15 3 1.5 -2.4 5.3 94.1
## 74 SF Callcusp FALSE 16 3 1.5 -2.4 5.3 95.6
## 75 SF Bromhord FALSE 17 3 1.5 -2.1 5.0 97.1
## 76 SF Rumeacet FALSE 18 2 1.0 -1.5 3.5 98.0
## 77 SF Cirsarve FALSE 19 2 1.0 -1.4 3.3 99.0
## 78 SF Achimill FALSE 20 1 0.5 -0.9 1.9 99.5
## 79 SF Chenalbu FALSE 21 1 0.5 -0.8 1.8 100.0
## logabun rankfreq
## 1 1.3 6.2
## 2 1.1 12.5
## 3 1.1 18.8
## 4 1.1 25.0
## 5 1.0 31.2
## 6 0.9 37.5
## 7 0.8 43.8
## 8 0.8 50.0
## 9 0.8 56.2
## 10 0.7 62.5
## 11 0.6 68.8
## 12 0.6 75.0
## 13 0.5 81.2
## 14 0.3 87.5
## 15 0.3 93.8
## 16 0.3 100.0
## 17 1.4 4.8
## 18 1.3 9.5
## 19 1.2 14.3
## 20 1.2 19.0
## 21 1.2 23.8
## 22 1.1 28.6
## 23 1.1 33.3
## 24 1.1 38.1
## 25 1.0 42.9
## 26 1.0 47.6
## 27 1.0 52.4
## 28 0.9 57.1
## 29 0.9 61.9
## 30 0.8 66.7
## 31 0.8 71.4
## 32 0.8 76.2
## 33 0.6 81.0
## 34 0.6 85.7
## 35 0.6 90.5
## 36 0.3 95.2
## 37 0.3 100.0
## 38 1.3 4.8
## 39 1.2 9.5
## 40 1.1 14.3
## 41 1.1 19.0
## 42 1.0 23.8
## 43 1.0 28.6
## 44 0.9 33.3
## 45 0.9 38.1
## 46 0.8 42.9
## 47 0.8 47.6
## 48 0.8 52.4
## 49 0.7 57.1
## 50 0.7 61.9
## 51 0.6 66.7
## 52 0.6 71.4
## 53 0.5 76.2
## 54 0.3 81.0
## 55 0.3 85.7
## 56 0.3 90.5
## 57 0.3 95.2
## 58 0.0 100.0
## 59 1.4 4.8
## 60 1.4 9.5
## 61 1.4 14.3
## 62 1.3 19.0
## 63 1.2 23.8
## 64 1.1 28.6
## 65 1.1 33.3
## 66 1.0 38.1
## 67 0.9 42.9
## 68 0.9 47.6
## 69 0.9 52.4
## 70 0.8 57.1
## 71 0.6 61.9
## 72 0.6 66.7
## 73 0.5 71.4
## 74 0.5 76.2
## 75 0.5 81.0
## 76 0.3 85.7
## 77 0.3 90.5
## 78 0.0 95.2
## 79 0.0 100.0
library(ggplot2)
library(ggrepel)
plotgg1 <- ggplot(data=bio, aes(x = rank, y = abundance)) +
scale_x_continuous(expand=c(0, 1), sec.axis = dup_axis(labels=NULL, name=NULL)) +
scale_y_continuous(expand=c(0, 1), sec.axis = dup_axis(labels=NULL, name=NULL)) +
geom_line(aes(colour=Grouping), size=1) +
geom_point(aes(colour=Grouping, shape=Grouping), size=5, alpha=0.7) +
geom_text_repel(data=subset(bio, labelit == TRUE),
aes(colour=Grouping, label=species),
angle=45, nudge_x=1, nudge_y=1, show.legend=FALSE) +
scale_color_brewer(palette = "Set1") +
labs(x = "rank", y = "abundance", colour = "Management", shape = "Management")
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
plotgg1
## Warning: ggrepel: Repulsion works correctly only for rotation angles multiple of
## 90 degrees
RA.data <- rankabuncomp(dune, y=dune.env, factor='Management',
return.data=TRUE, specnames=c(1:10), legend=FALSE)
plotgg2 <- ggplot(data=RA.data, aes(x = rank, y = abundance)) +
scale_x_continuous(expand=c(0, 1), sec.axis = dup_axis(labels=NULL, name=NULL)) +
scale_y_continuous(expand=c(0, 1), sec.axis = dup_axis(labels=NULL, name=NULL)) +
geom_line(aes(colour=Grouping), size=1) +
geom_point(aes(colour=Grouping), size=5, alpha=0.7) +
geom_text_repel(data=subset(RA.data, labelit == TRUE),
aes(label=species),
angle=45, nudge_x=1, nudge_y=1, show.legend=FALSE) +
scale_color_brewer(palette = "Set1") +
facet_wrap(~ Grouping) +
labs(x = "rank", y = "abundance", colour = "Management")
plotgg2
## Warning: ggrepel: Repulsion works correctly only for rotation angles multiple of 90 degrees
## ggrepel: Repulsion works correctly only for rotation angles multiple of 90 degrees
## ggrepel: Repulsion works correctly only for rotation angles multiple of 90 degrees
## ggrepel: Repulsion works correctly only for rotation angles multiple of 90 degrees
