radfitresult: Alternative Rank Abundance Fitting Results

Description Usage Arguments Details Value Author(s) References Examples

Description

Provides alternative methods of obtaining rank abundance curves than provided by functions radfit, fisherfit and prestonfit (vegan), although these same functions are called.

Usage

1
radfitresult(x,y="",factor="",level,plotit=T)

Arguments

x

Community data frame with sites as rows, species as columns and species abundance as cell values.

y

Environmental data frame.

factor

Variable of the environmental data frame that defines subsets to calculate fitted rank-abundance curves for.

level

Level of the variable to create the subset to calculate fitted rank-abundance curves.

plotit

Plot the results obtained by plot.radfit .

Details

These functions provide some alternative methods of obtaining fitted rank-abundance curves, although functions radfit, fisherfit and prestonfit (vegan) are called to calculate the actual results.

Value

The function returns the results from three methods of fitting rank-abundance curves:

radfit

results of radfit.

fisherfit

results of fisherfit.

prestonfit

results of prestonfit.

Optionally, a plot is provided of the radfit results by plot.radfit.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

Examples

1
2
3
4
library(vegan)
data(BCI)
BCIall <- t(as.matrix(colSums(BCI)))
radfitresult(BCIall)

Example output

Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
BiodiversityR 2.11-1: Use command BiodiversityRGUI() to launch the Graphical User Interface; 
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)

Warning message:
no DISPLAY variable so Tk is not available 
$radfit

Deviance for RAD models:

           Abarema.macradenia Vachellia.melanoceras Acalypha.diversifolia
Null                        0                     0                     0
Preemption                  0                     0                     0
Lognormal                   0                     0                     0
Zipf                        0                     0                     0
Mandelbrot                  0                     0                     0
           Acalypha.macrostachya Adelia.triloba Aegiphila.panamensis
Null                           0              0                    0
Preemption                     0              0                    0
Lognormal                      0              0                    0
Zipf                           0              0                    0
Mandelbrot                     0              0                    0
           Alchornea.costaricensis Alchornea.latifolia Alibertia.edulis
Null                             0                   0                0
Preemption                       0                   0                0
Lognormal                        0                   0                0
Zipf                             0                   0                0
Mandelbrot                       0                   0                0
           Allophylus.psilospermus Alseis.blackiana Amaioua.corymbosa
Null                             0                0                 0
Preemption                       0                0                 0
Lognormal                        0                0                 0
Zipf                             0                0                 0
Mandelbrot                       0                0                 0
           Anacardium.excelsum Andira.inermis Annona.spraguei Apeiba.glabra
Null                         0              0               0             0
Preemption                   0              0               0             0
Lognormal                    0              0               0             0
Zipf                         0              0               0             0
Mandelbrot                   0              0               0             0
           Apeiba.tibourbou Aspidosperma.desmanthum Astrocaryum.standleyanum
Null                      0                       0                        0
Preemption                0                       0                        0
Lognormal                 0                       0                        0
Zipf                      0                       0                        0
Mandelbrot                0                       0                        0
           Astronium.graveolens Attalea.butyracea Banara.guianensis
Null                          0                 0                 0
Preemption                    0                 0                 0
Lognormal                     0                 0                 0
Zipf                          0                 0                 0
Mandelbrot                    0                 0                 0
           Beilschmiedia.pendula Brosimum.alicastrum Brosimum.guianense
Null                           0                   0                  0
Preemption                     0                   0                  0
Lognormal                      0                   0                  0
Zipf                           0                   0                  0
Mandelbrot                     0                   0                  0
           Calophyllum.longifolium Casearia.aculeata Casearia.arborea
Null                             0                 0                0
Preemption                       0                 0                0
Lognormal                        0                 0                0
Zipf                             0                 0                0
Mandelbrot                       0                 0                0
           Casearia.commersoniana Casearia.guianensis Casearia.sylvestris
Null                            0                   0                   0
Preemption                      0                   0                   0
Lognormal                       0                   0                   0
Zipf                            0                   0                   0
Mandelbrot                      0                   0                   0
           Cassipourea.guianensis Cavanillesia.platanifolia Cecropia.insignis
Null                            0                         0                 0
Preemption                      0                         0                 0
Lognormal                       0                         0                 0
Zipf                            0                         0                 0
Mandelbrot                      0                         0                 0
           Cecropia.obtusifolia Cedrela.odorata Ceiba.pentandra Celtis.schippii
Null                          0               0               0               0
Preemption                    0               0               0               0
Lognormal                     0               0               0               0
Zipf                          0               0               0               0
Mandelbrot                    0               0               0               0
           Cespedesia.spathulata Chamguava.schippii Chimarrhis.parviflora
Null                           0                  0                     0
Preemption                     0                  0                     0
Lognormal                      0                  0                     0
Zipf                           0                  0                     0
Mandelbrot                     0                  0                     0
           Maclura.tinctoria Chrysochlamys.eclipes Chrysophyllum.argenteum
Null                       0                     0                       0
Preemption                 0                     0                       0
Lognormal                  0                     0                       0
Zipf                       0                     0                       0
Mandelbrot                 0                     0                       0
           Chrysophyllum.cainito Coccoloba.coronata Coccoloba.manzinellensis
Null                           0                  0                        0
Preemption                     0                  0                        0
Lognormal                      0                  0                        0
Zipf                           0                  0                        0
Mandelbrot                     0                  0                        0
           Colubrina.glandulosa Cordia.alliodora Cordia.bicolor
Null                          0                0              0
Preemption                    0                0              0
Lognormal                     0                0              0
Zipf                          0                0              0
Mandelbrot                    0                0              0
           Cordia.lasiocalyx Coussarea.curvigemma Croton.billbergianus
Null                       0                    0                    0
Preemption                 0                    0                    0
Lognormal                  0                    0                    0
Zipf                       0                    0                    0
Mandelbrot                 0                    0                    0
           Cupania.cinerea Cupania.latifolia Cupania.rufescens
Null                     0                 0                 0
Preemption               0                 0                 0
Lognormal                0                 0                 0
Zipf                     0                 0                 0
Mandelbrot               0                 0                 0
           Cupania.seemannii Dendropanax.arboreus Desmopsis.panamensis
Null                       0                    0                    0
Preemption                 0                    0                    0
Lognormal                  0                    0                    0
Zipf                       0                    0                    0
Mandelbrot                 0                    0                    0
           Diospyros.artanthifolia Dipteryx.oleifera Drypetes.standleyi
Null                             0                 0                  0
Preemption                       0                 0                  0
Lognormal                        0                 0                  0
Zipf                             0                 0                  0
Mandelbrot                       0                 0                  0
           Elaeis.oleifera Enterolobium.schomburgkii Erythrina.costaricensis
Null                     0                         0                       0
Preemption               0                         0                       0
Lognormal                0                         0                       0
Zipf                     0                         0                       0
Mandelbrot               0                         0                       0
           Erythroxylum.macrophyllum Eugenia.florida Eugenia.galalonensis
Null                               0               0                    0
Preemption                         0               0                    0
Lognormal                          0               0                    0
Zipf                               0               0                    0
Mandelbrot                         0               0                    0
           Eugenia.nesiotica Eugenia.oerstediana Faramea.occidentalis
Null                       0                   0                    0
Preemption                 0                   0                    0
Lognormal                  0                   0                    0
Zipf                       0                   0                    0
Mandelbrot                 0                   0                    0
           Ficus.colubrinae Ficus.costaricana Ficus.insipida Ficus.maxima
Null                      0                 0              0            0
Preemption                0                 0              0            0
Lognormal                 0                 0              0            0
Zipf                      0                 0              0            0
Mandelbrot                0                 0              0            0
           Ficus.obtusifolia Ficus.popenoei Ficus.tonduzii Ficus.trigonata
Null                       0              0              0               0
Preemption                 0              0              0               0
Lognormal                  0              0              0               0
Zipf                       0              0              0               0
Mandelbrot                 0              0              0               0
           Ficus.yoponensis Garcinia.intermedia Garcinia.madruno
Null                      0                   0                0
Preemption                0                   0                0
Lognormal                 0                   0                0
Zipf                      0                   0                0
Mandelbrot                0                   0                0
           Genipa.americana Guapira.myrtiflora Guarea.fuzzy Guarea.grandifolia
Null                      0                  0            0                  0
Preemption                0                  0            0                  0
Lognormal                 0                  0            0                  0
Zipf                      0                  0            0                  0
Mandelbrot                0                  0            0                  0
           Guarea.guidonia Guatteria.dumetorum Guazuma.ulmifolia
Null                     0                   0                 0
Preemption               0                   0                 0
Lognormal                0                   0                 0
Zipf                     0                   0                 0
Mandelbrot               0                   0                 0
           Guettarda.foliacea Gustavia.superba Hampea.appendiculata
Null                        0                0                    0
Preemption                  0                0                    0
Lognormal                   0                0                    0
Zipf                        0                0                    0
Mandelbrot                  0                0                    0
           Hasseltia.floribunda Heisteria.acuminata Heisteria.concinna
Null                          0                   0                  0
Preemption                    0                   0                  0
Lognormal                     0                   0                  0
Zipf                          0                   0                  0
Mandelbrot                    0                   0                  0
           Hirtella.americana Hirtella.triandra Hura.crepitans
Null                        0                 0              0
Preemption                  0                 0              0
Lognormal                   0                 0              0
Zipf                        0                 0              0
Mandelbrot                  0                 0              0
           Hieronyma.alchorneoides Inga.acuminata Inga.cocleensis
Null                             0              0               0
Preemption                       0              0               0
Lognormal                        0              0               0
Zipf                             0              0               0
Mandelbrot                       0              0               0
           Inga.goldmanii Inga.laurina Inga.semialata Inga.nobilis
Null                    0            0              0            0
Preemption              0            0              0            0
Lognormal               0            0              0            0
Zipf                    0            0              0            0
Mandelbrot              0            0              0            0
           Inga.oerstediana Inga.pezizifera Inga.punctata Inga.ruiziana
Null                      0               0             0             0
Preemption                0               0             0             0
Lognormal                 0               0             0             0
Zipf                      0               0             0             0
Mandelbrot                0               0             0             0
           Inga.sapindoides Inga.spectabilis Inga.umbellifera Jacaranda.copaia
Null                      0                0                0                0
Preemption                0                0                0                0
Lognormal                 0                0                0                0
Zipf                      0                0                0                0
Mandelbrot                0                0                0                0
           Lacistema.aggregatum Lacmellea.panamensis Laetia.procera
Null                          0                    0              0
Preemption                    0                    0              0
Lognormal                     0                    0              0
Zipf                          0                    0              0
Mandelbrot                    0                    0              0
           Laetia.thamnia Lafoensia.punicifolia Licania.hypoleuca
Null                    0                     0                 0
Preemption              0                     0                 0
Lognormal               0                     0                 0
Zipf                    0                     0                 0
Mandelbrot              0                     0                 0
           Licania.platypus Lindackeria.laurina Lonchocarpus.heptaphyllus
Null                      0                   0                         0
Preemption                0                   0                         0
Lognormal                 0                   0                         0
Zipf                      0                   0                         0
Mandelbrot                0                   0                         0
           Luehea.seemannii Macrocnemum.roseum Maquira.guianensis.costaricana
Null                      0                  0                              0
Preemption                0                  0                              0
Lognormal                 0                  0                              0
Zipf                      0                  0                              0
Mandelbrot                0                  0                              0
           Margaritaria.nobilis Marila.laxiflora Maytenus.schippii
Null                          0                0                 0
Preemption                    0                0                 0
Lognormal                     0                0                 0
Zipf                          0                0                 0
Mandelbrot                    0                0                 0
           Miconia.affinis Miconia.argentea Miconia.elata Miconia.hondurensis
Null                     0                0             0                   0
Preemption               0                0             0                   0
Lognormal                0                0             0                   0
Zipf                     0                0             0                   0
Mandelbrot               0                0             0                   0
           Mosannona.garwoodii Myrcia.gatunensis Myrospermum.frutescens
Null                         0                 0                      0
Preemption                   0                 0                      0
Lognormal                    0                 0                      0
Zipf                         0                 0                      0
Mandelbrot                   0                 0                      0
           Nectandra.cissiflora Nectandra.lineata Nectandra.purpurea
Null                          0                 0                  0
Preemption                    0                 0                  0
Lognormal                     0                 0                  0
Zipf                          0                 0                  0
Mandelbrot                    0                 0                  0
           Ochroma.pyramidale Ocotea.cernua Ocotea.oblonga Ocotea.puberula
Null                        0             0              0               0
Preemption                  0             0              0               0
Lognormal                   0             0              0               0
Zipf                        0             0              0               0
Mandelbrot                  0             0              0               0
           Ocotea.whitei Oenocarpus.mapora Ormosia.amazonica Ormosia.coccinea
Null                   0                 0                 0                0
Preemption             0                 0                 0                0
Lognormal              0                 0                 0                0
Zipf                   0                 0                 0                0
Mandelbrot             0                 0                 0                0
           Ormosia.macrocalyx Pachira.quinata Pachira.sessilis
Null                        0               0                0
Preemption                  0               0                0
Lognormal                   0               0                0
Zipf                        0               0                0
Mandelbrot                  0               0                0
           Perebea.xanthochyma Cinnamomum.triplinerve Picramnia.latifolia
Null                         0                      0                   0
Preemption                   0                      0                   0
Lognormal                    0                      0                   0
Zipf                         0                      0                   0
Mandelbrot                   0                      0                   0
           Piper.reticulatum Platymiscium.pinnatum Platypodium.elegans
Null                       0                     0                   0
Preemption                 0                     0                   0
Lognormal                  0                     0                   0
Zipf                       0                     0                   0
Mandelbrot                 0                     0                   0
           Posoqueria.latifolia Poulsenia.armata Pourouma.bicolor
Null                          0                0                0
Preemption                    0                0                0
Lognormal                     0                0                0
Zipf                          0                0                0
Mandelbrot                    0                0                0
           Pouteria.fossicola Pouteria.reticulata Pouteria.stipitata
Null                        0                   0                  0
Preemption                  0                   0                  0
Lognormal                   0                   0                  0
Zipf                        0                   0                  0
Mandelbrot                  0                   0                  0
           Prioria.copaifera Protium.costaricense Protium.panamense
Null                       0                    0                 0
Preemption                 0                    0                 0
Lognormal                  0                    0                 0
Zipf                       0                    0                 0
Mandelbrot                 0                    0                 0
           Protium.tenuifolium Pseudobombax.septenatum
Null                         0                       0
Preemption                   0                       0
Lognormal                    0                       0
Zipf                         0                       0
Mandelbrot                   0                       0
           Psidium.friedrichsthalianum Psychotria.grandis Pterocarpus.rohrii
Null                                 0                  0                  0
Preemption                           0                  0                  0
Lognormal                            0                  0                  0
Zipf                                 0                  0                  0
Mandelbrot                           0                  0                  0
           Quararibea.asterolepis Quassia.amara Randia.armata Sapium.broadleaf
Null                            0             0             0                0
Preemption                      0             0             0                0
Lognormal                       0             0             0                0
Zipf                            0             0             0                0
Mandelbrot                      0             0             0                0
           Sapium.glandulosum Schizolobium.parahyba Senna.dariensis
Null                        0                     0               0
Preemption                  0                     0               0
Lognormal                   0                     0               0
Zipf                        0                     0               0
Mandelbrot                  0                     0               0
           Simarouba.amara Siparuna.guianensis Siparuna.pauciflora
Null                     0                   0                   0
Preemption               0                   0                   0
Lognormal                0                   0                   0
Zipf                     0                   0                   0
Mandelbrot               0                   0                   0
           Sloanea.terniflora Socratea.exorrhiza Solanum.hayesii
Null                        0                  0               0
Preemption                  0                  0               0
Lognormal                   0                  0               0
Zipf                        0                  0               0
Mandelbrot                  0                  0               0
           Sorocea.affinis Spachea.membranacea Spondias.mombin
Null                     0                   0               0
Preemption               0                   0               0
Lognormal                0                   0               0
Zipf                     0                   0               0
Mandelbrot               0                   0               0
           Spondias.radlkoferi Sterculia.apetala
Null                         0                 0
Preemption                   0                 0
Lognormal                    0                 0
Zipf                         0                 0
Mandelbrot                   0                 0
           Swartzia.simplex.var.grandiflora Swartzia.simplex.continentalis
Null                                      0                              0
Preemption                                0                              0
Lognormal                                 0                              0
Zipf                                      0                              0
Mandelbrot                                0                              0
           Symphonia.globulifera Handroanthus.guayacan Tabebuia.rosea
Null                           0                     0              0
Preemption                     0                     0              0
Lognormal                      0                     0              0
Zipf                           0                     0              0
Mandelbrot                     0                     0              0
           Tabernaemontana.arborea Tachigali.versicolor Talisia.nervosa
Null                             0                    0               0
Preemption                       0                    0               0
Lognormal                        0                    0               0
Zipf                             0                    0               0
Mandelbrot                       0                    0               0
           Talisia.princeps Terminalia.amazonia Terminalia.oblonga
Null                      0                   0                  0
Preemption                0                   0                  0
Lognormal                 0                   0                  0
Zipf                      0                   0                  0
Mandelbrot                0                   0                  0
           Tetragastris.panamensis Tetrathylacium.johansenii Theobroma.cacao
Null                             0                         0               0
Preemption                       0                         0               0
Lognormal                        0                         0               0
Zipf                             0                         0               0
Mandelbrot                       0                         0               0
           Thevetia.ahouai Tocoyena.pittieri Trattinnickia.aspera
Null                     0                 0                    0
Preemption               0                 0                    0
Lognormal                0                 0                    0
Zipf                     0                 0                    0
Mandelbrot               0                 0                    0
           Trema.micrantha Trichanthera.gigantea Trichilia.pallida
Null                     0                     0                 0
Preemption               0                     0                 0
Lognormal                0                     0                 0
Zipf                     0                     0                 0
Mandelbrot               0                     0                 0
           Trichilia.tuberculata Trichospermum.galeottii Triplaris.cumingiana
Null                           0                       0                    0
Preemption                     0                       0                    0
Lognormal                      0                       0                    0
Zipf                           0                       0                    0
Mandelbrot                     0                       0                    0
           Trophis.caucana Trophis.racemosa Turpinia.occidentalis
Null                     0                0                     0
Preemption               0                0                     0
Lognormal                0                0                     0
Zipf                     0                0                     0
Mandelbrot               0                0                     0
           Unonopsis.pittieri Virola.multiflora Virola.sebifera
Null                        0                 0               0
Preemption                  0                 0               0
Lognormal                   0                 0               0
Zipf                        0                 0               0
Mandelbrot                  0                 0               0
           Virola.surinamensis Vismia.baccifera Vochysia.ferruginea
Null                         0                0                   0
Preemption                   0                0                   0
Lognormal                    0                0                   0
Zipf                         0                0                   0
Mandelbrot                   0                0                   0
           Xylopia.macrantha Zanthoxylum.ekmanii Zanthoxylum.juniperinum
Null                       0                   0                       0
Preemption                 0                   0                       0
Lognormal                  0                   0                       0
Zipf                       0                   0                       0
Mandelbrot                 0                   0                       0
           Zanthoxylum.panamense Zanthoxylum.setulosum Zuelania.guidonia
Null                           0                     0                 0
Preemption                     0                     0                 0
Lognormal                      0                     0                 0
Zipf                           0                     0                 0
Mandelbrot                     0                     0                 0

$fisherfit

Fisher log series model
No. of species: 225 
Fisher alpha:   35.05475 


$prestonfit

Preston lognormal model
Method: Quasi-Poisson fit to octaves 
No. of species: 225 

     mode     width        S0 
 4.885798  2.932690 32.022923 

Frequencies by Octave
                0        1        2      3        4        5        6        7
Observed 9.500000 16.00000 18.00000 19.000 30.00000 35.00000 31.00000 26.50000
Fitted   7.994154 13.31175 19.73342 26.042 30.59502 31.99865 29.79321 24.69491
                8        9       10     11
Observed 18.00000 13.00000 7.000000 2.0000
Fitted   18.22226 11.97021 7.000122 3.6443

BiodiversityR documentation built on April 20, 2021, 5:07 p.m.