vegan: Community Ecology Package

群集生態学のパッケージ

> library(vegan)
> data("BCI")
> data("BCI.env")
> data("varespec")
> data("varechem")

バージョン: 2.3.2

関数名 概略
BCI Barro Colorado Island Tree Counts
CCorA Canonical Correlation Analysis
MDSrotate Rotate First MDS Dimension Parallel to an External Variable
MOStest Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
RsquareAdj Adjusted R-square
SSarrhenius Self-Starting nls Species-Area Models
add1.cca Add or Drop Single Terms to a Constrained Ordination Model
adipart Additive Diversity Partitioning and Hierarchical Null Model Testing
adonis Permutational Multivariate Analysis of Variance Using Distance Matrices
anosim Analysis of Similarities
anova.cca Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of P rincipal Coordinates
as.mlm.cca Refit Constrained Ordination as a Multiple Response Linear Model
beals Beals Smoothing and Degree of Absence betadisper Multivariate homogeneity of groups dispersions (variances)
betadiver Indices of beta Diversity
bgdispersal Coefficients of Biogeographical Dispersal Direction
bioenv Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
biplot.rda PCA biplot
capscale [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
cascadeKM K-means partitioning using a range of values of K
cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.object Result Object from Constrained Ordination with cca, rda or capscale
clamtest Multinomial Species Classification Method (CLAM)
commsim Create a Object for Null Model Algorithms
contribdiv Contribution Diversity Approach
decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand Standardization Methods for Community Ecology
designdist Design your own Dissimilarities
deviance.cca Statistics Resembling Deviance and AIC for Constrained Ordination
dispindmorisita Morisita index of intraspecific aggregation
dispweight Dispersion-based weighting of species counts
distconnected Connectedness of Dissimilarities diversity Ecological Diversity Indices and Rarefaction Species Richness
dune Vegetation and Environment in Dutch Dune Meadows.
dune.taxon Taxonomic Classification and Phylogeny of Dune Meadow Species
eigenvals Extract Eigenvalues from an Ordination Object
envfit Fits an Environmental Vector or Factor onto an Ordination
eventstar Scale Parameter at the Minimum of the Tsallis Evenness Profile
fisherfit Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
goodness.cca Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
goodness.metaMDS Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
humpfit No-interaction Model for Hump-backed Species Richness vs. Biomass
indpower Indicator Power of Species
isomap Isometric Feature Mapping Ordination
kendall.global Kendall coefficient of concordance
linestack Plots One-dimensional Diagrams without Overwriting Labels
make.cepnames Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
mantel Mantel and Partial Mantel Tests for Dissimilarity Matrices
mantel.correlog Mantel Correlogram
metaMDS Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
mite Oribatid Mite Data with Explanatory Variables
model.matrix.cca Reconstruct Model Frame and Model Matrices of Constrained Ordination
monoMDS Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
mrpp Multi Response Permutation Procedure and Mean Dissimilarity Matrix
mso Functions for performing and displaying a spatial partitioning of cca or rda results
multipart Multiplicative Diversity Partitioning
nestedtemp Nestedness Indices for Communities of Islands or Patches
nobs.adonis Extract the Number of Observations from a vegan Fit.
nullmodel Null Model and Simulation
oecosimu Evaluate Statistics with Null Models of Biological Communities
ordiarrows Add Arrows and Line Segments to Ordination Diagrams
ordihull Display Groups or Factor Levels in Ordination Diagrams
ordilabel Add Text on Non-transparent Label to an Ordination Plot.
ordiplot Alternative plot and identify Functions for Ordination
ordipointlabel Ordination Plots with Points and Optimized Locations for Text
ordiresids Plots of Residuals and Fitted Values for Constrained Ordination
ordistep Choose a Model by Permutation Tests in Constrained Ordination
ordisurf Fit and Plot Smooth Surfaces of Variables on Ordination.
orditkplot Ordination Plot with Movable Labels
orditorp Add Text or Points to Ordination Plots
ordixyplot Trellis (Lattice) Plots for Ordination
pcnm Principal Coordinates of Neighbourhood Matrix
permatfull Matrix Permutation Algorithms for Presence-Absence and Count Data
permustats Extract, Analyse and Display Permutation Results
permutations Permutation tests in Vegan
permutest.betadisper Permutation test of multivariate homogeneity of groups dispersions (variances)
plot.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
prc Principal Response Curves for Treatments with Repeated Observations
predict.cca Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
procrustes Procrustes Rotation of Two Configurations and PROTEST
pyrifos Response of Aquatic Invertebrates to Insecticide Treatment
radfit Rank - Abundance or Dominance / Diversity Models
rankindex Compares Dissimilarity Indices for Gradient Detection
raupcrick Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
read.cep Reads a CEP (Canoco) data file
renyi Renyi and Hill Diversities and Corresponding Accumulation Curves
reorder.hclust Reorder a Hierarchical Clustering Tree
scores Get Species or Site Scores from an Ordination
screeplot.cca Screeplots for Ordination Results and Broken Stick Distributions
simper Similarity Percentages
simulate.rda Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
sipoo Birds in the Archipelago of Sipoo (Sibbo)
spantree Minimum Spanning Tree
specaccum Species Accumulation Curves
specpool Extrapolated Species Richness in a Species Pool
stepacross Stepacross as Flexible Shortest Paths or Extended Dissimilarities
stressplot.wcmdscale Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
taxondive Indices of Taxonomic Diversity and Distinctness
tolerance Species tolerances and sample heterogeneities
treedive Functional Diversity and Community Distances from Species Trees
tsallis Tsallis Diversity and Corresponding Accumulation Curves
varespec Vegetation and environment in lichen pastures
varpart Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegan-deprecated Deprecated Functions in vegan package
vegan-package Community Ecology Package: Ordination, Diversity and Dissimilarities
vegandocs Display Package Documentation
vegdist Dissimilarity Indices for Community Ecologists
vegemite Display Compact Ordered Community Tables
wascores Weighted Averages Scores for Species
wcmdscale Weighted Classical (Metric) Multidimensional Scaling

BCI / BCI.env

バロコロラド島1haプロットにおける樹木の個体数(BCI)とプロットに関する情報(BCI.env)

50地点での225種分のデータ

> data("BCI")
> BCI %>% {
+   print(class(.))
+   dplyr::glimpse(.)
+ }

[1] "data.frame"
Observations: 50
Variables: 225
$ Abarema.macradenia               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,...
$ Acacia.melanoceras               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Acalypha.diversifolia            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Acalypha.macrostachya            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Adelia.triloba                   (int) 0, 0, 0, 3, 1, 0, 0, 0, 5, 0,...
$ Aegiphila.panamensis             (int) 0, 0, 0, 0, 1, 0, 1, 0, 0, 1,...
$ Alchornea.costaricensis          (int) 2, 1, 2, 18, 3, 2, 0, 2, 2, 2...
$ Alchornea.latifolia              (int) 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,...
$ Alibertia.edulis                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Allophylus.psilospermus          (int) 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,...
$ Alseis.blackiana                 (int) 25, 26, 18, 23, 16, 14, 18, 1...
$ Amaioua.corymbosa                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Anacardium.excelsum              (int) 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,...
$ Andira.inermis                   (int) 0, 0, 0, 0, 1, 1, 0, 0, 1, 0,...
$ Annona.spraguei                  (int) 1, 0, 1, 0, 0, 0, 0, 1, 1, 0,...
$ Apeiba.glabra                    (int) 13, 12, 6, 3, 4, 10, 5, 4, 5,...
$ Apeiba.tibourbou                 (int) 2, 0, 1, 1, 0, 0, 0, 1, 0, 0,...
$ Aspidosperma.desmanthum          (int) 0, 0, 0, 1, 1, 1, 0, 0, 0, 1,...
$ Astrocaryum.standleyanum         (int) 0, 2, 1, 5, 6, 2, 2, 0, 2, 1,...
$ Astronium.graveolens             (int) 6, 0, 1, 3, 0, 1, 2, 2, 0, 0,...
$ Attalea.butyracea                (int) 0, 1, 0, 0, 0, 1, 1, 0, 0, 0,...
$ Banara.guianensis                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Beilschmiedia.pendula            (int) 4, 5, 7, 5, 8, 6, 5, 9, 11, 1...
$ Brosimum.alicastrum              (int) 5, 2, 4, 3, 2, 2, 6, 4, 3, 6,...
$ Brosimum.guianense               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Calophyllum.longifolium          (int) 0, 2, 0, 2, 1, 2, 2, 2, 2, 0,...
$ Casearia.aculeata                (int) 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,...
$ Casearia.arborea                 (int) 1, 1, 3, 2, 4, 1, 2, 3, 9, 7,...
$ Casearia.commersoniana           (int) 0, 0, 1, 0, 1, 0, 0, 0, 1, 0,...
$ Casearia.guianensis              (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Casearia.sylvestris              (int) 2, 1, 0, 0, 0, 3, 1, 0, 1, 1,...
$ Cassipourea.guianensis           (int) 2, 0, 1, 1, 3, 4, 4, 0, 2, 1,...
$ Cavanillesia.platanifolia        (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Cecropia.insignis                (int) 12, 5, 7, 17, 21, 4, 0, 7, 2,...
$ Cecropia.obtusifolia             (int) 0, 0, 0, 0, 1, 0, 0, 2, 0, 2,...
$ Cedrela.odorata                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ceiba.pentandra                  (int) 0, 1, 1, 0, 1, 0, 0, 1, 0, 1,...
$ Celtis.schippii                  (int) 0, 0, 0, 2, 2, 0, 1, 0, 0, 0,...
$ Cespedezia.macrophylla           (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Chamguava.schippii               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Chimarrhis.parviflora            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Maclura.tinctoria                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Chrysochlamys.eclipes            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Chrysophyllum.argenteum          (int) 4, 1, 2, 2, 6, 2, 3, 2, 4, 2,...
$ Chrysophyllum.cainito            (int) 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,...
$ Coccoloba.coronata               (int) 0, 0, 0, 1, 2, 0, 0, 1, 2, 1,...
$ Coccoloba.manzinellensis         (int) 0, 0, 0, 0, 0, 0, 0, 2, 0, 0,...
$ Colubrina.glandulosa             (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Cordia.alliodora                 (int) 2, 3, 3, 7, 1, 1, 2, 0, 0, 2,...
$ Cordia.bicolor                   (int) 12, 14, 35, 23, 13, 7, 5, 10,...
$ Cordia.lasiocalyx                (int) 8, 6, 6, 11, 7, 6, 6, 3, 0, 4...
$ Coussarea.curvigemma             (int) 0, 0, 0, 1, 0, 2, 1, 0, 1, 1,...
$ Croton.billbergianus             (int) 2, 2, 0, 11, 6, 0, 0, 4, 2, 0...
$ Cupania.cinerea                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Cupania.latifolia                (int) 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,...
$ Cupania.rufescens                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Cupania.seemannii                (int) 2, 2, 1, 0, 3, 0, 1, 2, 2, 0,...
$ Dendropanax.arboreus             (int) 0, 3, 6, 0, 5, 2, 1, 6, 1, 3,...
$ Desmopsis.panamensis             (int) 0, 0, 4, 0, 0, 0, 0, 0, 0, 1,...
$ Diospyros.artanthifolia          (int) 1, 1, 1, 1, 0, 0, 0, 0, 0, 1,...
$ Dipteryx.oleifera                (int) 1, 1, 3, 0, 0, 0, 0, 2, 1, 2,...
$ Drypetes.standleyi               (int) 2, 1, 2, 0, 0, 0, 0, 0, 0, 0,...
$ Elaeis.oleifera                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Enterolobium.schomburgkii        (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Erythrina.costaricensis          (int) 0, 0, 0, 0, 0, 3, 0, 0, 1, 0,...
$ Erythroxylum.macrophyllum        (int) 0, 1, 0, 0, 0, 0, 0, 1, 1, 1,...
$ Eugenia.florida                  (int) 0, 1, 0, 7, 2, 0, 0, 1, 1, 3,...
$ Eugenia.galalonensis             (int) 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,...
$ Eugenia.nesiotica                (int) 0, 0, 1, 0, 0, 0, 5, 4, 3, 0,...
$ Eugenia.oerstediana              (int) 3, 2, 5, 1, 5, 2, 2, 3, 3, 3,...
$ Faramea.occidentalis             (int) 14, 36, 39, 39, 22, 16, 38, 4...
$ Ficus.colubrinae                 (int) 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.costaricana                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.insipida                   (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.maxima                     (int) 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.obtusifolia                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.popenoei                   (int) 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,...
$ Ficus.tonduzii                   (int) 0, 0, 1, 2, 1, 0, 0, 0, 0, 0,...
$ Ficus.trigonata                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ficus.yoponensis                 (int) 1, 0, 0, 0, 0, 1, 1, 0, 0, 0,...
$ Garcinia.intermedia              (int) 0, 1, 1, 3, 2, 1, 2, 2, 1, 0,...
$ Garcinia.madruno                 (int) 4, 0, 0, 0, 1, 0, 0, 0, 0, 1,...
$ Genipa.americana                 (int) 0, 0, 1, 0, 0, 0, 1, 0, 1, 1,...
$ Guapira.myrtiflora               (int) 3, 1, 0, 1, 1, 7, 3, 1, 1, 1,...
$ Guarea.fuzzy                     (int) 1, 1, 0, 1, 3, 0, 0, 2, 0, 3,...
$ Guarea.grandifolia               (int) 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,...
$ Guarea.guidonia                  (int) 2, 6, 2, 5, 3, 4, 4, 0, 1, 5,...
$ Guatteria.dumetorum              (int) 6, 16, 6, 3, 9, 7, 8, 6, 2, 2...
$ Guazuma.ulmifolia                (int) 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,...
$ Guettarda.foliacea               (int) 1, 5, 1, 2, 1, 0, 0, 4, 1, 3,...
$ Gustavia.superba                 (int) 10, 5, 0, 1, 3, 1, 8, 4, 4, 4...
$ Hampea.appendiculata             (int) 0, 0, 1, 0, 0, 0, 0, 0, 2, 1,...
$ Hasseltia.floribunda             (int) 5, 9, 4, 11, 9, 2, 7, 6, 3, 4...
$ Heisteria.acuminata              (int) 0, 0, 0, 0, 1, 1, 0, 0, 0, 0,...
$ Heisteria.concinna               (int) 4, 5, 4, 6, 4, 8, 2, 5, 1, 5,...
$ Hirtella.americana               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Hirtella.triandra                (int) 21, 14, 5, 4, 6, 6, 7, 14, 8,...
$ Hura.crepitans                   (int) 0, 0, 0, 0, 0, 2, 1, 1, 0, 0,...
$ Hieronyma.alchorneoides          (int) 0, 2, 0, 0, 0, 0, 0, 0, 1, 0,...
$ Inga.acuminata                   (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Inga.cocleensis                  (int) 2, 4, 4, 6, 0, 0, 1, 6, 4, 5,...
$ Inga.goldmanii                   (int) 0, 0, 1, 0, 2, 1, 0, 1, 1, 2,...
$ Inga.laurina                     (int) 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,...
$ Inga.semialata                   (int) 0, 0, 2, 4, 0, 0, 0, 4, 1, 1,...
$ Inga.nobilis                     (int) 0, 0, 1, 3, 1, 0, 2, 2, 2, 3,...
$ Inga.oerstediana                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Inga.pezizifera                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Inga.punctata                    (int) 3, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Inga.ruiziana                    (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Inga.sapindoides                 (int) 2, 0, 3, 2, 5, 0, 0, 1, 1, 0,...
$ Inga.spectabilis                 (int) 0, 2, 0, 1, 0, 0, 0, 0, 0, 0,...
$ Inga.umbellifera                 (int) 0, 0, 0, 1, 0, 0, 0, 2, 2, 1,...
$ Jacaranda.copaia                 (int) 6, 10, 9, 2, 3, 7, 4, 8, 5, 1...
$ Lacistema.aggregatum             (int) 1, 0, 0, 1, 1, 2, 1, 0, 0, 2,...
$ Lacmellea.panamensis             (int) 1, 0, 0, 2, 2, 1, 3, 2, 0, 0,...
$ Laetia.procera                   (int) 0, 1, 1, 0, 1, 0, 0, 1, 0, 0,...
$ Laetia.thamnia                   (int) 0, 1, 1, 0, 0, 0, 0, 2, 1, 1,...
$ Lafoensia.punicifolia            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Licania.hypoleuca                (int) 0, 0, 0, 0, 1, 0, 0, 1, 0, 1,...
$ Licania.platypus                 (int) 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,...
$ Lindackeria.laurina              (int) 0, 0, 0, 0, 0, 0, 1, 0, 2, 2,...
$ Lonchocarpus.heptaphyllus        (int) 7, 7, 3, 9, 2, 1, 4, 2, 2, 4,...
$ Luehea.seemannii                 (int) 1, 0, 0, 0, 1, 1, 2, 0, 1, 0,...
$ Macrocnemum.roseum               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Maquira.guianensis.costaricana   (int) 4, 3, 7, 7, 10, 4, 3, 4, 7, 3...
$ Margaritaria.nobilis             (int) 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,...
$ Marila.laxiflora                 (int) 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Maytenus.schippii                (int) 2, 0, 0, 1, 0, 1, 2, 0, 0, 1,...
$ Miconia.affinis                  (int) 0, 0, 0, 1, 0, 0, 0, 1, 0, 1,...
$ Miconia.argentea                 (int) 2, 0, 1, 0, 1, 0, 1, 4, 0, 0,...
$ Miconia.elata                    (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Miconia.hondurensis              (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Mosannona.garwoodii              (int) 1, 0, 0, 0, 1, 1, 1, 0, 0, 1,...
$ Myrcia.gatunensis                (int) 1, 0, 0, 0, 0, 0, 0, 0, 1, 0,...
$ Myrospermum.frutescens           (int) 0, 0, 0, 0, 0, 2, 0, 0, 0, 0,...
$ Nectandra.cissiflora             (int) 0, 1, 2, 2, 2, 0, 1, 2, 3, 5,...
$ Nectandra.lineata                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Nectandra.purpurea               (int) 1, 0, 0, 0, 0, 1, 0, 0, 0, 0,...
$ Ochroma.pyramidale               (int) 1, 0, 0, 0, 0, 0, 0, 3, 0, 0,...
$ Ocotea.cernua                    (int) 0, 0, 1, 1, 0, 0, 1, 0, 1, 0,...
$ Ocotea.oblonga                   (int) 0, 0, 1, 2, 0, 0, 0, 0, 0, 1,...
$ Ocotea.puberula                  (int) 0, 0, 0, 2, 0, 1, 0, 2, 0, 2,...
$ Ocotea.whitei                    (int) 1, 0, 2, 3, 16, 3, 0, 1, 1, 3...
$ Oenocarpus.mapora                (int) 22, 21, 14, 23, 17, 19, 20, 2...
$ Ormosia.amazonica                (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ormosia.coccinea                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Ormosia.macrocalyx               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Pachira.quinata                  (int) 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,...
$ Pachira.sessilis                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Perebea.xanthochyma              (int) 0, 1, 0, 0, 1, 0, 0, 0, 8, 6,...
$ Cinnamomum.triplinerve           (int) 0, 0, 1, 0, 1, 0, 2, 0, 1, 0,...
$ Picramnia.latifolia              (int) 0, 0, 1, 0, 0, 0, 0, 1, 0, 0,...
$ Piper.reticulatum                (int) 0, 0, 0, 0, 2, 0, 0, 0, 0, 0,...
$ Platymiscium.pinnatum            (int) 3, 3, 5, 1, 1, 1, 6, 0, 2, 0,...
$ Platypodium.elegans              (int) 2, 1, 3, 0, 0, 2, 3, 3, 1, 0,...
$ Posoqueria.latifolia             (int) 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Poulsenia.armata                 (int) 24, 16, 28, 15, 25, 15, 8, 13...
$ Pourouma.bicolor                 (int) 5, 3, 0, 0, 1, 0, 0, 1, 1, 0,...
$ Pouteria.fossicola               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Pouteria.reticulata              (int) 5, 7, 3, 6, 5, 4, 4, 4, 3, 0,...
$ Pouteria.stipitata               (int) 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,...
$ Prioria.copaifera                (int) 13, 12, 12, 5, 3, 26, 18, 5, ...
$ Protium.costaricense             (int) 5, 4, 1, 3, 7, 1, 0, 0, 4, 4,...
$ Protium.panamense                (int) 2, 0, 2, 3, 2, 1, 0, 3, 0, 1,...
$ Protium.tenuifolium              (int) 11, 8, 3, 9, 3, 2, 6, 7, 4, 6...
$ Pseudobombax.septenatum          (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Psidium.friedrichsthalianum      (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Psychotria.grandis               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Pterocarpus.rohrii               (int) 1, 0, 0, 2, 1, 1, 2, 2, 1, 0,...
$ Quararibea.asterolepis           (int) 11, 12, 15, 14, 9, 3, 21, 7, ...
$ Quassia.amara                    (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Randia.armata                    (int) 3, 2, 1, 4, 2, 9, 14, 4, 4, 1...
$ Sapium.broadleaf                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Sapium.glandulosum               (int) 0, 0, 1, 0, 2, 0, 0, 0, 0, 0,...
$ Schizolobium.parahyba            (int) 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,...
$ Senna.dariensis                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Simarouba.amara                  (int) 14, 6, 16, 8, 7, 7, 13, 14, 1...
$ Siparuna.guianensis              (int) 3, 2, 1, 2, 0, 1, 1, 0, 0, 0,...
$ Siparuna.pauciflora              (int) 0, 0, 1, 0, 3, 0, 0, 0, 1, 1,...
$ Sloanea.terniflora               (int) 1, 0, 2, 2, 3, 2, 1, 2, 1, 2,...
$ Socratea.exorrhiza               (int) 15, 22, 31, 9, 55, 44, 23, 22...
$ Solanum.hayesii                  (int) 0, 0, 0, 0, 1, 0, 0, 0, 0, 2,...
$ Sorocea.affinis                  (int) 1, 1, 1, 1, 0, 1, 0, 0, 0, 1,...
$ Spachea.membranacea              (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Spondias.mombin                  (int) 1, 1, 0, 1, 1, 0, 0, 1, 0, 2,...
$ Spondias.radlkoferi              (int) 2, 0, 3, 3, 5, 0, 5, 0, 1, 1,...
$ Sterculia.apetala                (int) 1, 2, 0, 0, 0, 1, 1, 0, 0, 0,...
$ Swartzia.simplex.var.grandiflora (int) 3, 3, 0, 1, 1, 9, 9, 5, 5, 0,...
$ Swartzia.simplex.continentalis   (int) 1, 4, 2, 2, 1, 5, 7, 0, 0, 0,...
$ Symphonia.globulifera            (int) 0, 1, 1, 1, 2, 0, 0, 1, 1, 0,...
$ Handroanthus.guayacan            (int) 1, 0, 1, 0, 0, 1, 0, 0, 0, 0,...
$ Tabebuia.rosea                   (int) 1, 2, 1, 2, 3, 0, 1, 0, 0, 0,...
$ Tabernaemontana.arborea          (int) 9, 5, 6, 10, 16, 11, 9, 8, 12...
$ Tachigali.versicolor             (int) 6, 1, 3, 3, 0, 1, 2, 0, 3, 1,...
$ Talisia.nervosa                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Talisia.princeps                 (int) 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Terminalia.amazonia              (int) 1, 0, 0, 0, 1, 1, 0, 0, 0, 0,...
$ Terminalia.oblonga               (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Tetragastris.panamensis          (int) 5, 7, 10, 10, 7, 17, 8, 9, 5,...
$ Tetrathylacium.johansenii        (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Theobroma.cacao                  (int) 1, 1, 0, 0, 1, 0, 0, 0, 0, 0,...
$ Thevetia.ahouai                  (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Tocoyena.pittieri                (int) 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Trattinnickia.aspera             (int) 3, 1, 1, 0, 2, 0, 0, 2, 2, 1,...
$ Trema.micrantha                  (int) 0, 0, 0, 2, 1, 0, 0, 0, 0, 0,...
$ Trichanthera.gigantea            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Trichilia.pallida                (int) 0, 1, 0, 1, 0, 0, 1, 0, 0, 0,...
$ Trichilia.tuberculata            (int) 18, 27, 28, 35, 15, 31, 27, 3...
$ Trichospermum.galeottii          (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Triplaris.cumingiana             (int) 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,...
$ Trophis.caucana                  (int) 2, 0, 0, 0, 2, 0, 0, 0, 0, 0,...
$ Trophis.racemosa                 (int) 1, 1, 0, 1, 0, 0, 1, 0, 0, 2,...
$ Turpinia.occidentalis            (int) 0, 1, 1, 4, 2, 1, 0, 1, 1, 1,...
$ Unonopsis.pittieri               (int) 1, 5, 12, 3, 4, 3, 3, 2, 5, 9...
$ Virola.multiflora                (int) 0, 0, 0, 0, 0, 2, 0, 0, 0, 1,...
$ Virola.sebifera                  (int) 17, 12, 11, 16, 31, 19, 8, 19...
$ Virola.surinamensis              (int) 4, 3, 2, 2, 6, 1, 1, 1, 1, 2,...
$ Vismia.baccifera                 (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Vochysia.ferruginea              (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Xylopia.macrantha                (int) 1, 0, 0, 0, 0, 0, 0, 0, 0, 4,...
$ Zanthoxylum.ekmanii              (int) 3, 4, 8, 13, 3, 1, 2, 4, 13, ...
$ Zanthoxylum.juniperinum          (int) 0, 0, 1, 1, 0, 0, 0, 0, 1, 10...
$ Zanthoxylum.panamense            (int) 2, 2, 2, 5, 5, 3, 0, 2, 4, 4,...
$ Zanthoxylum.setulosum            (int) 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,...
$ Zuelania.guidonia                (int) 0, 0, 0, 1, 0, 2, 0, 0, 0, 0,...

> data("BCI.env")
> BCI.env %>% {
+   print(class(.))
+   dplyr::glimpse(.)
+ }

[1] "data.frame"
Observations: 50
Variables: 6
$ UTM.EW        (dbl) 625754, 625754, 625754, 625754, 625754, 625854, ...
$ UTM.NS        (dbl) 1011569, 1011669, 1011769, 1011869, 1011969, 101...
$ Precipitation (int) 2530, 2530, 2530, 2530, 2530, 2530, 2530, 2530, ...
$ Elevation     (int) 120, 120, 120, 120, 120, 120, 120, 120, 120, 120...
$ Age.cat       (fctr) c3, c3, c3, c3, c3, c3, c3, c3, c3, c3, c3, c3,...
$ Geology       (fctr) Tb, Tb, Tb, Tb, Tb, Tb, Tb, Tb, Tb, Tb, Tb, Tb,...

decostand

群集生態学でよく使われる標準化を行う

Arguments

  • x
  • methods
  • MARGIN
  • range.global
  • logbase
  • na.rm
  • ...
> data("varespec")
> sptrans <- decostand(varespec, "max")
> summary(sptrans)

    Callvulg           Empenigr           Rhodtome         Vaccmyrt      
 Min.   :0.000000   Min.   :0.008125   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:0.000000   1st Qu.:0.114531   1st Qu.:0.0000   1st Qu.:0.00000  
 Median :0.003108   Median :0.356250   Median :0.0000   Median :0.00000  
 Mean   :0.077825   Mean   :0.395807   Mean   :0.0874   Mean   :0.11565  
 3rd Qu.:0.045379   3rd Qu.:0.607812   3rd Qu.:0.0000   3rd Qu.:0.04379  
 Max.   :1.000000   Max.   :1.000000   Max.   :1.0000   Max.   :1.00000  
    Vaccviti         Pinusylv          Descflex          Betupube      
 Min.   :0.0792   Min.   :0.00000   Min.   :0.00000   Min.   :0.00000  
 1st Qu.:0.2669   1st Qu.:0.02500   1st Qu.:0.00000   1st Qu.:0.00000  
 Median :0.4500   Median :0.08333   Median :0.00000   Median :0.00000  
 Mean   :0.4584   Mean   :0.14271   Mean   :0.06306   Mean   :0.04833  
 3rd Qu.:0.5819   3rd Qu.:0.12708   3rd Qu.:0.01351   3rd Qu.:0.00000  
 Max.   :1.0000   Max.   :1.00000   Max.   :1.00000   Max.   :1.00000  
    Vacculig          Diphcomp            Dicrsp           Dicrfusc       
 Min.   :0.00000   Min.   :0.000000   Min.   :0.00000   Min.   :0.000000  
 1st Qu.:0.00000   1st Qu.:0.000000   1st Qu.:0.00000   1st Qu.:0.006744  
 Median :0.00000   Median :0.000000   Median :0.00000   Median :0.014432  
 Mean   :0.07829   Mean   :0.065217   Mean   :0.07202   Mean   :0.127596  
 3rd Qu.:0.03302   3rd Qu.:0.008454   3rd Qu.:0.01120   3rd Qu.:0.093674  
 Max.   :1.00000   Max.   :1.000000   Max.   :1.00000   Max.   :1.000000  
    Dicrpoly           Hylosple          Pleuschr            Polypili     
 Min.   :0.000000   Min.   :0.00000   Min.   :0.0004284   Min.   :0.0000  
 1st Qu.:0.000000   1st Qu.:0.00000   1st Qu.:0.0190633   1st Qu.:0.0000  
 Median :0.006667   Median :0.00000   Median :0.0981722   Median :0.0000  
 Mean   :0.084167   Mean   :0.07539   Mean   :0.2248858   Mean   :0.1017  
 3rd Qu.:0.069167   3rd Qu.:0.00000   3rd Qu.:0.3193988   3rd Qu.:0.0800  
 Max.   :1.000000   Max.   :1.00000   Max.   :1.0000000   Max.   :1.0000  
    Polyjuni          Polycomm         Pohlnuta          Ptilcili      
 Min.   :0.00000   Min.   :0.0000   Min.   :0.00000   Min.   :0.00000  
 1st Qu.:0.00394   1st Qu.:0.0000   1st Qu.:0.09375   1st Qu.:0.00000  
 Median :0.02579   Median :0.0000   Median :0.21875   Median :0.00300  
 Mean   :0.08268   Mean   :0.1183   Mean   :0.34115   Mean   :0.05838  
 3rd Qu.:0.03582   3rd Qu.:0.0000   3rd Qu.:0.59375   3rd Qu.:0.02275  
 Max.   :1.00000   Max.   :1.0000   Max.   :1.00000   Max.   :1.00000  
    Barbhatc          Cladarbu           Cladrang          Cladstel       
 Min.   :0.00000   Min.   :0.004359   Min.   :0.01475   Min.   :0.000000  
 1st Qu.:0.00000   1st Qu.:0.077949   1st Qu.:0.08284   1st Qu.:0.001275  
 Median :0.00000   Median :0.184103   Median :0.17322   Median :0.035884  
 Mean   :0.04431   Mean   :0.272489   Mean   :0.27451   Mean   :0.240564  
 3rd Qu.:0.00000   3rd Qu.:0.414359   3rd Qu.:0.40470   3rd Qu.:0.345196  
 Max.   :1.00000   Max.   :1.000000   Max.   :1.00000   Max.   :1.000000  
    Cladunci           Cladcocc        Cladcorn          Cladgrac     
 Min.   :0.002112   Min.   :0.000   Min.   :0.02113   Min.   :0.0000  
 1st Qu.:0.010557   1st Qu.:0.110   1st Qu.:0.08979   1st Qu.:0.3300  
 Median :0.030828   Median :0.440   Median :0.15141   Median :0.4600  
 Mean   :0.099029   Mean   :0.465   Mean   :0.18251   Mean   :0.4283  
 3rd Qu.:0.102090   3rd Qu.:0.720   3rd Qu.:0.17606   3rd Qu.:0.5000  
 Max.   :1.000000   Max.   :1.000   Max.   :1.00000   Max.   :1.0000  
    Cladfimb       Cladcris          Cladchlo         Cladbotr      
 Min.   :0.00   Min.   :0.01124   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:0.40   1st Qu.:0.03933   1st Qu.:0.0000   1st Qu.:0.00000  
 Median :0.72   Median :0.10393   Median :0.0400   Median :0.00000  
 Mean   :0.66   Mean   :0.17486   Mean   :0.1933   Mean   :0.07833  
 3rd Qu.:1.00   3rd Qu.:0.14045   3rd Qu.:0.2000   3rd Qu.:0.08000  
 Max.   :1.00   Max.   :1.00000   Max.   :1.0000   Max.   :1.00000  
    Cladamau           Cladsp           Cetreric         Cetrisla      
 Min.   :0.00000   Min.   :0.00000   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:0.00000   1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:0.00000  
 Median :0.00000   Median :0.00000   Median :0.0641   Median :0.02985  
 Mean   :0.07292   Mean   :0.08667   Mean   :0.1923   Mean   :0.12624  
 3rd Qu.:0.00000   3rd Qu.:0.08000   3rd Qu.:0.2532   3rd Qu.:0.13433  
 Max.   :1.00000   Max.   :1.00000   Max.   :1.0000   Max.   :1.00000  
    Flavniva          Nepharct         Stersp            Peltapht      
 Min.   :0.00000   Min.   :0.000   Min.   :0.000000   Min.   :0.00000  
 1st Qu.:0.00000   1st Qu.:0.000   1st Qu.:0.000000   1st Qu.:0.00000  
 Median :0.00000   Median :0.000   Median :0.006323   Median :0.00000  
 Mean   :0.04923   Mean   :0.045   Mean   :0.071012   Mean   :0.09596  
 3rd Qu.:0.01271   3rd Qu.:0.000   3rd Qu.:0.065905   3rd Qu.:0.01515  
 Max.   :1.00000   Max.   :1.000   Max.   :1.000000   Max.   :1.00000  
    Icmaeric          Cladcerv          Claddefo          Cladphyl     
 Min.   :0.00000   Min.   :0.00000   Min.   :0.00000   Min.   :0.0000  
 1st Qu.:0.00000   1st Qu.:0.00000   1st Qu.:0.04822   1st Qu.:0.0000  
 Median :0.00000   Median :0.00000   Median :0.12690   Median :0.0000  
 Mean   :0.09167   Mean   :0.08333   Mean   :0.21637   Mean   :0.1333  
 3rd Qu.:0.00000   3rd Qu.:0.00000   3rd Qu.:0.21193   3rd Qu.:0.0000  
 Max.   :1.00000   Max.   :1.00000   Max.   :1.00000   Max.   :1.0000

> apply(varespec, 2, max) # original

Callvulg Empenigr Rhodtome Vaccmyrt Vaccviti Pinusylv Descflex Betupube 
   24.13    16.00     4.00    18.27    25.00     1.20     3.70     0.25 
Vacculig Diphcomp   Dicrsp Dicrfusc Dicrpoly Hylosple Pleuschr Polypili 
    8.10     2.07    23.43    37.07     3.00     9.97    70.03     0.25 
Polyjuni Polycomm Pohlnuta Ptilcili Barbhatc Cladarbu Cladrang Cladstel 
    6.98     0.25     0.32    10.00     3.00    39.00    59.00    84.30 
Cladunci Cladcocc Cladcorn Cladgrac Cladfimb Cladcris Cladchlo Cladbotr 
   23.68     0.25     1.42     0.50     0.25     1.78     0.25     0.25 
Cladamau   Cladsp Cetreric Cetrisla Flavniva Nepharct   Stersp Peltapht 
    0.08     0.25     0.78     0.67    10.03     4.87    10.28     0.33 
Icmaeric Cladcerv Claddefo Cladphyl 
    0.10     0.05     1.97     0.25

> apply(sptrans, 2, max)

Callvulg Empenigr Rhodtome Vaccmyrt Vaccviti Pinusylv Descflex Betupube 
       1        1        1        1        1        1        1        1 
Vacculig Diphcomp   Dicrsp Dicrfusc Dicrpoly Hylosple Pleuschr Polypili 
       1        1        1        1        1        1        1        1 
Polyjuni Polycomm Pohlnuta Ptilcili Barbhatc Cladarbu Cladrang Cladstel 
       1        1        1        1        1        1        1        1 
Cladunci Cladcocc Cladcorn Cladgrac Cladfimb Cladcris Cladchlo Cladbotr 
       1        1        1        1        1        1        1        1 
Cladamau   Cladsp Cetreric Cetrisla Flavniva Nepharct   Stersp Peltapht 
       1        1        1        1        1        1        1        1 
Icmaeric Cladcerv Claddefo Cladphyl 
       1        1        1        1

make.cepnames

学名を省略する際に便利。

> make.cepnames(c("Aa maderoi", "Poa sp.", "Cladina rangiferina", "Cladonia cornuta", "Cladonia cornuta var. groenlandica", "Cladonia rangiformis", "Bryoerythrophyllum"))

[1] "Aamade"     "Poasp"      "Cladrang"   "Cladcorn"   "Cladgroe"  
[6] "Cladrang.1" "Bryrythr"

> data("BCI")
> colnames(BCI) <- make.cepnames(colnames(BCI))

radfit

renyi

simper

specaccum

累積種数曲線（SAC）

ref) picante::specaccum.psr()

Arguments

  • comm
  • method... collector, random, exact, coleman, rarefaction
  • permutations
  • conditioned
  • w
  • subset
  • x
  • add
  • random
  • ci
  • col
  • ci.col
  • ci.lty
  • xlab, ylab
  • ylim
  • xvar
  • object
  • model
  • lty
  • newdata
  • interpolation
  • at
  • ...
> specaccum(BCI)

Warning in cor(x > 0): the standard deviation is zero

Species Accumulation Curve
Accumulation method: exact
Call: specaccum(comm = BCI) 


Sites     1.00000   2.00000   3.00000   4.00000   5.00000   6.00000
Richness 90.78000 121.60980 139.04587 150.71157 159.23634 165.83062
sd        6.93481   7.19336   7.00199   6.63577   6.24812   5.89474

Sites      7.00000   8.00000   9.00000  10.00000  11.00000  12.00000
Richness 171.14214 175.55318 179.30561 182.56044 185.42917 187.99142
sd         5.59124   5.33703   5.12587   4.95014   4.80256   4.67674

Sites     13.00000  14.0000  15.00000  16.00000  17.00000  18.00000
Richness 190.30560 192.4155 194.35454 196.14879 197.81879 199.38098
sd         4.56741   4.4703   4.38202   4.29995   4.22206   4.14681

Sites     19.00000  20.00000  21.00000  22.00000  23.00000  24.00000
Richness 200.84871 202.23287 203.54250 204.78512 205.96707 207.09370
sd         4.07304   3.99989   3.92675   3.85313   3.77873   3.70328

Sites     25.00000  26.00000  27.00000  28.00000  29.00000  30.0000
Richness 208.16959 209.19868 210.18438 211.12965 212.03708 212.9090
sd         3.62663   3.54864   3.46921   3.38823   3.30563   3.2213

Sites     31.00000  32.00000  33.00000  34.00000  35.00000  36.00000
Richness 213.74738 214.55410 215.33078 216.07889 216.79978 217.49467
sd         3.13514   3.04702   2.95678   2.86426   2.76922   2.67142

Sites     37.00000  38.00000  39.00000  40.00000  41.00000  42.00000
Richness 218.16469 218.81087 219.43418 220.03550 220.61567 221.17546
sd         2.57053   2.46617   2.35786   2.24501   2.12687   2.00249

Sites     43.00000  44.00000  45.00000  46.00000  47.00000  48.0000
Richness 221.71561 222.23680 222.73968 223.22488 223.69296 224.1445
sd         1.87058   1.72938   1.57635   1.40765   1.21639   0.9916

Sites     49.00000  50
Richness 224.58000 225
sd         0.69541   0

> specaccum(BCI, method = "random") %>% summary()

 1 sites          2 sites         3 sites         4 sites        
 Min.   : 77.00   Min.   :108.0   Min.   :126.0   Min.   :134.0  
 1st Qu.: 86.00   1st Qu.:117.0   1st Qu.:135.8   1st Qu.:147.0  
 Median : 91.00   Median :122.0   Median :140.0   Median :150.5  
 Mean   : 90.66   Mean   :121.6   Mean   :139.7   Mean   :151.2  
 3rd Qu.: 93.25   3rd Qu.:126.0   3rd Qu.:144.0   3rd Qu.:156.0  
 Max.   :109.00   Max.   :135.0   Max.   :155.0   Max.   :165.0  
 5 sites         6 sites         7 sites         8 sites        
 Min.   :145.0   Min.   :151.0   Min.   :158.0   Min.   :164.0  
 1st Qu.:155.0   1st Qu.:162.0   1st Qu.:168.0   1st Qu.:172.0  
 Median :159.0   Median :165.0   Median :171.0   Median :175.0  
 Mean   :159.2   Mean   :165.6   Mean   :171.0   Mean   :175.4  
 3rd Qu.:163.0   3rd Qu.:169.0   3rd Qu.:174.2   3rd Qu.:179.0  
 Max.   :173.0   Max.   :176.0   Max.   :182.0   Max.   :187.0  
 9 sites         10 sites        11 sites        12 sites       
 Min.   :167.0   Min.   :169.0   Min.   :175.0   Min.   :176.0  
 1st Qu.:176.0   1st Qu.:180.0   1st Qu.:182.8   1st Qu.:185.0  
 Median :180.0   Median :183.0   Median :186.0   Median :188.0  
 Mean   :179.3   Mean   :182.6   Mean   :185.5   Mean   :187.9  
 3rd Qu.:182.2   3rd Qu.:185.2   3rd Qu.:189.0   3rd Qu.:191.0  
 Max.   :192.0   Max.   :192.0   Max.   :195.0   Max.   :198.0  
 13 sites        14 sites        15 sites        16 sites       
 Min.   :176.0   Min.   :178.0   Min.   :180.0   Min.   :181.0  
 1st Qu.:186.8   1st Qu.:189.8   1st Qu.:191.0   1st Qu.:192.0  
 Median :191.0   Median :193.0   Median :194.5   Median :197.0  
 Mean   :190.1   Mean   :192.3   Mean   :194.2   Mean   :195.7  
 3rd Qu.:193.0   3rd Qu.:195.0   3rd Qu.:197.2   3rd Qu.:199.2  
 Max.   :200.0   Max.   :203.0   Max.   :204.0   Max.   :205.0  
 17 sites        18 sites      19 sites        20 sites       
 Min.   :184.0   Min.   :188   Min.   :188.0   Min.   :188.0  
 1st Qu.:195.0   1st Qu.:196   1st Qu.:197.8   1st Qu.:199.0  
 Median :198.0   Median :200   Median :201.0   Median :202.0  
 Mean   :197.4   Mean   :199   Mean   :200.4   Mean   :201.6  
 3rd Qu.:201.0   3rd Qu.:203   3rd Qu.:204.0   3rd Qu.:204.0  
 Max.   :208.0   Max.   :210   Max.   :210.0   Max.   :212.0  
 21 sites      22 sites        23 sites        24 sites       
 Min.   :188   Min.   :191.0   Min.   :194.0   Min.   :195.0  
 1st Qu.:200   1st Qu.:202.0   1st Qu.:203.0   1st Qu.:204.0  
 Median :203   Median :205.0   Median :206.0   Median :207.5  
 Mean   :203   Mean   :204.4   Mean   :205.8   Mean   :206.9  
 3rd Qu.:206   3rd Qu.:207.0   3rd Qu.:208.2   3rd Qu.:210.0  
 Max.   :213   Max.   :214.0   Max.   :216.0   Max.   :217.0  
 25 sites        26 sites        27 sites        28 sites       
 Min.   :198.0   Min.   :198.0   Min.   :198.0   Min.   :198.0  
 1st Qu.:206.0   1st Qu.:206.0   1st Qu.:207.0   1st Qu.:209.0  
 Median :208.0   Median :209.0   Median :210.5   Median :211.0  
 Mean   :207.9   Mean   :208.9   Mean   :210.2   Mean   :211.1  
 3rd Qu.:210.0   3rd Qu.:211.2   3rd Qu.:213.0   3rd Qu.:214.0  
 Max.   :217.0   Max.   :218.0   Max.   :219.0   Max.   :220.0  
 29 sites        30 sites        31 sites        32 sites       
 Min.   :201.0   Min.   :206.0   Min.   :207.0   Min.   :208.0  
 1st Qu.:210.0   1st Qu.:210.0   1st Qu.:211.8   1st Qu.:212.0  
 Median :212.0   Median :213.0   Median :214.0   Median :214.0  
 Mean   :211.9   Mean   :212.8   Mean   :213.8   Mean   :214.4  
 3rd Qu.:214.0   3rd Qu.:214.2   3rd Qu.:216.0   3rd Qu.:217.0  
 Max.   :220.0   Max.   :221.0   Max.   :222.0   Max.   :223.0  
 33 sites        34 sites        35 sites        36 sites       
 Min.   :208.0   Min.   :208.0   Min.   :209.0   Min.   :209.0  
 1st Qu.:213.0   1st Qu.:214.0   1st Qu.:215.0   1st Qu.:216.0  
 Median :215.0   Median :216.0   Median :217.0   Median :218.0  
 Mean   :215.2   Mean   :216.1   Mean   :216.9   Mean   :217.6  
 3rd Qu.:217.0   3rd Qu.:218.0   3rd Qu.:219.0   3rd Qu.:219.0  
 Max.   :223.0   Max.   :223.0   Max.   :224.0   Max.   :224.0  
 37 sites        38 sites        39 sites        40 sites       
 Min.   :211.0   Min.   :212.0   Min.   :214.0   Min.   :215.0  
 1st Qu.:217.0   1st Qu.:218.0   1st Qu.:218.8   1st Qu.:219.0  
 Median :219.0   Median :219.0   Median :220.0   Median :220.0  
 Mean   :218.3   Mean   :218.9   Mean   :219.5   Mean   :220.2  
 3rd Qu.:220.0   3rd Qu.:221.0   3rd Qu.:221.0   3rd Qu.:221.2  
 Max.   :224.0   Max.   :224.0   Max.   :224.0   Max.   :225.0  
 41 sites        42 sites        43 sites        44 sites       
 Min.   :215.0   Min.   :215.0   Min.   :216.0   Min.   :216.0  
 1st Qu.:220.0   1st Qu.:220.0   1st Qu.:221.0   1st Qu.:221.0  
 Median :221.0   Median :221.5   Median :222.0   Median :222.0  
 Mean   :220.7   Mean   :221.2   Mean   :221.6   Mean   :222.1  
 3rd Qu.:222.0   3rd Qu.:222.0   3rd Qu.:223.0   3rd Qu.:223.0  
 Max.   :225.0   Max.   :225.0   Max.   :225.0   Max.   :225.0  
 45 sites        46 sites        47 sites        48 sites       
 Min.   :217.0   Min.   :217.0   Min.   :219.0   Min.   :220.0  
 1st Qu.:222.0   1st Qu.:222.0   1st Qu.:223.0   1st Qu.:224.0  
 Median :223.0   Median :223.0   Median :224.0   Median :224.0  
 Mean   :222.7   Mean   :223.2   Mean   :223.7   Mean   :224.2  
 3rd Qu.:224.0   3rd Qu.:224.0   3rd Qu.:224.0   3rd Qu.:225.0  
 Max.   :225.0   Max.   :225.0   Max.   :225.0   Max.   :225.0  
 49 sites        50 sites     
 Min.   :222.0   Min.   :225  
 1st Qu.:224.0   1st Qu.:225  
 Median :225.0   Median :225  
 Mean   :224.6   Mean   :225  
 3rd Qu.:225.0   3rd Qu.:225  
 Max.   :225.0   Max.   :225

> BCI %>% purrr::by_row(sum) %$% .out

 [1] 448 435 463 508 505 412 416 431 409 483 401 366 409 438 462 437 381
[18] 347 433 429 408 418 340 392 442 407 417 387 364 475 421 459 436 447
[35] 601 430 435 447 424 489 402 414 407 409 444 430 425 415 427 432

> # specaccum(BCI, method = "coleman") %>% plot()
> 
> # data.frame(sp1 = c(0, 1, 1, 2, 4),
> #            sp2 = c(1, 2, 2, 1, 2),
> #            sp3 = c(0, 0, 4, 6, 3),
> #            sp4 = c(2, 3, 2, 4, 5)) %>% 
> #   specaccum() %>% plot()

tolerance

treedive

tsallis

varespec

植生と環境データ

> data("varespec") # 種のデータ
> data("varechem") # 環境要因のデータ

vegemite