vegsoup: Classes and Methods for Phytosociology

S4 classes for phytosociological data. The classes document community samples, sites data, taxonomy and spatial representation. Methods are provided for data manipulation, multivariate analysis, indicator species analysis and typesetting of LaTex tables.

AuthorRoland Kaiser [aut, cre]
Date of publication2017-01-10 19:25:36
MaintainerRoland Kaiser <kardinal.eros@gmail.com>
LicenseGPL (>= 2)
Version0.2-6
http://vegsoup.r-forge.r-project.org/

View on R-Forge

Man pages

abbr: Get Abbreviations used to Encode Species and Layer Replicates

accuracy: Accuracy Statistics for Objects of class VegsoupPartition

apriori: Grouping Variable of 'Vegsoup*' Objects

as.data.frame: Coerce to data.frame

as.data.list: Coercion to '"data.lists"'

as.dendrogram: Dendrograms of Partitions

as.matrix: Retrieve Species Matrix with Specified Storage Mode

barmstein: Test Data Set

berchtesgaden: Grassland survey in National Park Berchtesgaden

bind: Combine 'Vegsoup*' objects

BraunBlanquetReduce: Reduce 9 Point Braun-Blanquet Abundance Scale to 7 Point

coerce: Coerce Methods for 'Vegsoup*' objects

coldiss: Plots of the Dissimilarity Matrix of an Object of class...

colSums: Row and Column Sums for Objects of Class VegsoupData*

combine: Combine taxa

compress: Compress Object and Retain Minimal Information

confusion: Confusionion Matrix for VegsoupPartition Objects

coverscale: Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects

Coverscale-class: Coverscale Class

decostand: Standardization Methods

dim: Number or Rows, Columns, and Cells

elevation: Query Elevation

extract: Indexing to Extract Values of a Vegsoup* Object

fidelity: Calculate Fidelity Values

fill: Matrix fill of species matrix

googletiles: Geocoding Using Tile Map Service Protocol

head: Return the First or Last Part of the Species Matrix

hist: Plot Histogram of Fidelity Values

identical: Intersect plot names

Indpower: Indicator Power of Species

Indspc: Compositional Indicator Species Analysis

intersect: Intersect plot names

Isamic: Indicator Species Analysis to Minimize Intermediate Constancy

isolate: Manually Modifiy Partitions

KML: Write KML Files to Disk

Latex: Typesetting Tables in LaTeX

layer: Return Stratum/Layer

layers: Get or Modify Layers

map: Draw Map of Plot Locations

misc: Utility Functions

multipatt: Methods for Function Multipatt

murdoch: Indicator Species Analysis by Murdoch Preference Function

names: Row and Column Names of 'Vegsoup*' objects

nndist: Nearest Neighbor Distances

optimize: Optimize Partitioning

OptimStride: Compute a Series of Partitions/Clusterings

outlier: Outlier Detection

Partitioning: Partitioning Vector of VegsoupPartition objects

plot: Plotting methods

plotPCO: Plot Principal Coordinates

quantile: Sample Quantiles for a Community Matrix

raster: Extract values from Raster objects

read.XML: Read From TurboVeg XML Files

rectangles: Plot Matrix Dimensions

reshape: Reshape Species Matrix

reverseGeocode: Reverse geocoding

richness: Species Richness

sample: Random Samples and Permutations for 'Vegsoup*' Objects

seriation: Reorder as to Reflect a Vegetation Table

shared: Shared Species

SigFidelity: Experimental Function

sites: Methods for the Sites Slot of 'Vegsoup*' Objects

Sites-class: Sites Class

spatial: Spatial Methods for 'Vegsoup*' Objects

species: Methods to Retrieve or Manipulate Slot Species of 'Vegsoup*'...

Species-class: Species Class

SpeciesTaxonomy: Compare Species Abbreviations to Taxonomic Reference List

SpeciesTaxonomy-class: SpeciesTaxonomy Class

splitAbbr: Deparse Species Layer Replication of 'Vegsoup*' Objects

spread: List Occurences of Species in Partitions

stable: Classification Stability

stack: Stack Species Matrix, Sites Data or Spatial Coordinates

summary-methods: Summary of Object

tables: Constancy and Contingency Tables

taxalist: Species and Relevee Listings

taxon: Get or Subset Object by Scientific Taxon Name

Taxonomy-class: Class Taxonomy

templates: LaTex template files

typical: Typical Samples of an Object of Class Vegsoup*

validate: Partition Quality Assessment for '"VegsoupPartition"' Objects

vegdist: Dissimilarity Matrices from 'Vegsoup*' Objects

Vegsoup: Create an object of class Vegsoup

Vegsoup-class: Class Vegsoup

VegsoupOptimstride-class: VegsoupOptimstride Class

vegsoup-package: An overview of the functions in this package

VegsoupPartition: Partition a Vegsoup object

VegsoupPartition-class: VegsoupPartition Class

VegsoupPartitionFidelity-class: VegsoupPartitionFidelity Class

verbatim: Read or Write Fixed-Column-Width Community Tables From or To...

windsfeld: Alpine Vegetation

Files in this package

vegsoup/ChangeLog
vegsoup/DESCRIPTION
vegsoup/NAMESPACE
vegsoup/R
vegsoup/R/AAA.R vegsoup/R/Class-Coverscale.R vegsoup/R/Class-Sites.R vegsoup/R/Class-Species.R vegsoup/R/Class-SpeciesTaxonomy.R vegsoup/R/Class-Taxonomy.R vegsoup/R/Class-Vegsoup.R vegsoup/R/Class-VegsoupOptimstride.R vegsoup/R/Class-VegsoupPartition.R vegsoup/R/Class-VegsoupPartitionFidelity.R vegsoup/R/Coverscale-Methods.R vegsoup/R/Coverscale-VegsoupMethods.R vegsoup/R/Indval.R vegsoup/R/KML.R vegsoup/R/Latex.R vegsoup/R/OptimStride.R vegsoup/R/Phi.R vegsoup/R/Sites-methods.R vegsoup/R/Species-methods.R vegsoup/R/SpeciesTaxonomy-Methods.R vegsoup/R/SpeciesTaxonomy.R vegsoup/R/Taxonomy-methods.R vegsoup/R/Vegsoup-Import.R vegsoup/R/Vegsoup-Internal.R vegsoup/R/Vegsoup-OutputMethods.R vegsoup/R/Vegsoup-RasterMethods.R vegsoup/R/Vegsoup-SpatialMethods.R vegsoup/R/Vegsoup-VisualisationMethods.R vegsoup/R/Vegsoup.R vegsoup/R/VegsoupOptimstride-BaseMethods.R vegsoup/R/VegsoupOptimstride-VisualisationMethods.R vegsoup/R/VegsoupPartition-BaseMethods.R vegsoup/R/VegsoupPartition-ClassificationStabilityMethods.R vegsoup/R/VegsoupPartition-FidelityMethods.R vegsoup/R/VegsoupPartition-OutputMethods.R vegsoup/R/VegsoupPartition-OutputMethodsMore.R vegsoup/R/VegsoupPartition-VisualisationMethods.R vegsoup/R/VegsoupPartition.R vegsoup/R/VegsoupPartitionFidelity-BaseMethods.R vegsoup/R/ZZZ.R vegsoup/R/accuracy.R vegsoup/R/as.coenocline.Vegsoup.R vegsoup/R/as.data.frame.R vegsoup/R/as.dendrogram.R vegsoup/R/as.dist.R vegsoup/R/as.matrix.R vegsoup/R/average.R vegsoup/R/bind.R vegsoup/R/castFooter.R vegsoup/R/coenoflex.R vegsoup/R/coerce.R vegsoup/R/coldiss.R vegsoup/R/combine.R vegsoup/R/compress.R vegsoup/R/confusion.R vegsoup/R/constancy.R vegsoup/R/contingency.R vegsoup/R/decostand.R vegsoup/R/dim.R vegsoup/R/disdiam.R vegsoup/R/elevation.R vegsoup/R/ellipsoidhull.R vegsoup/R/extract.R vegsoup/R/fidelity.R vegsoup/R/fisher.test.R vegsoup/R/fivenum.R vegsoup/R/googletiles.R vegsoup/R/grouping.R vegsoup/R/identical.R vegsoup/R/indpower.R vegsoup/R/indspc.R vegsoup/R/instantsoup.R vegsoup/R/intersect.R vegsoup/R/isamic.R vegsoup/R/isolate.R vegsoup/R/layers.R vegsoup/R/misc.R vegsoup/R/murdoch.R vegsoup/R/names.R vegsoup/R/optimize.R vegsoup/R/outlier.R vegsoup/R/over.R vegsoup/R/partition.R vegsoup/R/plainsoup.R vegsoup/R/plot.R vegsoup/R/quantile.R vegsoup/R/quicklook.R vegsoup/R/read.XML.R vegsoup/R/read.verbatim.R vegsoup/R/rectangles.R vegsoup/R/reorder.R vegsoup/R/reshape.R vegsoup/R/reverseGeocode.R vegsoup/R/richness.R vegsoup/R/rowSums.R vegsoup/R/sample.R vegsoup/R/seriation.R vegsoup/R/shared.R vegsoup/R/show.R vegsoup/R/silhouette.R vegsoup/R/sites.R vegsoup/R/species.R vegsoup/R/spread.R vegsoup/R/stable.R vegsoup/R/stack.coordinates.R vegsoup/R/stack.sites.R vegsoup/R/stack.species.R vegsoup/R/stride.R vegsoup/R/table.R vegsoup/R/taxon.R vegsoup/R/taxonomy.R vegsoup/R/templates.R vegsoup/R/typical.R vegsoup/R/validate.R vegsoup/R/vegdist.R vegsoup/R/verbatim.R vegsoup/R/write.verbatim.R
vegsoup/build
vegsoup/build/vignette.rds
vegsoup/data
vegsoup/data/barmstein.rda
vegsoup/data/berchtesgaden.rda
vegsoup/data/windsfeld.rda
vegsoup/inst
vegsoup/inst/doc
vegsoup/inst/doc/vegsoup.R
vegsoup/inst/doc/vegsoup.Rnw
vegsoup/inst/doc/vegsoup.pdf
vegsoup/inst/extdata
vegsoup/inst/extdata/Erschbamer1992Tab4.txt
vegsoup/inst/extdata/Erschbamer1992Tab4Locations.txt
vegsoup/inst/extdata/Erschbamer1992Tab4Tablefooter.txt
vegsoup/inst/extdata/Erschbamer1992Taxonomy.txt
vegsoup/inst/extdata/template.tex
vegsoup/inst/extdata/turboveg.xml
vegsoup/man
vegsoup/man/BraunBlanquetReduce.Rd vegsoup/man/Coverscale-class.Rd vegsoup/man/Indpower.Rd vegsoup/man/Indspc.Rd vegsoup/man/Isamic.Rd vegsoup/man/KML.Rd vegsoup/man/Latex.Rd vegsoup/man/OptimStride.Rd vegsoup/man/Partitioning.Rd vegsoup/man/SigFidelity.Rd vegsoup/man/Sites-class.Rd vegsoup/man/Species-class.Rd vegsoup/man/SpeciesTaxonomy-class.Rd vegsoup/man/SpeciesTaxonomy.Rd vegsoup/man/Taxonomy-class.Rd vegsoup/man/Vegsoup-class.Rd vegsoup/man/Vegsoup.Rd vegsoup/man/VegsoupOptimstride-class.Rd vegsoup/man/VegsoupPartition-class.Rd vegsoup/man/VegsoupPartition.Rd vegsoup/man/VegsoupPartitionFidelity-class.Rd vegsoup/man/abbr.Rd vegsoup/man/accuracy.Rd vegsoup/man/apriori.Rd vegsoup/man/as.data.frame.Rd vegsoup/man/as.data.list.Rd vegsoup/man/as.dendrogram.Rd vegsoup/man/as.matrix.Rd vegsoup/man/barmstein.Rd vegsoup/man/berchtesgaden.Rd vegsoup/man/bind.Rd vegsoup/man/coerce.Rd vegsoup/man/colSums.Rd vegsoup/man/coldiss.Rd vegsoup/man/combine.Rd vegsoup/man/compress.Rd vegsoup/man/confusion.Rd vegsoup/man/coverscale.Rd vegsoup/man/decostand.Rd vegsoup/man/dim.Rd vegsoup/man/elevation.Rd vegsoup/man/extract.Rd vegsoup/man/fidelity.Rd vegsoup/man/fill.Rd vegsoup/man/googletiles.Rd vegsoup/man/head.Rd vegsoup/man/hist.Rd vegsoup/man/identical.Rd vegsoup/man/intersect.Rd vegsoup/man/isolate.Rd vegsoup/man/layer.Rd vegsoup/man/layers.Rd vegsoup/man/map.Rd vegsoup/man/misc.Rd vegsoup/man/multipatt.Rd vegsoup/man/murdoch.Rd vegsoup/man/names.Rd vegsoup/man/nndist.Rd vegsoup/man/optimize.Rd vegsoup/man/outlier.Rd vegsoup/man/plot.Rd vegsoup/man/plotPCO.Rd vegsoup/man/quantile.Rd vegsoup/man/raster.Rd vegsoup/man/read.XML.Rd vegsoup/man/rectangles.Rd vegsoup/man/reshape.Rd vegsoup/man/reverseGeocode.Rd vegsoup/man/richness.Rd vegsoup/man/sample.Rd vegsoup/man/seriation.Rd vegsoup/man/shared.Rd vegsoup/man/sites.Rd vegsoup/man/spatial.Rd vegsoup/man/species.Rd vegsoup/man/splitAbbr.Rd vegsoup/man/spread.Rd vegsoup/man/stable.Rd vegsoup/man/stack.Rd vegsoup/man/summary-methods.Rd vegsoup/man/tables.Rd vegsoup/man/taxalist.Rd vegsoup/man/taxon.Rd vegsoup/man/templates.Rd vegsoup/man/typical.Rd vegsoup/man/validate.Rd vegsoup/man/vegdist.Rd vegsoup/man/vegsoup-package.Rd vegsoup/man/verbatim.Rd vegsoup/man/windsfeld.Rd
vegsoup/tests
vegsoup/tests/base.R
vegsoup/tests/plot.R
vegsoup/tests/profile.R
vegsoup/tests/vegdata.R
vegsoup/vignettes
vegsoup/vignettes/vegsoup.Rnw
vegsoup/vignettes/vegsoup.bib

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