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.

Author
Roland Kaiser [aut, cre]
Date of publication
2016-11-07 12:50:41
Maintainer
Roland Kaiser <kardinal.eros@gmail.com>
License
GPL (>= 2)
Version
0.2-6
URLs

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
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/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/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