classes and methods for phytosociology


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Documentation for package ‘vegsoup’ version 0.2-4

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A B C D E F G H I K L M N O P Q R S T V W misc

vegsoup-package An overview of the functions in this package

-- A --

abbr Get Abbreviations used to Encode Species and Layer Replicates
abbr-method Get Abbreviations used to Encode Species and Layer Replicates
abbr.layer Get Abbreviations used to Encode Species and Layer Replicates
abbr.layer-method Get Abbreviations used to Encode Species and Layer Replicates
abbr<- Get Abbreviations used to Encode Species and Layer Replicates
abbr<--method Get Abbreviations used to Encode Species and Layer Replicates
accuracy Accuracy Statistics for Objects of class VegsoupPartition
accuracy-method Accuracy Statistics for Objects of class VegsoupPartition
apriori Grouping Variable of 'Vegsoup*' Objects
apriori-method Grouping Variable of 'Vegsoup*' Objects
as-method Coerce Methods for 'Vegsoup*' objects
as.array Retrieve Species Matrix with Specified Storage Mode
as.array-method Retrieve Species Matrix with Specified Storage Mode
as.character Retrieve Species Matrix with Specified Storage Mode
as.character-method Retrieve Species Matrix with Specified Storage Mode
as.data.frame Coerce to data.frame
as.data.frame-method Coerce to data.frame
as.data.list Coercion to '"data.lists"'
as.data.list-method Coercion to '"data.lists"'
as.dendrogram Dendrograms of Partitions
as.dendrogram-method Dendrograms of Partitions
as.dist Dissimilarity Matrices from 'Vegsoup*' Objects
as.dist-method Dissimilarity Matrices from 'Vegsoup*' Objects
as.hclust Dendrograms of Partitions
as.hclust-method Dendrograms of Partitions
as.logical Retrieve Species Matrix with Specified Storage Mode
as.logical-method Retrieve Species Matrix with Specified Storage Mode
as.matrix Retrieve Species Matrix with Specified Storage Mode
as.matrix-method Retrieve Species Matrix with Specified Storage Mode
as.numeric Retrieve Species Matrix with Specified Storage Mode
as.numeric-method Retrieve Species Matrix with Specified Storage Mode
as.table Constancy and Contingency Tables
as.table-method Constancy and Contingency Tables
as.vector Retrieve Species Matrix with Specified Storage Mode
as.vector-method Retrieve Species Matrix with Specified Storage Mode
average Constancy and Contingency Tables
average-method Constancy and Contingency Tables

-- B --

barmstein Test Data Set
bbox Spatial Methods for 'Vegsoup*' Objects
bbox-method Spatial Methods for 'Vegsoup*' Objects
berchtesgaden Grassland survey in National Park Berchtesgaden
bind Combine 'Vegsoup*' objects
bind-method Sites Class
bind-method Species Class
bind-method SpeciesTaxonomy Class
bind-method Class '"Taxonomy"'
bind-method Combine 'Vegsoup*' objects
BraunBlanquetReduce Reduce 9 Point Braun-Blanquet Abundance Scale to 7 Point
BraunBlanquetReduce-method Reduce 9 Point Braun-Blanquet Abundance Scale to 7 Point

-- C --

castFooter Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files
coenoflex Create an object of class Vegsoup
coerce Coerce Methods for 'Vegsoup*' objects
coerce-method Coverscale Class
coerce-method Coerce Methods for 'Vegsoup*' objects
coldiss Plots of the Dissimilarity Matrix of an Object of class Vegsoup*
coldiss-method Plots of the Dissimilarity Matrix of an Object of class Vegsoup*
colMeans Row and Column Sums for Objects of Class VegsoupData*
colMeans-method Row and Column Sums for Objects of Class VegsoupData*
colnames Row and Column Names of 'Vegsoup*' objects
colnames-method Row and Column Names of 'Vegsoup*' objects
colSums Row and Column Sums for Objects of Class VegsoupData*
colSums-method Row and Column Sums for Objects of Class VegsoupData*
compass Utility functions
compress Compress object and retain minimal information
compress-method Compress object and retain minimal information
configure LaTex template files
confusion Confusionion Matrix for VegsoupPartition Objects
confusion-method Confusionion Matrix for VegsoupPartition Objects
constancy Constancy and Contingency Tables
constancy-method Constancy and Contingency Tables
contingency Constancy and Contingency Tables
contingency-method Constancy and Contingency Tables
coordinates Spatial Methods for 'Vegsoup*' Objects
coordinates-method Spatial Methods for 'Vegsoup*' Objects
coordinates<- Spatial Methods for 'Vegsoup*' Objects
coordinates<--method Spatial Methods for 'Vegsoup*' Objects
Coverscale Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
coverscale Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
Coverscale-class Coverscale Class
coverscale-method Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
coverscale<- Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
coverscale<--method Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects

-- D --

decostand Standardization Methods for 'Vegsoup*' objects.
decostand-method Standardization Methods for 'Vegsoup*' objects.
decostand<- Standardization Methods for 'Vegsoup*' objects.
decostand<--method Standardization Methods for 'Vegsoup*' objects.
dim Number or Rows, Columns, and Cells
dim-method Number or Rows, Columns, and Cells
dimnames Row and Column Names of 'Vegsoup*' objects
dimnames-method Species Class
dimnames-method Row and Column Names of 'Vegsoup*' objects
disdiam Partition Quality Assessment for '"VegsoupPartition"' Objects
disdiam-method Partition Quality Assessment for '"VegsoupPartition"' Objects
disdiam-methods Partition Quality Assessment for '"VegsoupPartition"' Objects
distconnected Dissimilarity Matrices from 'Vegsoup*' Objects
distconnected-method Dissimilarity Matrices from 'Vegsoup*' Objects

-- E --

elevation Query Elevation
elevation-method Query Elevation
ellipsoidhull Draw Map of Plot Locations
ellipsoidhull-method Draw Map of Plot Locations
extent Spatial Methods for 'Vegsoup*' Objects
extent-method Spatial Methods for 'Vegsoup*' Objects
Extract Indexing to Extract Values of a Vegsoup* Object
extract Extract values from Raster objects
extract-method Extract values from Raster objects

-- F --

fidelity Calculate Fidelity Values
fidelity-method Calculate Fidelity Values
fill Matrix fill of species matrix
fill-method Matrix fill of species matrix
FisherTest Calculate Fidelity Values
FisherTest-method Calculate Fidelity Values

-- G --

getK Partitioning Vector of VegsoupPartition objects
getK-method Compute a Series of Partitions/Clusterings
getK-method Partitioning Vector of VegsoupPartition objects
getStat Calculate Fidelity Values
getStat-method Calculate Fidelity Values

-- H --

hcr Random Samples and Permutations for 'Vegsoup*' Objects
hcr-method Random Samples and Permutations for 'Vegsoup*' Objects
head Return the First or Last Part of the Species Matrix
head-method Return the First or Last Part of the Species Matrix
header Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files
hist Plot Histogram of Fidelity Values
hist-method Plot Histogram of Fidelity Values

-- I --

identical Intersect plot names
identical-method Intersect plot names
indices Retrieve Species Matrix with Specified Storage Mode
indices-method Retrieve Species Matrix with Specified Storage Mode
Indpower Indicator Power of Species
Indpower-method Indicator Power of Species
Indspc Compositional Indicator Species Analysis
Indspc-method Compositional Indicator Species Analysis
Indval Calculate Fidelity Values
Indval-method Calculate Fidelity Values
instantsoup Create an object of class Vegsoup
intersect Intersect plot names
intersect-method Intersect plot names
is.continuous Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
is.continuous-method Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
is.occurence Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
is.occurence-method Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
is.ordinal Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
is.ordinal-method Set or Retrieve an Abundance Scale for 'Vegsoup*' Objects
isamic Indicator Species Analysis to Minimize Intermediate Constancy
isamic-method Indicator Species Analysis to Minimize Intermediate Constancy
isamic-methods Indicator Species Analysis to Minimize Intermediate Constancy

-- K --

KML Write KML Files to Disk
KML-method Write KML Files to Disk

-- L --

Latex Typesetting Tables in LaTeX
Latex-method Typesetting Tables in LaTeX
latlng2tile Geocoding Using Tile Map Service Protocol
layer Return Stratum/Layer
layer-method Return Stratum/Layer
layers Get or Modify Layers
layers-method Get or Modify Layers
layers<- Get or Modify Layers
layers<--method Get or Modify Layers

-- M --

map Draw Map of Plot Locations
map-method Draw Map of Plot Locations
method Compute a Series of Partitions/Clusterings
method-method Compute a Series of Partitions/Clusterings
Multipatt-method Methods for Function Multipatt
Multipatt-methods Methods for Function Multipatt
murdoch Indicator Species Analysis by Murdoch Preference Function
murdoch-method Indicator Species Analysis by Murdoch Preference Function
murdoch-methods Indicator Species Analysis by Murdoch Preference Function

-- N --

names Row and Column Names of 'Vegsoup*' objects
names-method Row and Column Names of 'Vegsoup*' objects
names<- Row and Column Names of 'Vegsoup*' objects
names<--method Row and Column Names of 'Vegsoup*' objects
ncell Number or Rows, Columns, and Cells
ncell-method Number or Rows, Columns, and Cells
ncol Number or Rows, Columns, and Cells
ncol-method Number or Rows, Columns, and Cells
nndist Nearest Neighbor Distances
nndist-method Nearest Neighbor Distances
nrow Number or Rows, Columns, and Cells
nrow-method Sites Class
nrow-method Species Class
nrow-method Class '"Taxonomy"'
nrow-method Number or Rows, Columns, and Cells

-- O --

optimclass1 Compute a Series of Partitions/Clusterings
optimclass1-method Compute a Series of Partitions/Clusterings
optimclass2 Compute a Series of Partitions/Clusterings
optimclass2-method Compute a Series of Partitions/Clusterings
OptimStride Compute a Series of Partitions/Clusterings
optindval Optimize Partitioning
optindval-method Optimize Partitioning
optindval-methods Optimize Partitioning
optsil Optimize Partitioning
optsil-method Optimize Partitioning
optsil-methods Optimize Partitioning
outlier Outlier Detection
outlier-method Outlier Detection
over Spatial Methods for 'Vegsoup*' Objects
over-method Spatial Methods for 'Vegsoup*' Objects

-- P --

partana Partition Quality Assessment for '"VegsoupPartition"' Objects
partana-method Partition Quality Assessment for '"VegsoupPartition"' Objects
partana-methods Partition Quality Assessment for '"VegsoupPartition"' Objects
partition Indexing to Extract Values of a Vegsoup* Object
partition-method Indexing to Extract Values of a Vegsoup* Object
partitioning Partitioning Vector of VegsoupPartition objects
partitioning-method Partitioning Vector of VegsoupPartition objects
partitioningCombinations Partitioning Vector of VegsoupPartition objects
partitioningCombinations-method Partitioning Vector of VegsoupPartition objects
partitioningMatrix Partitioning Vector of VegsoupPartition objects
partitioningMatrix-method Partitioning Vector of VegsoupPartition objects
peaks Compute a Series of Partitions/Clusterings
peaks-method Compute a Series of Partitions/Clusterings
Phi Calculate Fidelity Values
Phi-method Calculate Fidelity Values
plainsoup Create an object of class Vegsoup
plot-method Plotting methods
plot-methods Plotting methods
plotPCO Plot Principal Coordinates
preamble LaTex template files
proj4string Spatial Methods for 'Vegsoup*' Objects
proj4string-method Spatial Methods for 'Vegsoup*' Objects
proj4string<- Spatial Methods for 'Vegsoup*' Objects
proj4string<--method Spatial Methods for 'Vegsoup*' Objects

-- Q --

quantile Sample Quantiles for a Community Matrix
quantile-method Sample Quantiles for a Community Matrix
quicklook Draw Map of Plot Locations
quicklook-method Draw Map of Plot Locations

-- R --

read.verbatim Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files
read.verbatim.append Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files
read.XML Read From TurboVeg XML Files
rectangles Plot Matrix Dimensions
rectangles-method Plot Matrix Dimensions
relevee Return Species List for an 'Vegsoup*' object
relevee-method Return Species List for an 'Vegsoup*' object
relevee-methods Return Species List for an 'Vegsoup*' object
reorder Dendrograms of Partitions
reorder-method Dendrograms of Partitions
reshapeSpecies Reshape Species Matrix
reverseGeocode Reverse geocoding
reverseGeocode-method Reverse geocoding
richness Species Richness
richness-method Species Richness
row.names Row and Column Names of 'Vegsoup*' objects
row.names-method Row and Column Names of 'Vegsoup*' objects
row.names<- Row and Column Names of 'Vegsoup*' objects
row.names<--method Row and Column Names of 'Vegsoup*' objects
rowMeans Row and Column Sums for Objects of Class VegsoupData*
rowMeans-method Row and Column Sums for Objects of Class VegsoupData*
rownames Row and Column Names of 'Vegsoup*' objects
rownames-method Row and Column Names of 'Vegsoup*' objects
rownames<- Row and Column Names of 'Vegsoup*' objects
rownames<--method Row and Column Names of 'Vegsoup*' objects
rowSums Row and Column Sums for Objects of Class VegsoupData*
rowSums-method Row and Column Sums for Objects of Class VegsoupData*

-- S --

sample Random Samples and Permutations for 'Vegsoup*' Objects
sample-method Random Samples and Permutations for 'Vegsoup*' Objects
seriation Reorder as to Reflect a Vegetation Table
seriation-method Reorder as to Reflect a Vegetation Table
shapeSpecies Reshape Species Matrix
shared Shared Species
shared-method Shared Species
SigFidelity Experimental Function
SigFidelity-method Experimental Function
silhouette Partition Quality Assessment for '"VegsoupPartition"' Objects
silhouette-method Partition Quality Assessment for '"VegsoupPartition"' Objects
sim100 Simulated Test Data
singleton Utility functions
singletons Utility functions
sites Methods for the Sites Slot of 'Vegsoup*' Objects
Sites-class Sites Class
sites-method Sites Class
sites-method Methods for the Sites Slot of 'Vegsoup*' Objects
sites<- Methods for the Sites Slot of 'Vegsoup*' Objects
sites<--method Methods for the Sites Slot of 'Vegsoup*' Objects
SpatialPointsVegsoup Spatial Methods for 'Vegsoup*' Objects
SpatialPointsVegsoup-method Spatial Methods for 'Vegsoup*' Objects
SpatialPolygonsVegsoup Spatial Methods for 'Vegsoup*' Objects
SpatialPolygonsVegsoup-method Spatial Methods for 'Vegsoup*' Objects
spc Test Data Set
species Species Class
Species-class Species Class
species-method Species Class
species-method Methods to Retrieve or Manipulate the Species Slot of 'Vegsoup*' Objects
species-method SpeciesTaxonomy Class
species<- Methods to Retrieve or Manipulate the Species Slot of 'Vegsoup*' Objects
species<--method Methods to Retrieve or Manipulate the Species Slot of 'Vegsoup*' Objects
species<--method SpeciesTaxonomy Class
SpeciesTaxonomy Compare Species Abbreviations to Taxonomic Reference List
SpeciesTaxonomy-class SpeciesTaxonomy Class
splitAbbr Deparse Species Layer Replication of 'Vegsoup*' Objects
splitAbbr-method Deparse Species Layer Replication of 'Vegsoup*' Objects
spread List Occurences of Species in Partitions
spread-method List Occurences of Species in Partitions
spread-methods List Occurences of Species in Partitions
spTransform Spatial Methods for 'Vegsoup*' Objects
spTransform-method Spatial Methods for 'Vegsoup*' Objects
stable Classification Stability
stable-method Classification Stability
stack Stack Species Matrix, Sites Data or Spatial Coordinates
stackCoordinates Stack Species Matrix, Sites Data or Spatial Coordinates
stackSites Stack Species Matrix, Sites Data or Spatial Coordinates
stackSpecies Stack Species Matrix, Sites Data or Spatial Coordinates
str2latlng Geocoding Using Tile Map Service Protocol
stride Compute a Series of Partitions/Clusterings
stride-method Compute a Series of Partitions/Clusterings
sts Test Data Set
subset Get or Subset Object by Scientific Taxon Name
subset-method Get or Subset Object by Scientific Taxon Name
summary Summary of Object
summary,VegsoupOptimstride-methods VegsoupOptimstride Class
summary-method Summary of Object
summary-methods Summary of Object

-- T --

tabdev Partition Quality Assessment for '"VegsoupPartition"' Objects
tabdev-method Partition Quality Assessment for '"VegsoupPartition"' Objects
tabdev-methods Partition Quality Assessment for '"VegsoupPartition"' Objects
tail Return the First or Last Part of the Species Matrix
tail-method Return the First or Last Part of the Species Matrix
taxalist Return Species List for an 'Vegsoup*' object
taxalist-method Return Species List for an 'Vegsoup*' object
taxalist-methods Return Species List for an 'Vegsoup*' object
taxon Get or Subset Object by Scientific Taxon Name
taxon-method Get or Subset Object by Scientific Taxon Name
taxonomy Class '"Taxonomy"'
Taxonomy-class Class '"Taxonomy"'
taxonomy-method SpeciesTaxonomy Class
taxonomy-method Class '"Taxonomy"'
taxonomy<- SpeciesTaxonomy Class
taxonomy<--method SpeciesTaxonomy Class
taxonomy<--method Class '"Taxonomy"'
template LaTex template files
threshold Compute a Series of Partitions/Clusterings
threshold-method Compute a Series of Partitions/Clusterings
tile2latlng Geocoding Using Tile Map Service Protocol
txn Test Data Set
typical Typical Samples of an Object of Class Vegsoup*
typical-method Typical Samples of an Object of Class Vegsoup*

-- V --

variable Sites Class
variable-method Sites Class
variable<- Sites Class
variable<--method Sites Class
variables Sites Class
variables-method Sites Class
vegdist Dissimilarity Matrices from 'Vegsoup*' Objects
vegdist-method Dissimilarity Matrices from 'Vegsoup*' Objects
vegdist<- Dissimilarity Matrices from 'Vegsoup*' Objects
vegdist<--method Dissimilarity Matrices from 'Vegsoup*' Objects
Vegsoup Create an object of class Vegsoup
vegsoup An overview of the functions in this package
Vegsoup-class Class Vegsoup
VegsoupOptimstride-class VegsoupOptimstride Class
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 Plain Text Files

-- W --

whatshere2lnglat Geocoding Using Tile Map Service Protocol
which.max Compute a Series of Partitions/Clusterings
which.max-method Compute a Series of Partitions/Clusterings
windsfeld Alpine Vegetation
write.verbatim Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files
write.verbatim-method Read or Write Fixed-Column-Width Community Tables From or To Plain Text Files

-- misc --

$ Row and Column Names of 'Vegsoup*' objects
$-method Sites Class
$-method Species Class
$-method SpeciesTaxonomy Class
$-method Class '"Taxonomy"'
$-method Row and Column Names of 'Vegsoup*' objects
$<- Row and Column Names of 'Vegsoup*' objects
$<--method Sites Class
$<--method Species Class
$<--method Row and Column Names of 'Vegsoup*' objects
[ Indexing to Extract Values of a Vegsoup* Object
[-method Sites Class
[-method Species Class
[-method SpeciesTaxonomy Class
[-method Class '"Taxonomy"'
[-method Indexing to Extract Values of a Vegsoup* Object