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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
KML | Write KML Files to Disk |
KML-method | Write KML Files to Disk |
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 |
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 |
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 |
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 |
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 |
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 |
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* |
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 |
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* |
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 |
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 |
$ | 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 |