# Functions for "Data Analysis in Vegetation Ecology"

## Documentation for package ‘dave’ version 2.0

- DESCRIPTION file.

## Help Pages

A C D E F L M N O P R S T V W

## -- A --

aoc | Analysis of concentration (AOC)
aocc | Analysis of concentration (AOC)
aocc.default | Analysis of concentration (AOC)

## -- C --

ccost | Cost function of 2 alternative classifications of rows in vegetation data
ccost.default | Cost function of 2 alternative classifications of rows in vegetation data
ccost2 | Cost function of 2 alternative classifications of rows in vegetation data
centroid | Centroids of row groups (vegetation releves)
centroid.default | Centroids of row groups (vegetation releves)

## -- D --

dave | Data Analysis in Vegetation Ecology
davesil | Modified version of silhouette plotting
davesil.default | Modified version of silhouette plotting
dircor | Directional mantel correlation
dircor.default | Directional mantel correlation
dircor2 | Directional mantel correlation
dsil | Modified version of silhouette plotting

## -- E --

EKs | Swiss forest vegetation data base 1972, site information
EKv | Swiss forest vegetation data base 1972, vegetation information

## -- F --

fitmarkov | Approximating a Markov chain
fitmarkov.default | Approximating a Markov chain
fspa | Flexible shortest path adjustment
fspa.default | Flexible shortest path adjustment
fspa2 | Flexible shortest path adjustment

## -- L --

ltim | Lippe et al. 1985 data set, yr of observation
lveg | Lippe et al. 1985 data set, vegetation data

## -- M --

matrixplot | Matrixplot of groups similarities
mtab | Structuring vegetation data tables
Mtabs | Structuring vegetation data tables
Mtabs.default | Structuring vegetation data tables
mveg | Ellenberg's 1956 meadow data
mxplot | Matrixplot of groups similarities
mxplot.default | Matrixplot of groups similarities

## -- N --

nsit | European beach forest data, site factors
nveg | European beach forest data, vegetation

## -- O --

orank | Ranking by orthogonal components (RANK)
orank.default | Ranking by orthogonal components (RANK)
orank1 | Ranking by orthogonal components (RANK)
outlier | Outlier detection
outlier.default | Outlier detection
outly | Outlier detection
overly | Overly of multivariate time series
overly.default | Overly of multivariate time series
overly2 | Overly of multivariate time series

## -- P --

pcaser | Connecting time series in ordinations
pcaser.default | Connecting time series in ordinations
pcaser2 | Connecting time series in ordinations
pcoatest | Plotting 6 variants of principal coordinates analysis
pcobiplot | Computing and plotting a biplot ordination using principal coordinates analysis
pcobiplot.default | Computing and plotting a biplot ordination using principal coordinates analysis
pcocoor | Computing and plotting a biplot ordination using principal coordinates analysis
pcovar | Plotting 6 variants of principal coordinates analysis
pcovar.default | Plotting 6 variants of principal coordinates analysis
plot.aocc | Analysis of concentration (AOC)
plot.davesil | Modified version of silhouette plotting
plot.dircor | Directional mantel correlation
plot.fitmarkov | Approximating a Markov chain
plot.fspa | Flexible shortest path adjustment
plot.Mtabs | Structuring vegetation data tables
plot.mxplot | Matrixplot of groups similarities
plot.orank | Ranking by orthogonal components (RANK)
plot.outlier | Outlier detection
plot.overly | Overly of multivariate time series
plot.pcaser | Connecting time series in ordinations
plot.pcobiplot | Computing and plotting a biplot ordination using principal coordinates analysis
plot.pcovar | Plotting 6 variants of principal coordinates analysis
plot.SNPsm | The spatial and temporal model of succession in the Swiss National Park
plot.SNPtm | The temporal model of succession in the Swiss National Park
plot.speedprof | Plotting velocity profiles of multivariate time series
plot.vvelocity | Printing ordinations of velocity and acceleration and differently transformed speed profiles
plottab | Structuring vegetation data tables
plottabl | Structuring vegetation data tables
print.ccost | Cost function of 2 alternative classifications of rows in vegetation data
print.centroid | Centroids of row groups (vegetation releves)
print.outlier | Outlier detection
print.srank | Ranking species by IndVal or F-value
psit | Time scale (yr) for Soppensee pollen data
pveg | Soppensee pollen data

## -- R --

rcentroid | Centroids of row groups (vegetation releves)
rfitmarkov | Approximating a Markov chain

## -- S --

setgroupsize | Structuring vegetation data tables
sn59sit | Time series from the Swiss National Park, 59 plots. Site data.
sn59veg | Time series from the Swiss National Park, 59 plots. Vegetation data.
sn6sit | Time series from the Swiss National Park, 6 plots. Site data.
sn6veg | Time series from the Swiss National Park, 6 plots. Vegetation data.
sn7sit | Time series from the Swiss National Park, 7 plots. Site data.
sn7veg | Time series from the Swiss National Park, 6 plots. Vegetation data.
SNPsm | The spatial and temporal model of succession in the Swiss National Park
SNPsm.default | The spatial and temporal model of succession in the Swiss National Park
SNPsm2 | The spatial and temporal model of succession in the Swiss National Park
SNPtm | The temporal model of succession in the Swiss National Park
SNPtm.default | The temporal model of succession in the Swiss National Park
SNPtm2 | The temporal model of succession in the Swiss National Park
speedprof | Plotting velocity profiles of multivariate time series
speedprof.default | Plotting velocity profiles of multivariate time series
speedprof2 | Plotting velocity profiles of multivariate time series
srank | Ranking species by IndVal or F-value
srank.default | Ranking species by IndVal or F-value
srank2 | Ranking species by IndVal or F-value
ssind | Indicator values of all species in data set "sveg"
ssit | Schlaenggli site data
sspft | Selected plant functional traits of all species in data set "sveg"
summary.Mtabs | Structuring vegetation data tables
summary.orank | Ranking by orthogonal components (RANK)
sveg | Schlaenggli vegetation data

## -- T --

tsit | Time series from the Swiss National Park, Plot Tr6. Site data.
tveg | Time series from the Swiss National Park, Plot Tr6. Vegetation data.

## -- V --

vrsit | Vraconnaz time series data, site factors and dates
vrveg | Vraconnaz time series data, vegetation
vvelocity | Printing ordinations of velocity and acceleration and differently transformed speed profiles
vvelocity.default | Printing ordinations of velocity and acceleration and differently transformed speed profiles
vvelocity2 | Printing ordinations of velocity and acceleration and differently transformed speed profiles

## -- W --

wetsit | Random sample of Swiss wetland vegetation, site information.
wetveg | Random sample of Swiss wetland vegetation, vegetation information.
ws200 | Four kilometre grid forest data of Switzerland, 200m2 plots
ws30 | Four kilometre grid forest data of Switzerland, 30m2 plots
ws500 | Four kilometre grid forest data of Switzerland, 500m2 plots
wssit | Four kilometre grid forest data of Switzerland, site information