ecodist-package {ecodist}R Documentation

Dissimilarity-Based Functions for Ecological Analysis

Description

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.

Details

This package contains well-established dissimilarity-based ecological analyses, such as nmds and mantel, and experimental/research analyses such as xmantel. Helper functions such as crosstab and cor2m facilitate analysis of community data.

Because many of the analyses are time-consuming, this package includes worked examples that can be loaded using data().

Index of help topics:

MRM                     Multiple Regression on distance Matrices
addord                  Fit new points to an existing NMDS
                        configuration.
bcdist                  Bray-Curtis distance
bump                    Nine-bump spatial pattern
bump.pmgram             Nine-bump spatial pattern
cor2m                   Two-matrix correlation table
corgen                  Generate correlated data
crosstab                Data formatting
distance                Calculate dissimilarity/distance metrics
ecodist-package         Dissimilarity-Based Functions for Ecological
                        Analysis
fixdmat                 Distance matrix conversion
full                    Full symmetric matrix
graze                   Site information and grazed vegetation data.
iris.fit                Example of adding to an ordination
iris.nmds               Example for nmds
iris.vf                 Example for vector fitting on ordination
iris.vfrot              Example for vector fitting on rotated
                        ordination
lower                   Lower-triangular matrix
mantel                  Mantel test
mgram                   Mantel correlogram
mgroup                  Mantel test for groups
min.nmds                Find minimum stress configuration
nmds                    Non-metric multidimensional scaling
pco                     Principal coordinates analysis
plot.mgram              Plot a Mantel correlogram
plot.nmds               Plot information about NMDS ordination
plot.vf                 Plots fitted vectors onto an ordination diagram
pmgram                  Partial Mantel correlogram
residuals.mgram         Residuals of a Mantel correlogram
vf                      Vector fitting
xdistance               Cross-distance between two datasets.
xmantel                 Cross-Mantel test
xmgram                  Cross-Mantel correlogram
z.no                    Example for pmgram
z.z1                    Example for pmgram

Author(s)

Sarah Goslee and Dean Urban

Maintainer: Sarah Goslee <Sarah.Goslee@ars.usda.gov>


[Package ecodist version 2.0.9 Index]