R: Dissimilarity-Based Functions for Ecological Analysis

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 2.0.7 Index]