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ecodist R package

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

CHANGES in ecodist 2.0

  • fixed bug in crosstab() that affected expansion of single-row or -column tables using allrows or allcols; changed result to data frame
  • added icov argument to distance() for use with Mahalanobis distance
  • changed stress calculation in nmds() to match vegan and MASS calculations; formerly was a similar method that was monotonically related, but not identical.
  • added plot.nmds to display stress and r2 for NMDS ordinations across a range of dimensions
  • added addord method to add new data to an existing NMDS ordination.
  • added clusterlevel to calculate Mantel tests for specified groupings
  • added logistic regression to MRM
  • added xdistance cross-distance function, and cross-dissimilarity analysis functions xmantel, xmgram
  • updated examples in help files to be more helpful
  • added a vignette listing dissimilarity-based analyses

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Version

Install

install.packages('ecodist')

Monthly Downloads

4,742

Version

2.0.9

License

GPL (>= 2)

Maintainer

Sarah Goslee

Last Published

May 5th, 2022

Functions in ecodist (2.0.9)

plot.mgram

Plot a Mantel correlogram
plot.nmds

Plot information about NMDS ordination
iris.vfrot

Example for vector fitting on rotated ordination
corgen

Generate correlated data
nmds

Non-metric multidimensional scaling
pco

Principal coordinates analysis
crosstab

Data formatting
plot.vf

Plots fitted vectors onto an ordination diagram
lower

Lower-triangular matrix
mantel

Mantel test
mgram

Mantel correlogram
MRM

Multiple Regression on distance Matrices
xmantel

Cross-Mantel test
addord

Fit new points to an existing NMDS configuration.
iris.fit

Example of adding to an ordination
bump

Nine-bump spatial pattern
graze

Site information and grazed vegetation data.
xdistance

Cross-distance between two datasets.
xmgram

Cross-Mantel correlogram
pmgram

Partial Mantel correlogram
z.no

Example for pmgram
mgroup

Mantel test for groups
fixdmat

Distance matrix conversion
min.nmds

Find minimum stress configuration
residuals.mgram

Residuals of a Mantel correlogram
z.z1

Example for pmgram
vf

Vector fitting
full

Full symmetric matrix
bump.pmgram

Nine-bump spatial pattern
bcdist

Bray-Curtis distance
cor2m

Two-matrix correlation table
distance

Calculate dissimilarity/distance metrics
iris.vf

Example for vector fitting on ordination
iris.nmds

Example for nmds
ecodist-package

Dissimilarity-Based Functions for Ecological Analysis