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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

4,252

Version

2.0.5

License

GPL (>= 2)

Maintainer

Sarah Goslee

Last Published

April 7th, 2020

Functions in ecodist (2.0.5)

bump

Nine-bump spatial pattern
addord

Fit new points to an existing NMDS configuration.
ecodist-package

Dissimilarity-Based Functions for Ecological Analysis
MRM

Multiple Regression on distance Matrices
corgen

Generate correlated data
bcdist

Bray-Curtis distance
iris.nmds

Example for nmds
lower

Lower-triangular matrix
bump.pmgram

Nine-bump spatial pattern
graze

Site information and grazed vegetation data.
fixdmat

Distance matrix conversion
distance

Calculate dissimilarity/distance metrics
plot.vf

Plots fitted vectors onto an ordination diagram
residuals.mgram

Residuals of a Mantel correlogram
iris.vfrot

Example for vector fitting on rotated ordination
full

Full symmetric matrix
mantel

Mantel test
iris.fit

Example of adding to an ordination
crosstab

Data formatting
mgroup

Mantel test for groups
plot.mgram

Plot a Mantel correlogram
min.nmds

Find minimum stress configuration
mgram

Mantel correlogram
pco

Principal coordinates analysis
iris.vf

Example for vector fitting on ordination
vf

Vector fitting
cor2m

Two-matrix correlation table
nmds

Non-metric multidimensional scaling
pmgram

Partial Mantel correlogram
xmgram

Cross-Mantel correlogram
z.no

Example for pmgram
xmantel

Cross-Mantel test
xdistance

Cross-distance between two datasets.
z.z1

Example for pmgram
plot.nmds

Plot information about NMDS ordination