R Programming/Ordination

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Overview[edit]

This page provides basic code for creating a distance matrix and running and plotting a Non-metric Multidimensional Scaling (NMDS) ordination.

Read more about Ordination on Wikipedia.

This code relies on package vegan in R by Jari Oksanen.

Data[edit]

First, import data and load required libraries:

require(MASS)
require(vegan)
data(varespec)   # species data
data(varechem)   # environmental data

Distance matrix[edit]

bray <- vegdist(varespec, method = "bray")				# calculate a distance matrix
 
# There are many distance measure options for 'dist', 
# discoverable by running '?dist'. Common distance measures include:
       # 'bray' = Bray-Curtis
       # 'canb' = Canberra
       # 'euclidean' = Euclidean

Unconstrained Ordination[edit]

Displaying dissimilarity using NMDS[edit]

NMDS analysis and plotting:

nmds <- metaMDS(varespec, k = 2, 
          distance = 'bray', autotransform = FALSE) 	# semi-black box NMDS function
 
ordiplot(nmds, type = "text")			      # Plot NMDS ordination
fit <- envfit(nmds, varechem[ ,1:4])			   # Calculates environmental vectors
fit						        # Lists vector endpoint coordinates and r-squared values
plot(fit)						   # adds environmental vectors
# a linear representation of environmental variables is not always appropiate
# we could also add a smooth surface of the variable to the plot
ordisurf(nmds, varechem$N, add = TRUE, col = "darkgreen")
nmds$stress                                             # stress value
resulting nmds plot


In the metaMDS function, k is user-defined and relates to how easily the projection fits the dataframe when contrained to k dimensions. Conventional wisdom seems to suggest that stress should not exceed 10-12%. Stress is reduced by increasing the number of dimensions. However, increasing dimensionality might decrease the "realism" of a 2-dimensional plot of the first two NMDS axes.


We can also run a nMDS with 3 dimensions, fit environmental vectors and create a dynamic graph:

nmds3d <- metaMDS(varespec, k = 3, 
  distance = 'bray', autotransform = FALSE)              # run nmds with 3 dimensions
nmds3d$stress                                            # stress drops
fit3d <- envfit(nmds3d, varechem[ ,1:4], choices = 1:3)  # fit environmental vectors to 3d space
ordirgl(nmds3d, envfit = fit3d)                          # dynamic 3D graph

Running a principle component analysis (PCA) on environmental data[edit]

chem_pca <- rda(varechem, scale = TRUE)    # Run PCA
biplot(chem_pca, scaling = 2)              # display biplot
PCA biplot

Constrained Ordination[edit]