Theory, R functions & Examples
Section: Ordination analysis
vegan) - if the environmental data matrix in this function is not specified, the
rdafunction from package
veganperforms unconstrained ordination (PCA). To calculate tb-PCA, first pre-transform the compositional data (using
vegan, with argument
chord) and then use
plotdraws ordination diagram, but species are drawn like centroids, not like vectors (the same in function
vegan) to draw variables as vectors, or consider using function
cleanplot.pca(from Numerical Ecology with R, definition here), which is intended for drawing PCA results.
princomp- functions, which are a part of preinstalled library
plotfunction does not draw ordination diagram, but draws the barplot with eigenvalues (but you can use functions
labdsv) - another option, how to calculate pca. The library
labdsvprovides its own
plot.pcaand other (e.g.
points.pca) functions, because the results of
pcafunction are not compatible with
PCA(P. Legendre in Numerical Ecology with R) - custom build function (called
PCA.newrin the second edition), with
biplotfor ploting. You can find the definition here.
applied on the object returned by
BiodiversityR) - adds the circle of equivalent contribution onto the ordination diagram plotted by
biplot. Note that the ordination diagram needs to be stored into an object, and the name of this object needs to come in the argument
ordiplotof this function.