# Analysis of community ecology data in R

David Zelený

### Others

Author: David Zelený en:pca_r

Section: Ordination analysis

## PCA & tb-PCA (linear unconstrained ordination)

### R functions

• `rda` (library `vegan`) - if the environmental data matrix in this function is not specified, the `rda` function from package `vegan` performs unconstrained ordination (PCA). To calculate tb-PCA, first pre-transform the compositional data (using `decostand` from `vegan`, with argument `method` either `hellinger` or `chord`) and then use `rda` function. Function `plot` draws ordination diagram, but species are drawn like centroids, not like vectors (the same in function `ordiplot`); use `biplot` (library `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.
• `prcomp` and `princomp`- functions, which are a part of preinstalled library `stats`. Beware: `plot` function does not draw ordination diagram, but draws the barplot with eigenvalues (but you can use functions `ordiplot` or `biplot` from `vegan` package instead).
• `pca` (library `labdsv`) - another option, how to calculate pca. The library `labdsv` provides its own `plot.pca` and other (e.g. `points.pca`) functions, because the results of `pca` function are not compatible with `ordiplot` from `vegan`.
• `PCA` (P. Legendre in Numerical Ecology with R) - custom build function (called `PCA.newr` in the second edition), with `biplot` for ploting. You can find the definition here.

applied on the object returned by `vegan`'s function `rda`.

• `ordiequilibriumcircle` (library `BiodiversityR`) - adds the circle of equivalent contribution onto the ordination diagram plotted by `vegan`'s functions `ordiplot` or `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 `ordiplot` of this function. 