Analysis of community ecology data in R

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Section: [[en:ordination]]
===== PCA & tb-PCA (linear unconstrained ordination) =====
 
[[{|width: 7em; background-color: white; color: navy}pca|Theory]]
[[{|width: 7em; background-color: light; color: firebrick}pca_R|**R functions**]]
[[{|width: 7em; background-color: white; color: navy}pca_examples|Examples]]

==== 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 [[en:numecolr|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 [[en:numecolr|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.