User Tools

Site Tools


en:tbpca_examples

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

en:tbpca_examples [2018/03/28 23:21]
David Zelený
en:tbpca_examples [2018/03/30 23:04]
Line 1: Line 1:
-====== Unconstrained ordination ====== 
-===== Transformation-based principal component analysis (tb-PCA) ===== 
- 
-[[{|width: 7em; background-color:​ white; color: navy}tbpca|Theory]] 
-[[{|width: 7em; background-color:​ white; color: navy}tbpca_R|R functions]] 
-[[{|width: 7em; background-color:​ light; color: firebrick}tbpca_examples|**Examples**]] 
-[[{|width: 7em; background-color:​ white; color: navy}tbpca_exercise|Exercise {{::​lock-icon.png?​nolink|}}]] 
- 
- 
-==== Example 1: PCA on species data transformed using Hellinger transformation ==== 
-In this example we will use vegetation data from [[en:​data:​vltava|Vltava river valley dataset]], and we will analyse them by PCA after pre-transformation by Hellinger transformation. 
- 
-<code rsplus> 
-vltava.spe <- read.delim ('​http://​www.davidzeleny.net/​anadat-r/​data-download/​vltava-spe.txt',​ row.names = 1) 
-vltava.spe.hel <- decostand (log1p (vltava.spe),​ '​hellinger'​) # the species data (percentage scale) are first log transformed,​ and then transformed using Hellinger transformation 
- 
-PCA <- rda (vltava.spe.hel) 
- 
-source ('​http://​www.davidzeleny.net/​anadat-r/​doku.php/​en:​numecolr:​cleanplot.pca?​do=export_code&​codeblock=0'​) # define the cleanplot.pca function 
-cleanplot.pca (PCA) 
-</​code>​ 
- 
-{{:​obrazky:​ordination_unc18.png?​900&​direct|}} 
- 
-These ordination diagrams do not look too helpful (you need to click to enlarge them to see more details) - but we will see [[en:​indirect_ordination_viz|later]] how to visualize the results of ordination more effectively. ​ 
- 
  
en/tbpca_examples.txt · Last modified: 2018/03/30 23:04 (external edit)