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en:tbpca_examples [2018/03/28 23:21]
David Zelený
en:tbpca_examples [2018/03/30 23:04]
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-====== 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) 
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-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)