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en:tbpca_examples [2018/03/28 23:20]
David Zelený created
en:tbpca_examples [2018/03/30 23:04] (current)
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 [[{|width: 7em; background-color:​ white; color: navy}tbpca|Theory]] [[{|width: 7em; background-color:​ white; color: navy}tbpca|Theory]]
 [[{|width: 7em; background-color:​ white; color: navy}tbpca_R|R functions]] [[{|width: 7em; background-color:​ white; color: navy}tbpca_R|R functions]]
-[[{|width: 7em; background-color: ​white; color: ​navy}tbpca_examples|Examples]] +[[{|width: 7em; background-color: ​light; color: ​firebrick}tbpca_examples|**Examples**]] 
-[[{|width: 7em; background-color: ​light; color: ​firebrick}tbpca_exercise|**Exercise** {{::​lock-icon.png?​nolink|}}]]+[[{|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 ('​https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​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.1522250440.txt.gz · Last modified: 2018/03/28 23:20 by David Zelený