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en:ordiagrams_r [2019/02/05 13:13]
David Zelený
en:ordiagrams_r [2019/02/26 23:34]
David Zelený
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-====== Ordination analysis ======+Section: [[en:​ordination]]
 ===== Ordination diagrams ===== ===== Ordination diagrams =====
 [[{|width: 7em; background-color:​ white; color: navy}ordiagrams|Theory]] [[{|width: 7em; background-color:​ white; color: navy}ordiagrams|Theory]]
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 //Custom functions://​ //Custom functions://​
 +  * **''​screestick''​** ([[references|Borcard et al. 2018]], definition [[en:​numecolr|here]]) - plots the screeplot of eigenvalues and adds broken stick model and Keiser-Guttman criterion to help decide which ordination axes should be selected for interpretation.
 +  * **''​evplot''​** ([[references|Borcard et al. 2011]], definition [[en:​numecolr|here]]) - an older function doing the same thing as ''​screestick''​ function above, with differnt plotting strategy.
 +  * **''​PCAsignificance''​** (library ''​BiodiversityR''​) - calculates broken-stick model for PCA axes. Function can be 
   * **''​ordicenter''​** - adds labels to centroids of groups onto ordination diagrams. Similar to ''​ordispider''​ with argument ''​label = TRUE'',​ but does not draw spider plot. Arguments and use are analogous to ''​ordispider'' ​ and ''​ordihull''​. Definition [[en:​customized_functions:​ordicenter|here]].   * **''​ordicenter''​** - adds labels to centroids of groups onto ordination diagrams. Similar to ''​ordispider''​ with argument ''​label = TRUE'',​ but does not draw spider plot. Arguments and use are analogous to ''​ordispider'' ​ and ''​ordihull''​. Definition [[en:​customized_functions:​ordicenter|here]].
   * **''​orglhull''​** - adds 3D convexhulls wrapping groups of samples (possibly transparent). Custom function not in ''​vegan''​ or ''​vegan3d'',​ requires ''​library (geometry)''​. Definition [[en:​customized_functions:​orglhull|here]].   * **''​orglhull''​** - adds 3D convexhulls wrapping groups of samples (possibly transparent). Custom function not in ''​vegan''​ or ''​vegan3d'',​ requires ''​library (geometry)''​. Definition [[en:​customized_functions:​orglhull|here]].
en/ordiagrams_r.txt · Last modified: 2019/02/26 23:34 by David Zelený