David Zelený

en:ordiagrams_r

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 en:ordiagrams_r [2019/02/05 13:13]David Zelený en:ordiagrams_r [2019/02/26 23:34]David Zelený Both sides previous revision Previous revision 2019/02/26 23:34 David Zelený 2019/02/21 18:04 David Zelený [R functions] 2019/02/06 17:05 David Zelený [R functions] 2019/02/05 13:13 David Zelený 2019/01/26 19:48 David Zelený 2018/04/14 18:01 David Zelený 2018/04/14 17:59 David Zelený [R functions] 2017/10/11 20:36 external edit2017/04/10 23:38 David Zelený [R functions] 2017/02/16 21:19 David Zelený created Next revision Previous revision 2019/02/26 23:34 David Zelený 2019/02/21 18:04 David Zelený [R functions] 2019/02/06 17:05 David Zelený [R functions] 2019/02/05 13:13 David Zelený 2019/01/26 19:48 David Zelený 2018/04/14 18:01 David Zelený 2018/04/14 17:59 David Zelený [R functions] 2017/10/11 20:36 external edit2017/04/10 23:38 David Zelený [R functions] 2017/02/16 21:19 David Zelený created Line 1: Line 1: - ====== 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]] Line 27: Line 27: //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]].