User Tools

Site Tools


en:pcoa_nmds_r

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
en:pcoa_nmds_r [2019/01/21 01:07]
David Zelený [R functions]
en:pcoa_nmds_r [2019/01/26 18:35]
David Zelený
Line 1: Line 1:
-====== ​Unconstrained ordination ​====== +====== ​Ordination analysis ​====== 
-===== Distance-based ordination methods (PCoA & NMDS) =====+===== PCoA & NMDS (unconstrained ordination) ===== 
 [[{|width: 7em; background-color:​ white; color: navy}pcoa_nmds|Theory]] [[{|width: 7em; background-color:​ white; color: navy}pcoa_nmds|Theory]]
 [[{|width: 7em; background-color:​ light; color: firebrick}pcoa_nmds_R|**R functions**]] [[{|width: 7em; background-color:​ light; color: firebrick}pcoa_nmds_R|**R functions**]]
Line 11: Line 12:
   * **''​wcmdscale''​** (library ''​vegan''​) - based on ''​cmdscale''​ function, but allows to weight the importance of samples in the PCoA. If arguments ''​eig = TRUE''​ or  ''​x.ret = TRUE'',​ the function returns an object of class "​wcmdscale"​ with print, plot, scores, eigenvals and stressplot methods.   * **''​wcmdscale''​** (library ''​vegan''​) - based on ''​cmdscale''​ function, but allows to weight the importance of samples in the PCoA. If arguments ''​eig = TRUE''​ or  ''​x.ret = TRUE'',​ the function returns an object of class "​wcmdscale"​ with print, plot, scores, eigenvals and stressplot methods.
   * **''​pcoa''​** (library ''​ape''​) - another way how to achieve PCoA analysis. Use ''​biplot.pcoa''​ function (or simply generic ''​biplot''​) to project ordination diagram. Does not work with ''​vegan'''​s functions ''​ordiplot''​ or ''​scores''​.   * **''​pcoa''​** (library ''​ape''​) - another way how to achieve PCoA analysis. Use ''​biplot.pcoa''​ function (or simply generic ''​biplot''​) to project ordination diagram. Does not work with ''​vegan'''​s functions ''​ordiplot''​ or ''​scores''​.
-  *   * **''​metaMDS''​** (library ''​vegan''​) - rather advanced function, composed of many subroutine steps. See example below for details.+  * **''​metaMDS''​** (library ''​vegan''​) - rather advanced function, composed of many subroutine steps. See example below for details.
   * **''​stressplot''​** (library ''​vegan''​) - draws Shepards stress plot, which is the relationship between real distances between samples in resulting //m// dimensional ordination solution, and their particular compositional dissimilarities expressed by selected dissimilarity measure.   * **''​stressplot''​** (library ''​vegan''​) - draws Shepards stress plot, which is the relationship between real distances between samples in resulting //m// dimensional ordination solution, and their particular compositional dissimilarities expressed by selected dissimilarity measure.
   * **''​goodness''​** (library ''​vegan''​) - returns goodness-of-fit of particular samples. See example how can be this result visualized (inspired by [[references|Borcard et al. 2011]]).   * **''​goodness''​** (library ''​vegan''​) - returns goodness-of-fit of particular samples. See example how can be this result visualized (inspired by [[references|Borcard et al. 2011]]).
en/pcoa_nmds_r.txt · Last modified: 2019/02/26 23:33 by David Zelený