David Zelený

en:pcoa_nmds_r

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 en:pcoa_nmds_r [2019/01/21 01:07]David Zelený [R functions] en:pcoa_nmds_r [2019/01/26 18:35]David Zelený Both sides previous revision Previous revision 2019/02/26 23:33 David Zelený 2019/01/26 18:40 David Zelený 2019/01/26 18:35 David Zelený 2019/01/21 01:07 David Zelený [R functions] 2019/01/21 01:07 David Zelený [R functions] 2019/01/21 01:04 David Zelený [Principal Coordinate Analysis (PCoA)] 2019/01/21 00:59 David Zelený [Principal Coordinate Analysis (PCoA)] 2019/01/21 00:59 David Zelený created Next revision Previous revision 2019/02/26 23:33 David Zelený 2019/01/26 18:40 David Zelený 2019/01/26 18:35 David Zelený 2019/01/21 01:07 David Zelený [R functions] 2019/01/21 01:07 David Zelený [R functions] 2019/01/21 01:04 David Zelený [Principal Coordinate Analysis (PCoA)] 2019/01/21 00:59 David Zelený [Principal Coordinate Analysis (PCoA)] 2019/01/21 00:59 David Zelený created Next revision Both sides next revision 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]]).