User Tools

Site Tools


en:forward_sel_examples

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
en:forward_sel_examples [2019/04/06 08:43]
David Zelený [Example 2: CCA with forward selection on data from Carpathian wetlands]
en:forward_sel_examples [2019/04/06 08:46] (current)
David Zelený [Example 2: CCA with forward selection on data from Carpathian wetlands]
Line 628: Line 628:
 </​file>​ </​file>​
  
-The first five variables (Ca, conductivity,​ Si, NH3 and NO3) are the same as in tb-RDA analysis above, the last two differ. If we increase the number of permutations to 49,000 (to reduce the lowest P-value we can obtain - but this takes quite some time!) and adjust the P-values with Holm's correction for multiple testing issue, only the first four variables will be selected (compared to the first five in the case of tb-RDA):+The first five variables (Ca, conductivity,​ Si, NH3 and NO3) are the same as in tb-RDA analysis above, the last two differ. If we increase the number of permutations to 49,999 (to reduce the lowest P-value we can obtain - but this takes quite some time!) and adjust the P-values with Holm's correction for multiple testing issue, only the first four variables will be selected (compared to the first five in the case of tb-RDA):
 <code rsplus> <code rsplus>
 sel.osR2.cca <- ordiR2step (cca.0, scope = formula (cca.all), direction = '​forward',​ R2scope = adjRsq.cca, permutations = 49999, trace = F) sel.osR2.cca <- ordiR2step (cca.0, scope = formula (cca.all), direction = '​forward',​ R2scope = adjRsq.cca, permutations = 49999, trace = F)
Line 648: Line 648:
 </​file>​ </​file>​
  
-You may have noticed that the use of ''​ordiR2step''​ function with CCA takes considerably longer than when applied on RDA (or tb-RDA as above). This is because in the case of CCA, [[en:​expl_var#​adjusted_r2|adjusted R2 needs to be calculated using the permutation method]] introduced by [[en:​references|Peres-Neto et al. (2006)]], while in the case of RDA the adjusted R<​sup>​2</​sup>​ can be calculated analytically by Ezekiel'​s formula. This also means that the resulting adjusted R<​sup>​2</​sup>​ values will slightly change between calculations.+You may have noticed that the use of ''​ordiR2step''​ function with CCA takes considerably longer than when applied on RDA (or tb-RDA as above). This is because in the case of CCA, [[en:​expl_var#​adjusted_r2|adjusted R2 needs to be calculated using the permutation method]] introduced by [[en:​references|Peres-Neto et al. (2006)]], while in the case of RDA the adjusted R<​sup>​2</​sup>​ can be calculated analytically by Ezekiel'​s formula. This also means that the resulting adjusted R<​sup>​2</​sup>​ values will slightly change between calculations, because the adjusted value calculation is using mean of R2 explained by randomized environmental variables (by default 1000 randomizations is used; this number can be increased by including the argument ''​R2permutations''​ in the ''​ordiR2step''​ function with higher number).
  
  
  
  
en/forward_sel_examples.txt · Last modified: 2019/04/06 08:46 by David Zelený