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Section: Ordination analysis

Variable selection (constrained ordination)

R functions

  • ordistep (library vegan) - forward selection function applicable with functions rda, cca or cmdscale. Comparison of variables is based on AIC criteria and P-values from Monte Carlo permutation test.
  • ordiR2step (library vegan) - similar to previous, but based on R2adj, and implements three stopping criteria: selection of variables will stop if R2adj of the selected model starts to degrees, or R2adj of global model (defined in scope is exceeded, or any remaining variable is not significant at predefined P-value. It can be used with rda, cca or capscale 1).
  • forward.sel (library adespatial) - forward selection method using rda only, and containing stopping rules from Borcard et al. 2008. Has different logic for setting of arguments than the two functions above, but basically returns the same results as ordiR2step.
ordir2step used to be limited to only rda and capscale before; recently, vegan implements the permutation method of estimating adjusted R2 for CCA (Peres-Neto et al. 2006) into the function RsquareAdj, and since that time the ordir2step function can handle also formula with cca function.
en/forward_sel_r.txt · Last modified: 2021/03/03 19:54 by David Zelený