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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] |
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| - | 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) | ||
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| </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
