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en:rda_cca

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en:rda_cca [2019/02/10 09:40] David Zelený [Canonical correspondence analysis (CCA)] |
en:rda_cca [2019/02/25 20:56] David Zelený |
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- | ====== Ordination analysis ====== | + | Section: [[en: |

===== RDA, tb-RDA, CCA & db-RDA (constrained ordination) ===== | ===== RDA, tb-RDA, CCA & db-RDA (constrained ordination) ===== | ||

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Unimodal constrained ordination method, related to correspondence analysis (CA), with an algorithm derived from redundancy analysis (RDA). The algorithm of RDA is modified in the way that instead of raw species composition data, the set of regressions is done on the < | Unimodal constrained ordination method, related to correspondence analysis (CA), with an algorithm derived from redundancy analysis (RDA). The algorithm of RDA is modified in the way that instead of raw species composition data, the set of regressions is done on the < | ||

- | Note that CCA calculates **two sets of sample scores**: LC scores, and WA scores. **LC scores** are linear combinations of the columns in the environmental matrix, while **WA scores** are weighted averages of the species scores. Default plotting of ordination diagrams differ between programs; e.g. in R (library //vegan//), the samples in CCA ordination plots are using WA scores, while in CANOCO 5 they are plotted using LC scores. Use of each scoring method has its proponents and opponents. Some (e.g. ter Braak, one of two CANOCO 5 authors) that LC scores are more meaningful, since they are not influenced by species composition;The difference when plotted onto the ordination diagram is rather obvious when explanatory (environmental) variables are factors with several levels, or quantitative variables with evenly spaced values (<imgref cca-lc-wa-scores> | + | Note that CCA calculates **two sets of sample scores**: LC scores, and WA scores. **LC scores** are linear combinations of the columns in the environmental matrix, while **WA scores** are weighted averages of the species scores. Default plotting of ordination diagrams differ between programs; e.g. in R (library //vegan//), the samples in CCA ordination plots are using WA scores, while in CANOCO 5 they are plotted using LC scores. Use of each scoring method has its proponents and opponents. The difference when plotted onto the ordination diagram is rather obvious when explanatory (environmental) variables are factors with several levels, or quantitative variables with evenly spaced values (<imgref cca-lc-wa-scores> |

- | <Left column are WA scores, right LC scores. In the Figure (b), the sample scores are all hidden behind the centroids of the management factor. Note that species scores (red plus symbols) are not influenced by the choice of sample scores.> | + | <Diagrams in the left column are using WA scores, those in the right column are using LC scores. In Figure (b), the sample scores are all hidden behind the centroids of the management factor. Note that species scores (red plus symbols) are not influenced by the choice of sample scores.> |

en/rda_cca.txt · Last modified: 2020/04/16 08:35 by David Zelený