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en:similarity_r

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en:similarity_r [2019/02/05 22:58] David Zelený [R functions] |
en:similarity_r [2019/02/05 22:58] David Zelený [R functions] |
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* **''vegdist'' (library ''vegan'')** - default distance used in this function is Bray-Curtis distance, which is (in contrast to Euclidean distance) considered as more suitable for ecological data (it is a quantitative analog of Sørensen dissimilarity). | * **''vegdist'' (library ''vegan'')** - default distance used in this function is Bray-Curtis distance, which is (in contrast to Euclidean distance) considered as more suitable for ecological data (it is a quantitative analog of Sørensen dissimilarity). | ||

* **''dsvdis'' (library ''labdsv'')** - offers some other indices than ''vegdist'', e.g. ''ruzicka'' (Růžička, quantitative analogue of Jaccard) and ''roberts''. For full comparison of ''dist'', ''vegdist'' and ''dsvdis'', see [[http://ecology.msu.montana.edu/labdsv/R/labs/lab8/lab8.html|Table 1 in the website of Dave Roberts]]. | * **''dsvdis'' (library ''labdsv'')** - offers some other indices than ''vegdist'', e.g. ''ruzicka'' (Růžička, quantitative analogue of Jaccard) and ''roberts''. For full comparison of ''dist'', ''vegdist'' and ''dsvdis'', see [[http://ecology.msu.montana.edu/labdsv/R/labs/lab8/lab8.html|Table 1 in the website of Dave Roberts]]. | ||

- | * **dist.ldc** (library ''adespatial''** - includes 21 dissimilarity indiced described in Legendre & De Cáceres (2013), twelve of which are not readily available in other packages. Note that Bray-Curtis dissimilarity is called //percentage difference// (''method = "percentdiff"''). By default returns also informative message whether given dissimilarity index is Euclidean or not and whether it becomes Euclidean if square-rooted (as is the case of e.g. Bray-Curtis aka Percentage difference index). | + | * **''dist.ldc'' (library ''adespatial'')** - includes 21 dissimilarity indiced described in Legendre & De Cáceres (2013), twelve of which are not readily available in other packages. Note that Bray-Curtis dissimilarity is called //percentage difference// (''method = "percentdiff"''). By default returns also informative message whether given dissimilarity index is Euclidean or not and whether it becomes Euclidean if square-rooted (as is the case of e.g. Bray-Curtis aka Percentage difference index). |

* **''designdist'' (library ''vegan'')** - allows to design virtually any distance measure using the formula for their calculation. | * **''designdist'' (library ''vegan'')** - allows to design virtually any distance measure using the formula for their calculation. | ||

* **''daisy'' (library ''cluster'')** - offers euclidean, manhattan and gower distance. | * **''daisy'' (library ''cluster'')** - offers euclidean, manhattan and gower distance. | ||

* **''distance'' (library ''ecodist'')** - contains seven distance measures, but the function more than for practical use is for a demonstration of the script (for larger matrices, the calculation takes rather long). | * **''distance'' (library ''ecodist'')** - contains seven distance measures, but the function more than for practical use is for a demonstration of the script (for larger matrices, the calculation takes rather long). |

en/similarity_r.txt · Last modified: 2019/02/05 22:58 by David Zelený