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en:similarity_r [2018/03/22 08:48]
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).
   * **''​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