Theory, R functions & Examples
dist- offers just limited number of distance measures - e.g.
manhattan. The result is the distance matrix, an object of the class
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).
labdsv) - offers some other indices than
ruzicka(Růžička, quantitative analogue of Jaccard) and
roberts. For full comparison of
dsvdis, see Table 1 in the website of Dave Roberts.
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).
vegan) - allows to design virtually any distance measure using the formula for their calculation.
cluster) - offers euclidean, manhattan and gower distance.
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).