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rmatrixdistance
Catherine
Catherine

Reputation: 5417

How to use R to compute Tanimoto/Jacquard Score as distance matrix

I would like to calculate the distance matrix of the rows in an array in R using Tanimoto/Jacquard Score as distance matrix.

Is it possible to be done? If yes, could you mind to teach me how to do it?

Upvotes: 4

Views: 12476

Answers (2)

Roman Luštrik
Roman Luštrik

Reputation: 70643

vegan package has a vegdist function that can calculate, among other things, the Jaccard index. Assuming that's what you're after. It's use is pretty straightforward.

library(vegan)
data(varespec)
vare.dist <- vegdist(varespec, method = "jaccard")

Other available methods are 

method   Dissimilarity index, partial match to "manhattan", "euclidean",
 "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita",
 "horn", "mountford", "raup" , "binomial" or "chao"

Upvotes: 10

Ben Bolker
Ben Bolker

Reputation: 226192

I think you're going to have a lot more luck searching for "Jaccard" rather than "Jacquard".

  • Install the 'sos' package (install.packages("sos"))
  • Search for functions with these strings (library(sos); findFn("tanimoto jaccard")).
  • Poke through the results for something suitable (it looks to me like this is probably your best option; install.packages("ade4"); library("ade4"); ?dist.binary)
  • If you can't figure out how to use it, edit your question, giving a small reproducible example of what you want to do.

Upvotes: 7

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