Jaccard distance matric in Phyloseq
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Entering edit mode
16 months ago
MSRS ▴ 580

Hi, I am a little bit confused about the Jaccard distance matrix in phyloseq R package.

distance(esophagus, "jaccard", binary = TRUE) # vegdist jaccard


What is the meaning of binary = TRUE here?

It is not clear to me from the phyloseq package details.

Also, can we write: distance(esophagus, "bray", binary = TRUE)

R phyloseq • 804 views
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Entering edit mode
16 months ago

Hi,

If you specify jaccard as method, phyloseq will use the vegdist() function from the vegan R package (see source code line 237).

The argument binary = TRUE is an extra parameter, which in the function distance() from phyloseq appears represented by the three dots, i.e., .... These extra arguments will be passed to the function vegdist() (see source code line 138).

Therefore, the argument binary = TRUE according to the ?vegan::vegdist() means the following (see the link):

Perform presence/absence standardization before analysis using decostand.

António

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Great! Thank you so much.