Jaccard distance matric in Phyloseq

Question

[MSRS]

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)

Thank you for your assistance.

Answer 1

[antonioggsousa]

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.

I hope this answers your question.

António

[MSRS]

Great! Thank you so much.