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vegan::capscale ordination in phyloseq #312

iLivius opened this Issue Mar 17, 2014 · 5 comments

2 participants

iLivius commented Mar 17, 2014

Dear Dr. McMurdie,

I’m currently into microbial community analysis and an eager user of your package. Big fan!
We just got a paper accepted in PLOS ONE (about endophyte bugs in grapevines after several treatments, classic microbial ecology study, 16S rRNA pyroseqs) but still one reviewer made mincemeat out of me since I used a CCA for constraining variables. I would like to use then a Constrained Analysis of Principal Coordinates (CAP), since I’ve already used its PCoA counterpart as an unconstrained approach early in the analysis.

I’m almost sure that the vegan::capscale ( is not wrapped into phyloseq. Can you please suggest me how should I use that function as an ordination in phyloseq?

Thank you very much in advance


@joey711 joey711 added the Feature label Mar 18, 2014
joey711 commented Mar 18, 2014

This is an feature request that I will look into. Thanks for your interest!


joey711 commented Mar 24, 2014

This won't be difficult to include. I've partially completed. I'll test it and post an example here when I post the update.

@joey711 joey711 added a commit that referenced this issue Mar 26, 2014
@joey711 1.7.24 Support for CAP. Revised `ordinate`, added `formula` argument.…
… Additional ord unit tests.



	- Added support for [Partial] Constrained Analysis of Principal
Coordinates (CAP).

		- A supported/documented option in `ordinate`, supported by

		- This solves [Issue

	- The `ordinate` function now takes an explicit `formula` argument.

		- This facilitates reliable contrained ordination calls for:

			- CAP (this commit)

			- RDA (partial redundancy analysis)

			- CCA (constrained correspondence analysis)
joey711 commented Mar 26, 2014

This is also a specific case of the broader issue I suggested for supporting further ordination result classes (indicating other PCA classes as an example) in the following:


joey711 commented Mar 27, 2014

Done. See the "CAP" option in the ordinate function after updating your phyloseq version to 1.7.24+.

Thanks for the feedback. Always helpful.


@joey711 joey711 closed this Mar 27, 2014
iLivius commented Mar 27, 2014

Just got my data tested with the brand new 1.7.24 version. The ordinate() function is more powerful than ever, working like a charm!

Thank you so much, big fan


@joey711 joey711 was assigned by iLivius Mar 27, 2014
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