[R] ordination in vegan: what does downweight() do?

kelsmith kelsmith at usgs.gov
Mon Nov 7 19:24:07 CET 2011

Can anyone point me in the right direction of figuring out what downweight()
is doing?
I am using vegan to perform CCA on diatom assemblage data. I have a lot of
rare species, so I want to reduce the influence of rare species in my CCA. I
have read that some authors reduce rare species by only including species
with an abundance of at least 1% in at least one sample (other authors use
5% as a rule, but this removes at least half my species). If I code it as

cca(downweight(diatoms, fraction=5) ~ ., env)

It is clearly not removing these species entirely from analysis, as some
authors suggest. So I am wondering: what is downweight() doing exactly? I
assume it is somehow ranking the species and reducing their abundance values
based on their rank, but I'm not entirely sure and can't seem to figure out
how to look at the code (R novice here). Nor can I find a clear description
within the documentation (although I may be looking in all the wrong

So, my inclination is to remove species that are very rare (max abundance <
1%) prior to the CCA and then use the downweight function (fraction = 5?) in
my CCA (as above). This way, I can include most of my species, but overall
still reduce the impact of rare species. 

Any advice is appreciated. Thanks!

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