ordination in vegan: what does downweight() do?

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).

That is not what downweight() is for. If you want this sort of
selection, see chooseTaxa() in my analogue package

diat.sel <- chooseTaxa(diatoms, max.abun = 1, type = "AND")

or, if proportions not percent

diat.sel <- chooseTaxa(diatoms, max.abun = 0.01, type = "AND")

This sort of indexing is trivial (but I made a typo in the current
version so type = "OR" won't work) so you can study the code of
analogue:::chooseTaxa.default once I fix the CRAN version or on R-Forge
now:

https://r-forge.r-project.org/scm/viewvc.php/pkg/R/chooseTaxa.R?view=markup&root=analogue

Jari has addressed the other part of your question.

Jari also mentioned the issue about whether you should be removing or
downweighting rare species. Many people, especially diatomists, do this
for practical purposes in a routine fashion because their data sets are
especially speciose and have a large proportion of low abundance taxa.
As a general matter of routine practice, I don't think this is a very
good way of working, especially as we have no good ecological grounds
for doing so and who knows what information these species could be
telling us if we just listened to them instead of discarding them.

HTH

G

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