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 follows:
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 places). 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! -- View this message in context: http://r.789695.n4.nabble.com/ordination-in-vegan-what-does-downweight-do-tp4010352p4010352.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
