Hello, for the function envfit in package vegan, the manual suggests that "The function fits environmental vectors or factors onto an ordination" but since there are scores for both sites and species, does envfit correlate the environmental factors to the sites or to the species NMDS scores? Or to both, at the same time? Or am I missing something? thanks for any input on this! adrien
NMDS and envfit
2 messages · adrien, Gavin Simpson
On Wed, 2013-05-15 at 14:42 +0300, adrien wrote:
Hello, for the function envfit in package vegan, the manual suggests that "The function fits environmental vectors or factors onto an ordination" but since there are scores for both sites and species, does envfit correlate the environmental factors to the sites or to the species NMDS scores? Or to both, at the same time? Or am I missing something?
There are really only site scores in nMDS, and anyway, all versions of envfit would work on the site scores. So only the chosen axis scores are used in the envfit process. As for the species scores; metaMDS adds these as a convenience feature if the species data is available to it. They are added as a weighted average of the site scores and then possibly expanded. G
thanks for any input on this! adrien
Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology [f] +1 306 337 2410 Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada