anosim, mrpp and adonis
Roman,
On 17/12/2009 18:29, "Roman Lu?trik" <roman.lustrik at gmail.com> wrote:
I'm trying to see if samples within and between locations differ (in case they don't, I will have an argument to join subsamples into one). I have tried ANOSIM and mrpp. anosim.result <- with(environmental.sub, anosim(community.sub.dist, station)) #station is used as "strata" mrpp.result <- with(environmental.sub, mrpp(community.sub.dist, station))#ditto
My question would be, in what way can I see between and within differences in mrpp (can I plot this?)
Not directly in mrpp(), but you can use meandist() which is documented together with the mrpp() and has a plot method (in vegan 1.15-4 at CRAN and vegan devel). The meandist() function is just another formulation of mrpp (or vice versa).
and how would a similar method be done in adonis() (both ANOSIM and mrpp help files link to adonis as a more appropriate method)? I have tried as displayed below, but clearly this is not the solution (or am I missing something?). Can anyone advise on how to improve it to match what I'm trying to achieve with ANOSIM/mrpp? 1> adonis.result <- adonis(community.sub.dist ~., data=environmental.sub, strata=environmental.sub$station, permutations=999) 1> adonis.result
If you want to fit a similar model as with mrpp and anosim above, you should use adonis(community.sub.dist ~ station, data = environmental.sub) Then you cannot have 'strata = station' which would stratify all permutations so that in no case would the 'station' change in fitted models and all permutations would have identical statistics (within numerical accuracy). adonis() does not have plot method, but you can use betadisper for plots. Cheers, Jari Oksanen