Okey, I understood that, and I agree with you, but that is what I got wuth 4 dimensions... The graph is great, but what about the Stress?
Call: metaMDS(comm = sqrtABCD, distance = "bray", k = 4, trymax = 100, autotransform = F) Nonmetric Multidimensional Scaling using isoMDS (MASS package) Data: sqrtABCD Distance: bray shortest Dimensions: 4 Stress: 11.68632 Two convergent solutions found after 2 tries Scaling: centring, PC rotation, halfchange scaling Species: expanded scores based on sqrtABCD I am going to try with decorana now, I would see how it work... Cheers, Gian Gian, > > This looks very much like badly degenerate solution. You shouldn't use 23 > axes in NMDS, in particular with 40 x 20 source data. In Euclidean space > that data would give you rank of 20 or you could find at maximum 20 axes in > metric scaling. In the Bray-Curtis space the situation is more complicated, > but one random data set (Poisson random variates with lambda = 3.14) gave > 25 > positive and 14 negative eigenvalues. Probably the 23 dimensions you > specify > exhaust the real part of your space even in metric scaling, and probably > (and obviously) fail miserably in nonmetric scaling. You shouldn't get > stress of that magnitude with a decent model with data like that. > > It has never occurred to me that anybody would like to have NMDS with that > high number of dimensions. Usually we want to use two, sometimes one or two > more, but that's about the limit. Do the same and set k=2 to k=4 at > maximum. > If you want to have mapping of all of your real space (i.e., ignore the > complex space), you can use metric scaling. The standard R choice is > cmdscale(). The vegan alternatives are capscale() which also can do > unconstrained metric scaling, returns information both on the real and > imaginary components of your space, and has plot and other support > functions. The low level alternative in vegan is wcmdscale() which also is > used by capscale(), but does not have any support functions (lacks even > print.wcmdscale!) > > NMDS is really intended for nonlinear mapping onto *low* number of > dimensions. > > Cheers, Jari Oksanen > > >> NMS.trial > > > > Call: > > metaMDS(comm = sqrtABCD, distance = "bray", k = 23, trymax = 100, > > autotransform = F) > > > > Nonmetric Multidimensional Scaling using isoMDS (MASS package) > > > > Data: sqrtABCD > > Distance: bray shortest > > > > Dimensions: 23 > > Stress: 0.2548688 > > Two convergent solutions found after 8 tries > > Scaling: centring, PC rotation, halfchange scaling > > Species: expanded scores based on sqrtABCD > > > > With more than 23 dimensions R gave me that result: > > > >> metaMDS(sqrtABCD, distance = "bray", k = 30, trymax = 50, > > Using step-across dissimilarities: > > Too long or NA distances: 230 out of 780 (29.5%) > > Stepping across 780 dissimilarities... > > Errore in isoMDS(dist, k = k, trace = isotrace) : > > initial configuration must be complete > > Inoltre: Warning messages: > > 1: In cmdscale(d, k) : some of the first 30 eigenvalues are < 0 > > 2: In sqrt(ev) : Si è prodotto un NaN > >> > > > > ...Is normal I got better ordination (sepatation of different samples, > that > > I know they're different) with few dimension also if the Stress is high? > > > > ... I supposed, that If we use as many dimensions as there are variables, > > then we can perfectly reproduce the observed distance matrix. Isn't it? > But, > > of course, our goal is to reduce the observed complexity of nature, that > is, > > to explain the distance matrix in terms of fewer underlying dimensions... > > So what is best at the end?? > > And also wich is the function for plotting the stress values versus the > > number of dimnsions and how to read the plot? > > I hope I was clear, thank you so much! > > Yours, > > > > G. > > > > [[alternative HTML version deleted]]
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