search for: rstress

Among those users of Primer, stress values greater than 0.3 are interpreted as "questionable". Using both isoMDS and metaMDS (vegan package), the stress values returned are much higher using my own data and using examples provided in R Help. For example Rstress = 8.3, and the stressplot r2 = 0.99 indicating (to me) that the ordination is OK. I am guessing that the "stress" values across packages are not the same, and googling about has not returned a satisfactory answer ... thus this posting. My concern being that reporting a stress value of 8...

...e ## written by Jari Oksanen, which uses isoMDS from package MASS ## internally. ## you might want to look at metaMDSiter() in that package to do random ## starts to check you haven't converged to a sub-optimal local solution (stress <- sum((S$y - S$yf)^2) / sum(S$y^2)) ## intermediate calc (rstress <- 1 - stress) ## non-metric fit, R^2 (ralscal <- cor(S$y, S$yf)^2) ## Linear fit, R2 (stress <- sqrt(stress) * 100) ## compare with Dnmds$stress ## statistic minimised in nMDS algorithm In this example, the stress is quite low, hence quite a good fit. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~...