search for: initmd

...0 2 0 .... 071_Dona.4 0 2 6 .... ... I want to do an isoMDS-analysis with the dissimilarity index "bray/curtis" as discribed in the help-files of the package vegan: mds.test <- isoMDS(test.bc, initMDS(test.bc), maxit=200, trace=FALSE, tol=1e-7) Then I get following error message: "Error in isoMDS(test.bc, initMDS(test.bc), maxit = 200, trace = FALSE, : zero or negative distance between objects 19 and 20" The objects 19 and 20 have the same variables in the same way and th...

...unction of the vegan package, one uses plot(procrustes_object, kind=2) to obtain a plot of the residual differences. For instance: data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7) vare.proc <- procrustes(mds.alt, mds.null) plot(vare.proc, kind=2) In the resulting plot 3 horizontal lines (1 continuous and 2 dashed) are displayed and I was wondering what they actually represent. (Perhaps mean residual +/- 95% CI ?). I would al...

Dear useRs, last week I asked you about a problem related to isoMDS. It turned out that in my case isoMDS was trapped. Nonetheless, I still have some problems with other data sets. Therefore I would like to know if anyone here has experience with how well isoMDS performs in comparison to other non-metric MDS routines, like Minissa. I have the feeling that for large data sets with a high

...nctions I am using. This example, using data and functions from the vegan package illustrates the problem. require(vegan) require(lattice) data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) ## isoMDS mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7) vare.proc <- procrustes(mds.alt, mds.null) vare.proc groups <- factor(c(rep(1,16), rep(2,8)), labels = c("grazed","ungrazed")) source("xyplot.procrustes.R") xyplot(vare.proc, y ~ x | groups, data = as.data.frame(groups), kind = 1...

...t; Building/Updating help pages for package `vegan' Formats: text html latex example decorana text html latex example decostand text html latex example diversity text html latex example initMDS text html latex example postMDS text html latex example procrustes text html latex example rankindex text html latex example varechem...