search for: monomds

...cepin.f -o cepin.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c data2hill.c -o data2hill.o gfortran -g -O2 -pipe -c decorana.f -o decorana.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c goffactor.c -o goffactor.o gfortran -g -O2 -pipe -c monoMDS.f -o monoMDS.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c nestedness.c -o nestedness.o gfortran -g -O2 -pipe -c ordering.f -o ordering.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c pnpoly.c -o pnpoly.o gcc -I/usr/lib/R/include -DNDEBUG...

...t at the same time? If I have 100 iterations for metaMDS, then when I plot the result, does it give me result from best solution? How do I know that. Can you plot the Stress by Iteration number? parth.mds <- metaMDS(WorldPRSenv, distance = "bray", k = 2, trymax = 100, engine = c("monoMDS", "isoMDS"), autotransform =TRUE, wascores = TRUE, expand = TRUE, trace = 2) plot(parth.mds, type = "p") Thanks in advance, Kumar -- Section of Integrative Biology University of Texas at Austin Austin, Texas 78712, USA [[alternative HTML version deleted]]

Are you missing values coded as missing values? That is, are they NA? Such NA-values should be handled by vegan::monoMDS. Naturally, it can be possible that your data set cannot be meaningfully analysed if you have too many missing values or missing values are grouped in peculiar ways. Zero-values are not missing values, but they indicate 0-difference (= identical observations). The missing values must be coded as NA...

Dear All, I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I?m trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very much

...on at tamu.edu> Sent: 17 April 2018 21:13 To: Jessie Woodbridge <jessie.woodbridge at plymouth.ac.uk>; r-help at r-project.org Subject: RE: nMDS with R: missing values I think you will have to provide some more information. What function/package are you using for nMDS (eg. isoMDS in MASS, monoMDS in vegan)? What function/package are you using to compute your distance/dissimilarities (eg. dist in stats, vegdist in vegan)? Zero represents absence. It is not a missing value, so that part of your question is not clear. The dist() function computes distance ignoring missing values if they are...