[R] NMDS using Vegan
Hello R experts, I am new to Vegan and use trying to follow the tutorial to perform NMDS for my data. But after performing the metaMDS, when I plotted my results the default plot shows MDS1 vs MDS2. Thought according to the tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this difference? Accourding to tutorial it says: Function metaMDS is a wrapper to perform NMDS. Can anybody please help me to understand this? Thanks, Mitra [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] NMDS using Vegan
On Wed, 2013-05-15 at 12:06 +0800, Suparna Mitra wrote: Hello R experts, I am new to Vegan and use trying to follow the tutorial to perform NMDS for my data. But after performing the metaMDS, when I plotted my results the default plot shows MDS1 vs MDS2. Thought according to the tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this difference? Accourding to tutorial it says: Function metaMDS is a wrapper to perform NMDS. Can anybody please help me to understand this? Thanks, Mitra They are just labels and metaMDS **has** performed an NMDS. Not sure why Jari labelled these as MDSx. If this bothers you so, add your own labels: require(vegan) data(dune) sol - metaMDS(dune) plot(sol, xlab = NMDS1, ylab = NMDS2) HTH G -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental Change Society [e] gavin.simp...@uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] NMDS using Vegan
Dear Prof. Simpson, Thanks a lot for your reply. Yes I know that I can change the labels any time, but I was only worried if I am doing any mistake as default output didn't match with the output shown in the Vegan tutorial output. Thanks, Mitra On 15 May 2013 22:43, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Wed, 2013-05-15 at 12:06 +0800, Suparna Mitra wrote: Hello R experts, I am new to Vegan and use trying to follow the tutorial to perform NMDS for my data. But after performing the metaMDS, when I plotted my results the default plot shows MDS1 vs MDS2. Thought according to the tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this difference? Accourding to tutorial it says: Function metaMDS is a wrapper to perform NMDS. Can anybody please help me to understand this? Thanks, Mitra They are just labels and metaMDS **has** performed an NMDS. Not sure why Jari labelled these as MDSx. If this bothers you so, add your own labels: require(vegan) data(dune) sol - metaMDS(dune) plot(sol, xlab = NMDS1, ylab = NMDS2) HTH G -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental Change Society [e] gavin.simp...@uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
