search for: nmds

Hi, I'm using nmds command (library vegan) to analyze some fishing data. I'd like to plot not only points, but also the names of species and stations in a specified position. I used the command text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds $points),pos=3,cex=0.5) But the labels are sometimes ove...

Hello, I am using vegan to do an NMDS plot and I would like to suppress the labels for the loading vectors. Is this possible? Alternatively, how can I avoid overlap? Many thanks for the help. Example code: #perform NMDS using metaMDS() function spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS", au...

...g with the similarity matrix below and I would like to plot a two-dimensional MDS solution such as each point in the plot has a label. This is what I did: data <- read.table('c:/multivariate/mds/colour.txt',header=FALSE) similarity <- as.dist(data) distance <- 1-similarity result.nmds <- nmds(distance) plot(result.nmds) (nmds and plot.nmds as defined at labdsv.nr.usu.edu/splus_R/lab8/lab8.html; nmds simply calls isoMDS) Colour.txt, containing the similaity matrix, reads as follows: 1.0 .86 .42 .42 .18 .06 .07 .04 .02 .07 .09 .12 .13 .16 .86 1.0 .50 .44 .22 .09 .07 .07 .0...

Hi, I am looking for the best multidimensional configuration for my data (47*47 distance matrix). I ve tried classical metric (cmdscale) and non metric MDS (isoMDS, nmds) but it is now difficult to choose the best solution because of the uncertainties in the definitions of the "stress" function. So, same problem, several questions : 1. Statistical consideration : With "cmdscale" we get eigen values. What is the best way to choose optimal dimen...

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 ve...

Hello R experts, I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were i...

...00. If a locality did not have certain millennia represented you would just leave them out. David C -----Original Message----- From: Jessie Woodbridge <jessie.woodbridge at plymouth.ac.uk> Sent: Wednesday, April 18, 2018 3:42 AM To: David L Carlson <dcarlson at tamu.edu> Subject: RE: nMDS with R: missing values Dear Prof Carlson, Thank you for your reply. I'm using 'vegan' with 'vegdist' and 'bray'. I have a selection of datasets that cover different time periods (converted to z-scores), so a record that starts 5000 years ago would have missing data bef...

Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a l...

Dear List, This is Elaine, a postgraduate studying in bird distributions in East Asia. I want to calculate Simpson dissimilarity index, based on a presence/absence matrix of bird species in islands in East Asia. (matrix row: 36 islands/matrix column: species ID) (R package vegan to make NMDS and R package betapart) In most papers using vegan for NMDS and betapart for dissimilarity index, the dissimilarity index is generated by grid data in continents. The calculation of this index is done by comparing species presence/absence between a pair of grids adjacent to each other. Howe...

...ed it. Once I split them I can create unique graphical parameters for each to display within the plot; I know how to alter graphics and how to plot sites alone in the graphical output. Anyone know how to split these out? -- View this message in context: http://n4.nabble.com/How-to-split-data-for-NMDS-plots-tp1751101p1751101.html Sent from the R help mailing list archive at Nabble.com.

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16 different species (OTUs). Firstly I want to make a nmds plot and see ho...

hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti

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 yo...

Hi, I am currently working on some data and feel that NMDS would return an excellent result. With my current data set however I have been experiencing some problems and cannot carry out metaMDS. I have tried with a few smaller data sets which I created for practice sake and this has worked fine. I think it is the set up of my data set that is causing me...

...function over an ordination of floristic data. The problem is that every time that I run it changes the results. Sometimes dramatically, selecting variables that the first time were not significant. I do not get what could be the problem or if is normal given the permutations are different. # the NMDS ordination gap_flor_NMDS_chord <- metaMDS(gaps_flor, distance = "euclid", k = 2, trymax = 20, autotransform =TRUE, noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1, plot = FALSE, old.wa = FALSE, zerodist = "add") # the environmental variables to use with enfit exp...

Hi, I am stuck in one problem when doing nonmetric multidimensional scaling. I use the function 'metaMDS' in the package 'vegan' to work on the presence/absence community data. The problem is when two samples are identical (dissimilarity = 0), metaMDS cannot work with zero dissimilarity. I don't want to delete the duplicates as they are true samples from different locations.

I am trying to plot an nMDS plot using ggplot2. My rownames are coded so that they can be broken down by Site, Species, Treatment, or Replicate based on unique separators. There are no column headers. I am having trouble coding ggplot2 to plot by Site -or- Species -or- Treatment and NOT by all unique row names. This is pr...

Hi, I have used Vegan to construct an NMDS ordination plot. I plotted sites of three forest types with the site number in it. My reviewer has asked me to use different symbols for each of the forest types. Can anyone send me how I can do this in R in simple steps. I have used the options like ordiplot, sel and pl syntaxes that are not worki...

Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0...

Hello, I can draw a basic stress plot for NMDS with the following code in package Vegan. > stressplot(parth.mds, parth.dis) When I try to specify the line and point types, it gives me error message. > stressplot(parth.mds, parth.dis, pch=1, p.col="gray", lwd=2, l.col="red") Error in plot.xy(xy, type, ...) : invalid pl...