search for: nmds

Displaying 20 results from an estimated 28 matches for "nmds".

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2007 Nov 14
1
label plotting on nmds diagram
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...
2011 Sep 23
1
Envfit, inconsistant result?
...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...
2018 Apr 17
2
nMDS with R: missing values
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...
2008 Apr 14
1
Vegan R^2 and tau values for metaMDS
...axes of the ordination configuration that I get with metaMDS in the vegan package is there a way to do this- is it stored in some object returned by the function that I am unaware of- or is there another function inside of vegan or elsewhere- that I can use? I have seen mention of ecodist function nmds having an R^2 would this be the place to go? -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mam...
2018 Apr 18
0
nMDS with R: missing values
...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...
2010 Apr 04
3
How to split data for NMDS plots
...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.
2010 Feb 13
2
NMDS ordination
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...
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
...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....
2011 Sep 09
2
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
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...
2008 Sep 09
2
NMDS and varimax rotation
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
2018 Apr 17
0
nMDS with R: missing values
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. Than...
2010 Jan 12
1
Non-metric multidimensional scaling (NMDS) help
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...
2010 Apr 05
4
NMDS Ordination Graphics Problem
...15 19 10 8 9 Where: 1i-3i are "infested" sites, and 1c-3c are "control sites". A-F are species found at each site. I have several of these ordinations to perform on different variables (BA, density, RIV, cover, etc..., all in different matrices). I'm running NMDS (metaMDS) ordinations on each matrices, and producing ordination graphs for each cloud of points. The problem I have is that I cannot devise a way to split the cloud of points into infested and control so that I can deduce any significant groupings. A simple difference in symbols/color (Ex. g...
2008 Jul 05
2
p-value for Nonmetric Multidimentional Scaling?
Dear R-helpers, I am running metaMDS in the vegan package, which uses isoMDS in MASS, to perform Nonmetric Multidimentional Scaling (NMDS). I have seen some authors report a p-value for the NMDS ordination based on randomization of the dataset. As I understand it this is meant to compare the stress in your dataset to multiple runs of randomized data. I do not see a way to perform such a test in vegan or MASS. So my questions are: I...
2010 Jul 22
1
interpretation of stress in NMDS
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"
2018 Apr 22
0
nMDS with R: missing values
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
2008 Nov 04
1
ggplot2 scatterplot matrix
..."SC 2007/04", "SC 2007/06", "SC 2007/08"), class = "data.frame")) plotmatrix(d[,3:6]) I would like to either have a colour or more preferably a shape to correspond to Site this is what I have tried (along with many other combinations) plotmatrix(nmds.bug[,3:6])+scale_shape(nmds.bug, shape=Site, pch=1:12) thanks -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel...
2011 Oct 04
2
Adonis and nmds help and questions for a novice.
Hi, forgive me if someone has already posted about this but I have had a look and cannot find the answer, also I am very new to R and been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am looking at diversity in different soils with either woodland or grassland habitats. I have run the scripts library(vegan) library(ecodist) library(MASS) mydata <- read.table("ash_data.csv",...
2004 May 13
2
BIO-ENV procedure
I've been unable to find a R package that provides the means of performing Clarke & Ainsworth's BIO-ENV procedure or something comparable. Briefly, they describe a method for comparing two separate sample ordinations, one from species data and the second from environmental data. The analysis includes selection of the 'best' subset of environmental variables for explaining
2000 Aug 22
2
various ordinations
Colleagues, I'm developing a library of functions for community ecology analyses and have a couple of questions that I've not been able to answer via faqs or docs. 1) Are there existing functions for: a) Bray-Curtis (polar) ordination? b) non-metric multidimensional scaling (NMDS)? c) canonical correlation analyses (CCA and DCA)? d) TWINSPAN (doubtful...)? 2) If not, does anyone have these functions already? 3) I'm having difficulty figuring out how to dyn.load C object files in a windows environment, which I admittedly know little about. I'm using the Cy...