It's Data of dung beetle species associated with 5 mammals namely elephant, cow, goat, buffalo and pig in an agriculture habitat .
In the NMDS plot , Pig is in the lower part with -ve score on Y axis ;
Cow is with +ve scores on the y axis .
Goat is on the upper part with - ve value in y axis.
I understand it as the elephant and buffalo beetle communities are with similar distribution and others are different.
Positive and negative scale on the Y axis and the lower and higher position on the graph is not understood.
Thank you
The nMDS calculates the similarity using the distance matrix and the dissimilarity index. The meaning of the axes is not really relevant. What is relevant is the distance between each point in the graph, with objects closer having a more similar relationship. In the X-axis (NMDS 1) all animals are similar except for Cows, in the Y-axis (NMDS 2) all animals are similar except Goat and Pigs. However, if you combine both axes, as in the graph, you can see that Elephants and Buffalos are very similar in the trait you are measuring. What you can do if you wish is to include a third axes, NMDS 3 if you wish, and create a 3D graph to see if the Elephants and Buffalos differ within this extra dimension.
Apologies to my colleague above but the axes are important and should be labeled correctly including the units. You might try Peter Rouseuw, Finding Groups in Data. Available in the z-library google instructions for the z-library. Best wishes David Booth PS IF YOU want THE programs they are available in an R package. Best wishes, David Booth
I am quite interested in what the unit and correct labeling would be on the axes of a NMDS ordination plot. Perhaps you could elaborate and provide some sources that strengthen these suggestions. I have never previously seen any suggestions for a unit or labeling. David Eugene Booth
Dear Friend, did I say NMDS PLOT ? I did say plot. That is a common way of data exploration. If you see the reference above you will notice multiple types of plots that are important for example in finding dissimilar points which may be of some use. In grouping data. This text was a major addition to a robust analysis in the multivariate grouping.literature. Please try to read what is written and not what you hoped it might be. BTW I noticed that there's no question in the original post. Thus I attempted to supply helpful information. I didn't mean to confuse anyone with what is now standard robust multivariate analysis. Mea culpa to anyone that misunderstood my posts. David Booth
NMDS plot was done by using metaMDS {vegan}, with default setting in the package k= 2 (Number of dimensions).
Which package helps to draw a NMDS plot with K=3 (Number of dimensions)?
Otherwise, Will modifying the the syntax, will enable to get a three dimensional NMDS plot?
If that’s the solution, kindly modify the syntax to to get a three dimensional NMDS plot
We used the following syntax.
data(dune)
# Global NMDS using monoMDS
sol
Neethu V P You have two main options. You can use the regular plot-function to plot the axes, but you need to plot three plots, one with axis 1 and 2, one with axis 1 and 3 and one axis with 2 and 3. The alternative is to use the R-package plot3D. Using this package you can plot a 3D representation of all of your three axes. This 3D plot can be rotated to get a good view of the data.
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