Here i will present a real life example of how to go from your otu table to nmds plots and hypothesis testing in r.
Nmds f kinder.
The first three columns of my data have information about my samples so my abundance.
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A 2d nmds reaches a reasonable solution and the plot makes sense in this case there s a fair amount of overlap between the three groups.
Nmds does not use the absolute abundances of species in communities but rather their rank orders.
Function metamds performs nonmetric multidimensional scaling nmds and tries to find a stable solution using several random starts.
The relation between mds and nmds codes in the ordered metric and distri butions is the main motivation of the present study.
It s also where the non metric.
As was observed by skriganov.
The metamds function does not provide actual nmds but it calls another function for the purpose.
After some consideration i decided to remove one of the three groups and focus on the difference between the remaining two.
I will be checking the statistical significance of the groupings of time and type below.
The use of ranks omits some of the issues associated with using absolute distance e g sensitivity to transformation and as a result is much more flexible technique that accepts a variety of types of data.
In addition it standardizes the scaling in the result so that the configurations are easier to interpret and adds species scores to the site ordination.
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As a reminder this is the nmds figure we made in this tutorial.
F 1 f r f.
However now with n 10 the nmds is not successful stress too low and the.
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