Using a user-defined equation to create a distance matrix
May 9, 2018 12:53 PM(2352 views)
I am trying to create a distance matrix of similarity/dissimilarity values for community data. I would like to use a specific equation (Bray-Curtis) to construct the matrix of values; values will show similarity in multiple species abundances between multiple plots. I am aware of the method to create a distance matrix in JMP using hierarchial clustering, but do not know how to perform a similar command using my own equation. Is there a tool to do that, or how would I go about writing the script to do so?
Whatever you desire can be achieved with a script. JSL will set you free!
As for how to go about writing the script to do so, I recommend a computer keyboard.
Seriously, though, you will need to consider several things before you plow into writing a script: how your data sources are structured and organized, the data analysis steps necessary, the output you desire, and how the script will be used. You will probably want to write a function to implement the dissimilarity measure you choose.
Depending on your answers to these questions (there's a helpful checklist in Chapter 11 of the Second Edition of JSL Companion), the script could be more or less difficult to write.
And, if you do get to choose, I would recommend a different dissimilarity measure than Bray-Curtis. Please reference the enclosed paper if you wish.