Using a user-defined equation to create a distance matrix

hjh — Wed, 09 May 2018 19:53:46 GMT

Hello,

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?

Re: Using a user-defined equation to create a distance matrix

Kevin_Anderson — Wed, 09 May 2018 22:20:27 GMT

Hi, hjh!

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.

Good luck!

topic Using a user-defined equation to create a distance matrix in Discussions

Using a user-defined equation to create a distance matrix

Re: Using a user-defined equation to create a distance matrix