I grouped sites in six different clusters on the basis of fish species abundance using a self-organizing map (SOM). Now, I want to determine to what extent water chemistry variables can explain this grouping. However, I don't want to assess the linear relationship between the fish communities and water chemistry variables.
Since SOM is not a linear clustering method, can I use the LDA?
Would the same answer apply if I had used Cluster Analysis for grouping?
Hamed
Linear & non linear methods cannot produce similar results unless the data is linear by itself. However., the data in your case may not be linear and may have complex structure. I would therefore suggest you to use SOM [ https://au.mathworks.com/help/deeplearning/referencelist.html?type=function&category=self-organizing-maps&s_tid=CRUX_topnav ] for your final outcomes.
https://au.mathworks.com/help/deeplearning/ref/selforgmap.html
Dear Muhammad Ali thank you so much for your suggestion. If I understand well, you suggested using both SOM for biological and physicochemical variables. How does this work with R? I am not familiar with MATLAB.
Hamed
Dear Hamed,
I suggest instead of clustering only on the basis of fish species abundance to use multi dimension data which includes water chemistry variables.
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