In what file format is this Matrix that you want to import?
I do not want to transform these matrices to tables with a separate row for each species & replicate
What exactly do you mean by that?
"Replicate" means what?
Why do you not want a separate record for each row of the matrix?
Im OK with having a separate record for each row of the matrix but I don't want to have a separate record for each column of my matrix... And the number & type of the columns of my matrix (i.e. the type & number of species sampled) differ between sites.
Hope this makes sense!
Have you tried taking, just as a test, one of these excel files and then do a "drag and drop" to drop it on an icon for the FileMaker application?
This will automatically produce a new FileMaker file with a table that reproduces the structure shown above. Each row in excel will be a record and each column will be a different field in that record.
Import Records | File from the File menu or the Import Records script step can also do the same type of import to either create a new table or to add the data from an excel file to an existing table.
The problem here is that the target table must have at least the same number of columns as there are columns of data in the excel file and data for a given species will need to always be in the same column.
But ultimately, you may want to revisit that idea of having one record for each replicate-species count cell in the example table shown. You can still produce the "cross tab" like format shown above when you want to examine the data, but you gain a great deal of flexibility in what you can do with the imported data. This takes more work--especially since you can't just import a file like the one shown and get this result automatically, but there are potential, very substantial benefits as well. I can't make that call for you, but if the only reason that you don't want that result is that you need to see the columnar format shown above, be aware that this can still be produced even with one record for each "species count" imported.