Liviu,This shows some promise. The echo=T within the chunks overrides the SWeaveOpts command, and the although the code is suppressed you still get the output, which is fine for the figures but not for some of the numerical output
However, this all looks promising as you could create objects in the main text (rather than output)and then put the output into the appendix.
All told this looks very good. Many many thanks. lyx seems to triumph again. Graham
