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    <p>Too late for you here, but I use Sweave a lot, and most probably I'd have used a Sweave file from the beginning (e.g. if I know that the final product needs to be some kind of report). </p> <p>For repeating parts of the analysis a second and third time, there are then two options: </p> <ul> <li><p>if the results are rather "independent" (i.e. should produce 3 reports, comparison means the reports are inspected side by side), and the changed input comes in the form of new data files, that goes into its own directory together with a copy of the Sweave file, and I create separate reports (similar to source, but feels more natural for Sweave than for plain source).</p></li> <li><p>if I rather need to do the exactly same thing once or twice again inside one Sweave file I'd consider reusing code chunks. This is similar to the ugly for-loop.</p> <p>The reason is that then of course the results are together for the comparison, which would then be the last part of the report.</p></li> <li><p>If it is clear from the beginning that there will be some parameter sets and a comparison, I write the code in a way that as soon as I'm fine with each part of the analysis it is wrapped into a function (i.e. I'm acutally writing the function in the editor window, but evaluate the lines directly in the workspace while writing the function).</p></li> </ul> <p>Given that you are in the described situation, I agree with Nick - nothing wrong with <code>source</code> and everything else means much more effort now that you have it already as script.</p>
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