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copied!<p>It sounds like you're asking two separate questions. One question concerns workflow and the other concerns using ESS. As I use StatET and Eclipse, I'll just share my experience regarding the workflow aspect of your question.</p> <p>As with Vincent I also follow something like the workflow set out by Josh Reich here (also see Hadley's useful comments): <a href="https://stackoverflow.com/questions/1429907/workflow-for-statistical-analysis-and-report-writing">Workflow for statistical analysis and report writing</a></p> <p>Although it can vary between projects, I tend to have a couple of main R files</p> <ul> <li>import.R: this imports data files and does any necessary cleaning and manipulation</li> <li>analyse.R: This generates the output that I need for any final report</li> <li>main.R: This calls import.R and analyse.R </li> </ul> <p>The aim is for import.R and analyse.R to represent the complete and final workflow for producing the final results of any analyses.</p> <p>In terms of a directory structure for an analysis project, I'll often also have the following folders</p> <ul> <li><strong>data</strong>: for storing any raw data files</li> <li><strong>meta</strong>: for storing meta data, such as variable labels, scoring systems for tests, recoding information, etc.</li> <li><strong>output</strong>: for storing any graphics, tables, or text generated by my analyses that I might want to incorporate into an external program</li> <li><strong>temp</strong>: When exploring the data and brainstorming analyses, I like to type code into files instead of using the console. I tend to label these temp1.R, temp2.R, temp3.R. I store these in a temp folder. That way I have a permanent record that's easily accessible. If the analyses become final they get incorporated into one of the main R files (i.e., import.R or analysis.R)</li> <li><strong>functions</strong>: If I think that a function will be needed across a couple of projects, I often place it one function per file or a set of related functions in a file in a folder called functions. This makes it relatively easy to reuse functions across projects, when the formal requirements of package development are more than needed.</li> <li><strong>library</strong>: If I want to create some general functions that I think will be project specific, I'll place them in this folder</li> <li><strong>save</strong>: A folder to store any saved R objects</li> </ul> <p>StatET and Eclipse make it easy to interact with such a file system. Of course, given all the R gurus that use ESS and Emacs, I'm sure it also handles interactions with the file system well.</p>

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