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2) Setup files that each person can identify the location of each type of directory in their file structure. ADD MORE SPECIFICS.
3) A main do file that executes project do files in orderscript that begins with loading original data and ends by producing publication-ready tables. Note that you should nest do files scripts within other do filesscripts. For example, you might have a one stata .do file that executes all of the code to create your analysis files and another . Another do file could to execute all the scripts to do the data analysis. The main do file would call and execute both.
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We are also developing techniques to automate the production of tables for publication. See automate for more.