I am working in a project where I need to extract data from lots of files provided to me in different formats (.exe, .doc, .txt, .dbf, and even .pdf). The data I am interested in are water quality and hydrological variables measured at different sites, with different periodicities (monthly, daily, hourly) and sometimes at different depths. The organization of the files is not easy either. For example, some Excel files contain several tables in the same sheet.
So, I need some software, R package or Python module that can help me organize this mess and extract the relevant data. What do you suggest?