The emphasis of the current guide is on ‘Applied Statistics’. This means that even though the mathematical principles of different statistical methods are briefly described, the key aim is to make sure the reader understands what kind of data is being analysed, what type of test is the most appropriate, how to actually implement this test correctly using R, and how to properly interpret the results. The examples given throughout this guide are taken from the archaeological sciences. However, technical terms have been intentionally avoided so that these examples are understood by non-archaeologists and it should be easy for specialists from other disciplines to see how the analyses presented could be used with their types of data and research questions. These notes were written especially for users running the Windows version of R, but most of the material applies to the Mac and Linux versions as well. All the sample data files used in this guide are provided in the folder R_Files, which may be freely downloaded from the zenodo repository (DOI: 10.5281/zenodo.3837331). This document is an open resource and it is anticipated to be updated at regular intervals. I would greatly appreciate any feedback and recommendations for future improvement at e.nikita@cyi.ac.cy.