Two more points about R: using R inside Rstudio is a great help. You can still do analyses from the command line in the console, but have better control (IMO) over saving plots and other items. It’s a little easier to develop your own R functions and more in this setting. Use of RMarkdown allows you to generate reports in pdf, html, and Word format (I never use the last one, but it is possible), presentations. R Notebooks contain all output as well as code, and interested readers can download the source once your work is posted and not only examine the code but run it and tweak it as they might desire. Unless you have a need for a full-fledged stand-alone Latex installation you can install “Tinytex” and include Latex code in your work as desired.

Finally — a comment defending Microsoft’s R (MRO, Microsoft R Open, and MRS, Microsoft R Server). Everything you can do with the open source R can be done with it, and Microsoft R can be used with Rstudio. There are a few exceptions going from it to the open source version, but there are some packages available for Microsoft R that are not available for the open source version. The primary advantage of the Microsoft versions comes in high performance implementations of many procedures (glm, clustering, and others), the ability to work with larger data sets, tight integration with SQL, and good support for multithreading (the latter is something open source R isn’t so good at).