The main reason people switch from spreadsheet software such as Microsoft Excel to scripting languages such as Python and R is reproducibility, re-usability and the idea that code is an important means of communication.
Programming languages offer immense power. But with great power comes great responsibility. While analysis in code are less error prone to copy-and-paste errors as found in Excel and Co., or involuntary conversions to dates1, they can of course contain mistakes nonetheless.
A number of measures have been taken to ensure that the code presented here is safe, testable and easy to extend.
R at it’s heart is a functional programming language. Loosely speaking, this means that functions are first class citizens in this language. They can, for example, be passed to other functions (higher order functions) as arguments just like variables However, it is not a strict functional language and functions are not required to be pure, that is free of side-effects. A pure function acts like a mathematical function: When given the same input, it produces the same output and does not rely on any external, global state. I designed the functions that process your data in ShinyLipids to be pure. That means, if you put in the same data, rain of shine you get the same processed data out. Furthermore, this can guarantee that if some other part of ShinyLipids changes or is being worked on, the way the pure functions operate doesn’t change. Understanding and verifying one function does not require you to read and understand the whole source code of all other functions. Of course, mistakes can still happen, but the more the code aligns with conventions of pure functional programming, the easier they are to find and prevent. But what if we do want to change things? How can we make sure that ShinyLipids still works as a whole? This is where unit tests come into play.
Because the functions mentioned above only rely on their input, we can also test and verify them as independent units. Furthermore, we can automate the whole process! Every time a code change is pushed online, a whole bunch of tests are run to make sure that the app still works, automatically.