@schuemie This chapter is a fabulous start.
I’m using a few of the Atlas-generated PLE outputs right now and I have to be honest, 13.3.4 Running the study package needs more detail. The README file today is missing some key knowledge on how to actually execute a study package.
If not inside this exact section, we need a user guide that explains the code generated by Atlas (e.g. a brief explanation of each of the components, what they do, etc) and basic step-by-step of how to utilize the package. This is important because if the PLE package is being transmitted as a network study, it will undergo significant review by organizations receiving the package. We shouldn’t assume people automatically understand the outputs and should be clear there’s no funny business in here. I imagine some sites will be forced to explain to their IT group, “no we’re not getting hacked by OHDSI… this is clean and acceptable code. Here’s what it does…”
Right now, the README has placeholders inside the code where a user would need to add their own instructions of how to load the package, e.g.:
- In ‘R’, use the following code to install the [studyname] package:
To do: Need to provide some instructions for installing the study package itself.
Or maybe this was a note to yourself?
Maybe we can set-up a call and quickly chat through the general steps here? @George_Argyriou and I are testing @mattspotnitz’s package and admittedly we’re not sure what the ‘best practice’ is for loading. We both have different opinions
I will cover some of the nuances of executing a study in the Network Studies chapter, too… but I think the PLE chapter needs to explain the PLE side of things.