Mapping coverage

[MaximMoinat]

This generates an overview of concept mapping coverage directly from DQD results. For the main OMOP domains it takes the percentage of unique terms mapped and the percentage of all records with a mapping (dqd checks sourceValueCompleteness and standardConceptRecordCompleteness respectively).

@egarcialara We can start collecting your other DQD 'utility scripts' in the same way. And please take a look whether my code can be improved!

[egarcialara]

Awesome! I've just run it for ABUCASIS and it's really nice haha

A couple of things:

• Perhaps it could be added the absolute number of unique terms and records for each domain/unit, in order to have a more complete figure?
• How final are the scripts? Depending on that, we can think of a directory to save the figures and tables, a common theme/background, and increase the fontsize for the domain/unit.
• [just for myself] where could I find the "fig 6 in EHDEN DoA"?

[MaximMoinat]

• Perhaps it could be added the absolute number of unique terms and records for each domain/unit, in order to have a more complete figure?

I gave it a try, but it gets messy. This data can be found in the outputted table if someone wants to go in depth.

• How final are the scripts? Depending on that, we can think of a directory to save the figures and tables, a common theme/background, and increase the fontsize for the domain/unit.

Might be nice indeed to apply same style to all new plots (also your dqd compare). Let's come back to it later, when we integrate these in the shiny app.

just in case, if you want to make it general you can use separate: ... [prob not use for observation/observation_period, but here I leave it]

Nice! It actually also causes issues with e.g. CARE_SITE. But I liked the idea of generalising, I made it into the following mutate: domain = gsub("_(OCC\\w+|EXP\\w+|PLAN.+)$", "", CDM_TABLE_NAME),