Draft: Differences in mimic-iv definition

[mlondschien]

Thanks @dplecko for adding mimic-iv and adding sicdb.

See below for the diff between my definition of mimic-iv 2.2 and yours. In particular

• I have included some more variables, including caregiver_id, admit_provider_id, order_provider_id, formulary_drug_cd, and provider_id. Any reasons you excluded those? They are relevant for me (and the only reason I updated to 2.2 in the first place).
• I am getting the caregiver from the icu directory. See https://mimic.mit.edu/docs/iv/modules/icu/caregiver/.

[dplecko]

Thanks @mlondschien. These are indeed mistakes on my side.

In the current setup of ricu, we use the R files in inst/extdata/config/ to generate the concept dictionaries and the data sources specification. Even though it duplicates information, I am hoping that soon we will be moving into a source-specific setup for the configs, and then having the R files will be easier to generate the new setup, instead of copying and pasting huge jsons.

Could I ask you to edit the data-sources.R for this one, and add this to your PR? I am happy to accept after this. Otherwise, I can also do it myself based on what you suggested.

[dplecko]

Hi @mlondschien,

These edits were quite helpful. I included them in ricu 0.6.1. However, as you will see, I edited the data-sources.R instead of data-sources.json. Handling json files with 10k lines is quite annoying (and causes errors, including in your pull request), so for the time being, editing the R files is the preferred solution (in case you need to make a pull request in the future).