New way to edit thresholds

[MaximMoinat]

Adds function editThresholds(threshold_file) that can create a thresholds file from a table of modified thresholds.

As described under point 1 in this OHDSI 2021 collaborator showcase: https://www.ohdsi.org/2021-global-symposium-showcase-67/

Making it a draft as it needs to be moved from extras to the main codebase, with Roxygen doc. We do include a readme here. Any feedback at this stage is much appreciated.

[MaximMoinat]

Description from extras/edit_thresholds/Readme.md:

This script can be used to edit selected thresholds in a DQD result. This of course assumes that you have run the DQD, observed it, and have a list of checks for which you would like a different threshold.

About the thresholds

There are 20 different checks. The thresholds for these checks are recorded in one of 3 files: Table, Field or Concept level. This script is valid for editing the three of them simultaneously.
For more information about the checks and their thresholds, visit: https://ohdsi.github.io/DataQualityDashboard/articles/CheckTypeDescriptions.html

About this script

In the previous files, each check can be found using a combination of the check name itself, together with information from additional columns. In summary, the checks and additional columns are the following:

	Test	Additional columns
	TABLE LEVEL
1	measurePersonCompleteness	cdmTableName
	FIELD LEVEL
2	cdmField [not tested]	cdmTableName, cdmFieldName
3	isRequired	cdmTableName, cdmFieldName
4	cdmDatatype	cdmTableName, cdmFieldName
5	isPrimaryKey	cdmTableName, cdmFieldName
6	isForeignKey	cdmTableName, cdmFieldName, fkTableName
7	fkDomain	cdmTableName, cdmFieldName, fkDomain
8	fkClass	cdmTableName, cdmFieldName, fkClass
9	isStandardValidConcept	cdmTableName, cdmFieldName
10	measureValueCompleteness	cdmTableName, cdmFieldName
11	standardConceptRecordCompleteness	cdmTableName, cdmFieldName
12	sourceConceptRecordCompleteness	cdmTableName, cdmFieldName
13	sourceValueCompleteness	cdmTableName, cdmFieldName
14	plausibleValueLow	cdmTableName, cdmFieldName
15	plausibleValueHigh	cdmTableName, cdmFieldName
16	plausibleTemporalAfter	cdmTableName, cdmFieldName
17	plausibleDuringLife	cdmTableName, cdmFieldName
	CONCEPT LEVEL
18	plausibleValueLow	cdmTableName, cdmFieldName, conceptId, unitConceptId
19	plausibleValueHigh	cdmTableName, cdmFieldName, conceptId, unitConceptId
20	plausibleGender	cdmTableName, cdmFieldName, conceptId

How to run?

1. Define the checks for which you want to edit the thresholds in a .csv file, including all the 'additional columns', like this:

Level	checkName	cdmTableName	cdmFieldName	fkTableName	fkDomain	conceptId	unitConceptId	Threshold	Notes
Field	isRequired	MEASUREMENT	person_id					10	"one note"
Field	plausibleValueLow	PERSON	year_of_birth					100	"another note"
Field	isForeignKey	MEASUREMENT	person_id	PERSON				1
Field	fkDomain	PERSON	race_concept_id		Race			49	"and yet another one"
Concept	plausibleValueLow	MEASUREMENT	MEASUREMENT_CONCEPT_ID			2212333	8554	56	"note in another table"

2. Run edit_thresholds.R. Make sure to have the correct file names.

[katy-sadowski]

@MaximMoinat I strongly support making these long format files available. I'm wondering if instead of framing this as an edit threshold function, it's just a long<>wide converter. executeDqChecks can be updated to take either a long or a wide file as input (wide by default, at least for now, to ensure backwards compatibility). That would also allow users to edit other columns (check on/off toggle, notes, etc.) more easily.

The ideas of combining table/field/concept and 5.3/5.4 into a single file, I need to ponder more. Backwards compatibility with combined files might be more challenging to figure out.