add variables `ANRLO`, `ANRHI` to dataset `ADVS` & `ADLB`

[waddella]

Motivation

While developing the Patient profile module in TMC, we encountered multiple variables that were not present in random cdisc data (RCD) datasets and could be useful for future usage. See original issue.

Todo

In the function radvs and radlb add the variables:

• ANRLO: Analysis Normal Range Lower Limit
• ANRHI: Analysis Normal Range Upper Limit

Update NEWS.md

Definition of done

• Check the definition of the variable in the GDSR
• If the variable has an associated codelist adhere to it (see GDSR)
• For possible values of variable, can search at stream manual
• Are there any related variables that show inconsistencies with your new variable, i.e. would the data pass the sdmtchecks (see https://github.roche.com/Rpackages/sdtmchecks)
• radsl returns a tibble with the variables ETHNIC and DTHADY
• Check that the documentation is updated
• Check the variable labels are present, use View(x) in RStudio
• Rerun vignettes/rebuild_cached_data.Rmd, and update the cached data

[yli110-stat697]

Hi the document regarding the ANRLO and ANRHI variables can be found at https://docs.google.com/document/d/1pR_eLDuC-jxoa4upWRNqeZrYAyCifIP_LXMHdDoOzx8/edit?usp=sharing

Per the feedback from DSG, ADVS has this marked reference range, but it was only for Roche Internal use. Maybe we can discard the LOW LOW and HIGH HIGH level to make the random.cdisc.data easier?

[yli110-stat697]

Here's the issue where we did the helper function marked reference range. https://github.com/insightsengineering/tern/issues/230

[shajoezhu]

For ADLB

ALT 7 to 55 units per liter (U/L) CRP 8-10 mg/L IGA 0.8 - 3.0g/L

Reference: ALT, https://www.webmd.com/digestive-disorders/alanine-aminotransferase-test#:~:text=A%20normal%20ALT%20test%20result,Alcohol%20abuse CRP, https://www.testing.com/tests/c-reactive-protein-crp/#:~:text=Although%20%E2%80%9Cnormal%E2%80%9D%20CRP%20levels%20vary,lower%20than%200.3%20mg%2FdL. IGA https://www.ouh.nhs.uk/immunology/diagnostic-tests/tests-catalogue/immunoglobulins.aspx#:~:text=Reference%20range%2Funits,IgM%200.4%20%2D%202.5g%2FL

For ADVS

Diastolic Blood Pressure 80 - 120 Pulse Rate 60 - 100 Respiratory Rate 12 to 20 Systolic Blood Pressure 120 - 180 Temperature 36.1 - 37.2 Weight 40 - 100

If AVAL is NA, ANRLO and ANRHI takes NA values as well

[npaszty]

@shajoezhu am reviewing goshawk and see that the ADLB$LOQFL value is not being created in a way that would yield expected result. with the proposed range change of the three param values perhaps we can include an adjustment to the LBSTRESC, AVAL and thus LOQFL. setting LOQFL to "Y" if AVAL is <32 on line 154 should be adjusted.

The way that this works in a typical setting is that LBSTRESC values that include a ">" or "<" would indicate that the assay could not detect a value because it was either above or below the limit of quantitation (LOQ). here's what would be helpful...

1. randomly set a few LBSTRESC values within each PARAM to "<7" for ALT, "<8" for CRP and "<0.8" for IGA.
2. for these records AVAL would be the numeric portion of LBSTRESC/2 and LOQFL would be set to "Y".

Since your comments above are trying to introduce "sensible data" let's say, what we have now for LOQFL doesn't make sense.