Documentation: For BDS datasets with `PARAM`/`PARAMCD` variables, list out distinct values in documentation

[manciniedoardo]

Once #97 is merged, we'll have a nice documentation pipeline to create reference pages for each ADaM dataset we provide. It would be nice to detect if the dataset is "BDS" structure and thus contains PARAM/PARAMCD variables. If it does, we could list out distinct values in he documentation by adding an additional section. For instance, for ADVS it would look something like this (but in a table):

Available paraemters

This dataset contains the following PARAM/PARAMCD combinations:

• Body Mass Index(kg/m^2) - BMI
• Body Surface Area(m^2) - BSA
• Diastolic Blood Pressure (mmHg) - DIABP
• Height (cm) - HEIGHT
• Mean Arterial Pressure (mmHg) - MAP
• Pulse Rate (beats/min) - PULSE
• Systolic Blood Pressure (mmHg) - SYSBP
• Temperature (C) - TEMP
• Weight (kg) - WEIGHT

Note - this issue is similar to the corresponding one in pharmaversesdtm

[Fanny-Gautier]

Hi @manciniedoardo ,
I prepared some code to add the PARAMs and PARAMCDs in the documentation but I am facing the following error while running create_adams_data.R. Any idea how I could fixe that while working on R 4.2.3? Thanks

[manciniedoardo]

@pharmaverse/admiral any idea why this is happening? I'm flummoxed

[bundfussr]

When create_adams_data.R runs the templates, it calls Rscript on the operation system. The R version of Rscript may differ from the R version in RStudio.

Maybe it is better to use source() (and specifying an environment for local) for running the templates. This should avoid the issue.

[Fanny-Gautier]

When create_adams_data.R runs the templates, it calls Rscript on the operation system. The R version of Rscript may differ from the R version in RStudio.

Maybe it is better to use source() (and specifying an environment for local) for running the templates. This should avoid the issue.

This still gives me the same error messages using source() with several local set up. I contacted my IT to double check if it comes from my environment...

[Fanny-Gautier]

Thanks Stefan for the advice.
Finally locally fixed as following:

Sys.getenv("PATH")
PATH <- "my PATH with updated Rscript version number corresponding to the used R version"
Sys.setenv(PATH = PATH)
system("Rscript --version")

[Fanny-Gautier]

Any idea about that error? 🤔

[bms63]

Where is this from? Is this code from template checker program?

I would think res is a dataframe and you are using $ to find the column. but looks like res is now an atomic vector and you can't use $ or [], [[]] since it isn't a named list