add subject disposition

[samussiah]

Overview

This branch adds subject-level status using the study completion domain, then aggregates at the study, site, and country levels.

Test Notes/Sample Code

lSourceData <- list(
    Raw_STUDY = clindata::ctms_study,
    Raw_SITE = clindata::ctms_site,
    Raw_SUBJ = clindata::rawplus_dm,
    Raw_STUDCOMP = clindata::rawplus_studcomp
)
lWorkflows <- MakeWorkflowList(c('STUDY', 'SITE', 'COUNTRY', 'SUBJ', 'STUDCOMP'))
lSpec <- CombineSpecs(lWorkflows)
lRawData <- Ingest(lSourceData, lSpec)
lMappedData <- RunWorkflows(
    lWorkflows,
    lRawData
)
dfGroups <- RunWorkflow(
    MakeWorkflowList('Groups')[[1]],
    lMappedData
)
dfGroups %>% filter(Param == 'ActiveParticipants')

Connected Issues

• Closes Feature: Add subject disposition. #2003

[lauramaxwell]

we can remove this Status, right? looks like a duplicate

[samussiah]

This one captures subject status, to count the number of active subjects at the site.

[lauramaxwell]

Another duplicate Status as far as i can tell

[samussiah]

Nice catch!

[samussiah]

Oh wait, Mapped_SUBJ$Status is used to calculate the number of active subjects. Raw_STUDY$Status is a study-level attribute.

[lauramaxwell]

A few tiny yaml edits that will also require a rerun of tests to update snaps, but other than that (and some investigation into the check failueres), this is looking good!

[samussiah]

This PR kind of standardizes Status so the study and each site/participant will have a status, because the RBQM team can only follow up with active sites and participants.

[lauramaxwell]

Status' were not duplicates-misread the yamls. this looks great!