Incidence/Prevalence Shiny: some DB not appearing in specific tabs

[martapineda]

All DP who upload results included the Inc-prev attritions, and Inc-prev results files. However 3 DB are not seen/missing in specific tabs of the shiny:

• Turku: missing in Incidence attrition, Incidence estimates, and Prevalence estimates tabs
• INGEF: missing in Incidence attrition and Incidence estimates tabs
• ULSM: missing in Incidence attrition and Incidence estimates tabss
• UZB: missing in Incidence attrition and Incidence estimates tabss

[tiozab]

@martapineda

TURKU does not appear in the incidenceAttrition tab because they do not have any denominator_days_prior_observation == 30, since this does not show in the attrition, they wont have any estimates either.

that makes me question whether they have run the code correctly. I think they were playing with the code or have an older version? because also their incidence and prevalence in the csv have capital letters and that is why they are not detected by the shiny.
We need to ask them to re-run and not change anything in the RunIncidencePrevalence.R without confirming with us, so everything stays in the correct format.

[tiozab]

@martapineda INGEF and ULSM and UZB do not have denominator_days_prior_observation == 30 and therefore also no incidence results.
let's ask them if they have adapted the code:
cdm <- generateDenominatorCohortSet(
cdm = cdm,
name = "denominator",
cohortDateRange = as.Date(c("2010-01-01",NA)),
ageGroup = list(
c(0, 150),
c(0, 17),
c(18, 64),
c(65, 150)
),
sex = c("Both", "Female", "Male"),
daysPriorObservation = c(0,30), # 30 for incidence, 0 for prevalence
requirementInteractions = TRUE,
overwrite = TRUE
)

[mikaelhogerman]

Hi,

Turku had different database name in the first feasibility run that what we reported in main excel before anything was run. We named our files according to first reported names for incidence run. We exchanged few emails about this with Montse and Moncusi. @martapineda

The code didn't run without commenting "overwrite=TRUE" out.
Otherwise it gave error:
Error in generateDenominatorCohortSet(cdm = cdm, name = "denominator", :
unused argument (overwrite = TRUE)

[tiozab]

@mikaelhogerman thanks for your anwer.
did you employ the renv? if you receive this error, you did not use the correct version of the IncidencePrevalence Package #24,

What we are more interested in is whether you would expect your patients to have prior observation or not, because if so, s.th. did not work.
Can you retry with the renv?

[tiozab]

@mikaelhogerman re changing file names, if you must change s.th. in the file name, please do not amend the snippet that we provide (but work around it), thereby the files are seen in further processing, e.g. changing "incidence" to capital letter "Incidence" was not detected.

[tiozab]

@mikaelhogerman , one possibility why we do not see incident results could be that each hospital visit is a new observation, and we look back in the observation_period, therefore, unless a patient was in hospital for longer than 30 days and has received a medication of interest afterwards, that patient would be part of the incidence results. Just a thought

[mikaelhogerman]

Hi @tiozab
I was able to employ renv and re-run scripts without modifying them at all. I have submitted new zip-file now but I am not sure that it solved the problem.

[tiozab]

@martapineda can you check the results? we can also have a look together on friday.
@mikaelhogerman thank you for re-running the results. other than running code succesfully, it is also about looking at the results and questioning whether they make sense. Therefore, we asked whether you would expect patients to have prior observtion or not, and a reason why "no" may be the answer is that every hospital stay for the same person is a new "observation" and people not staying long enough in the hospital to accumulate sufficient observation days (>30). in any case, hospitals may not be the most reliable source for incidence results, so prevalence results are enough. Yet, it is always important to question what was going on ;-)

[tiozab]

@raeleesha-norris FYI

[raeleesha-norris]

@tiozab Thank you for guiding me here. We don't see the same issue in the DUS results which makes sense given the structure of our data and the available observation peirods for our patients, so I imagine that there was really a technical issue while running that will now be resolved. And as a heads-up, due to the long run time of the code, we will likely be able to share the results at the beginning of next week.

[mikaelhogerman]

Hi @tiozab,
It it still unclear to me how do you define "accumulate sufficient observation days"? I believe results are otherwise ok.

[tiozab]

@mikaelhogerman, happy to elaborate: with "accumulate sufficient observation days" I meant that if each hospital visit was a new observation then a patient would need to be in hospital for at least 30 days before he or she can be part of the denominator group that requires at least "prior observation of 30 days", however, like you said how you define your observation period, you would expect patients to have sufficient amount of time (like e.g. once in the hospital their observation remains intact until their next visit, thus they "accumulate sufficient observation days"). If things worked for DUS then there indeed was something wrong with the Inc/Prev run, looking forward to look at your results again.

[tiozab]

@mikaelhogerman we have just had a look again at your results, the denominator_days_prior_observation == 30 days is still not there. So there is a problem somewhere in your data maybe since you mentioned that there were no errors and that you would patients expect to have prior observation time? @janblom is an ETL expert, please liaise with him.

[tiozab]

@mikaelhogerman we will still use your prevalence results though, it is just the incidence that is missing. will be helpful for the future as well to get behind what is going on.