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ohdsi-studies / PioneerWatchfulWaiting

This study is part of the joint PIONEER - EHDEN - OHDSI studyathon in March 2021, and aims to advance understanding of clinical management and outcomes of watchful waiting in prostate cancer.
Apache License 2.0
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Update app on ShinyDeploy #39

Closed MaximMoinat closed 3 years ago

MaximMoinat commented 3 years ago

The last update of the PIONEER WatchfulWaiting shiny app on ShinyDeploy was over two months ago. We should update the code there to fix some issues with the currently deployed app (see #34).

Do we want to do an intermediate update or wait for fixing the time to event plot #38?

MaximMoinat commented 3 years ago

And who are authorised to do these updates? I know at least @keesvanbochove and @Anne0507 ~have access~ have done this before with a PR.

bdemeulder commented 3 years ago

I can commit the changes over to the ShinyDeploy server. It sometimes takes a while for someone at OHDSI to accept it.

keesvanbochove commented 3 years ago

Right @MaximMoinat I don't have push rights either (nor does Anne) but you can always open a PR to OHDSI/ShinyDeploy.

On Wed, 2 Jun 2021, 10:51 bdemeulder @.***> wrote:

I can commit the changes over to the ShinyDeploy server. It sometimes takes a while for someone at OHDSI to accept it.

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bdemeulder commented 3 years ago

Just updated the cohort.csv file.

bdemeulder commented 3 years ago

The cohort tab now shows the right list of cohorts. I still get the following in the compare cohort characteristics tab Shiny app 02062021

MaximMoinat commented 3 years ago

I cannot replicate this issue on the current master branch. For me it displays the cohort names nicely. It used to work for me as well without the cohort.csv updates. image

bdemeulder commented 3 years ago

@MaximMoinat I've downloaded the master branch again and I still get the same issue.

Which data are you using?

MaximMoinat commented 3 years ago

I am using the following file from our MS Teams, General channel: Cohort testing -> Task # 3 Second version of package -> Results -> Premerged.RData

bdemeulder commented 3 years ago

OK, with the same data I have the same result as you. I was using the task #4 results that I've uploaded in teams ('Cohort testing/Task #4 Third version o fthe package/Results/PreMerged.Rdata')

My guess is that the list of cohorts between those datasets and the cohorts.csv in the shiny app don't match, hence the issue I had.

MaximMoinat commented 3 years ago

I can confirm the issue is in the results file. Specifically, the covariate variable. So we should fix this in the study code. And maybe implement a quick fix to display the already collected results correctly in the shiny app. image