Data Quality Dashboard, Control files and Thresholds

tajanenp · September 28, 2021, 9:04am

Dear All, I created now a new topic for this as I have several questions related to DqD I’ll copy here also my original posting and Clair’s answer to it :

Dear All, referring to Don Torok’s posting, I suspect that we have a similar issue with the following tests:

combination of CONCEPT_ID 3015377 (CALCIUM [MOLES/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8753 (MILLIMOLE PER LITER), the number and percent of records that have a value less than 7.000 – our normal ranges with the unit 8753 (MILLIMOLE PER LITER) are 2.15 -2.7 and all our records have values under 7.000 ! I wonder if these plausible low and high values might actually be referring to the unit 8840 (mg/dl) ?

Further to this subject, are we allowed to modify the plausible values in the Control files? Or we should just modify the threshold and add a note explaining why we have so many records failing the check? Would be great if someone would comment, Thanks so much!

Reply

clairblacketer

4d

Thanks so much @tajanenp! I agree it seems like the units are off and it makes sense to update the plausible values in the control files. Would you be willing to send us a pull request to fix the issue?

Reply

tajanenp Pia Tajanen

1d

Dear Clair, thank you for your prompt reply! I will get back to the pull request a bit later as i suspect we have at lest one more case like that but may I ask you , or anyone , another more general question about the plausible values/thresholds; We seem to have quite some cases where we go slightly or significantly over the thresholds (% records 5.5 up to 50%) and at least at first glance I don’t see anything wrong with the data. So my question is that, how these plausible values are set? And as we are a University hospital, our patient population consist of lots of seriously ill patients, might that explain why we do not seem to fit in the default values/thresholds? Many thanks again, I appreciate all the advice we can get, as I am still at the beginning of the learning curve with this great project!

tajanenp · September 28, 2021, 9:17am

Me again after having gone through all our issues related to the plausible results with different combinations of CONCEPT_IDs and UNIT_CONCEPT_IDs, I’ve made the following findings. I am not sure if my conclusions are correct, perhaps the problem is not always in the control file’s plausible value ranges, but with my understanding or our data?! Never the less I would be so grateful if Clair or co would be able to comment again, so many Thanks already!

combination of CONCEPT_ID 3003458 (PHOSPHATE [MOLES/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8753 (MILLIMOLE PER LITER), the number and percent of records that have a value less than 1.000 - according to our/common Normal ranges, only children should have results over 1.0,for adults it seems to be okay to have values under 1, am I correct?
combination of CONCEPT_ID 3000620 (COMPLEMENT C3 [MASS/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8636 (GRAM PER LITER), the number and percent of records that have a value less than 1.000 – common normal ranges with the unit 8636 (GRAM PER LITER) are 0.8 to 1.6 so values under 1.0 should not be an issue? Should the plausible low value be adapted, or do we anyway want to make sure the percentage of these values under 1.0 is not too high?
combination of CONCEPT_ID 3019800 (TROPONIN T.CARDIAC [MASS/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8748 (MICROGRAM PER LITER), the number and percent of records that have a value higher than 10.00 - is this correct, or is this check actually referring to ng/L ?
combination of CONCEPT_ID 3024561 (ALBUMIN [MASS/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8636 (GRAM PER LITER), the number and percent of records that have a value higher than 18.00 - common normal ranges are 34-48 g/L, so yes, most values are over 18.0. Could the plausible values in CDM be referiing to g/dL ?
combination of CONCEPT_ID 3017766 (COMPLEMENT C4 [MASS/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8636 (GRAM PER LITER), the number and percent of records that have a value less than 1.000 - our ranges are 0.11 - 0.34 and almost all our values are well under 1, perhaps the check has incorrect plausible values for this unit?
combination of CONCEPT_ID 3022756 (CERULOPLASMIN [MASS/VOLUME] IN SERUM OR PLASMA) and UNIT_CONCEPT_ID 8636 (GRAM PER LITER), the number and percent of records that have a value less than 1.000 - commonly Normal Ranges with unit g/L are clearly below 1.0, so there might be a mistake in the plausible values set?

clairblacketer · September 29, 2021, 2:18pm

Hi @tajanenp we put these measurement plausibility values together with input from physicians who gave us values that they determined would be biologically implausible for each measurement-unit pair. That being said, we do have a long list of measurements and units and we have found some instances where there is a mismatch between the implausible value and the associate unit. Thank you for sharing some of your examples here. What would be great is if you alter the implausible values in the control files and send us a pull request we can grab your changes and test them our side.

Either way, if you have confidence that your measurement values are correct, feel free to alter the control files to fit your understanding of your data. That is a major feature the tool you are more than welcome to take advantage of.

Clair

tajanenp · September 30, 2021, 12:12pm

Thanks again Clair!! I’ll ask to go through these once again with my colleagues and if we all agree with my conclusion, we’ll go ahead and make the the changes to the control files and send you the pull request! I’m satified now and will leave you in peace for now

Minerva_Alvarez · October 11, 2021, 4:17pm

Hi Community

I have installed DQD in R studio and during the Testing I tried to open the json file, however it looks like that there is a problem opening this json in Google Chrome, because it is not able to find the path, and the Dashboard that shows is empty.
library(DataQualityDashboard)
viewDqDashboard(jsonPath=‘c:\myResults\ESJD\esjd-20211008144050.json’)

Do you have any idea about what I am missing?

Warning in open.connection(con, “rb”) :
cannot open file ‘c:\myResults\ESJD\esjd-20211008144050.json’: No such file or directory
Warning: Error in open.connection: cannot open the connection

Kind Regards,

clairblacketer · October 11, 2021, 6:03pm

hi @Minerva_Alvarez, I don’t think the issue is with chrome. I know this is going to sound like a silly question but are you sure the JSON file ended up in the location you gave it? This often happens to me and it invariably comes down to an incorrect character in my path.