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ARS-toscana / ConcePTIONAlgorithmPregnancies

Repository of the script of the ConcePTION Algorithm for Pregnancies
GNU Affero General Public License v3.0
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Error step_07_02 "pregnancies_description" (version 5.0.1) #72

Closed LAMaglan closed 1 year ago

LAMaglan commented 1 year ago

@GiorgioLimoncella There is an error when running step_07_02 (see screenshot) for us at UOSL. error_step_07_02_pregnancies_description

Note: the main HTML-file HTML_pregnancy_description.html is created (I guess this is the second part?)

GiorgioLimoncella commented 1 year ago

Hi @LAMaglan,

There seems to be an error in the calculation of the average gestational age at the first record for LOSTFU. The error occurs only when restricting the analysis to the years 2015-2019.

I cannot understand the error this way, I suggest commenting out lines 670-687 of the file "p_macro/pregnancies_description_HTML.Rmd" and complete the execution.

From the results we can understand what produces this error.

LAMaglan commented 1 year ago

update The rmarkdown script ran with the lines commented out. Is there something else you want me to show you / run?

LAMaglan commented 1 year ago

Follow-up: this only occurs for the UOSL ConcePTION dataset, not the (new) VAC4EU dataset

GiorgioLimoncella commented 1 year ago

Hi @LAMaglan ,

Many thanks!

I await your news on the analysis of the results.

I will send you instructions shortly explaining how to upload the results to DRE, but unfortunately I will have to ask you to run an added step which is to copy some metadata into the g_export_manuscript folder before the upload.This step will not affect the results in any way.

LAMaglan commented 1 year ago

We get this error again for v5.1.0. I did what you suggested before and it fixed it.

I cannot understand the error this way, I suggest commenting out lines 670-687 of the file "p_macro/pregnancies_description_HTML.Rmd" and complete the execution.

Again, this only happens for the ConcePTION data at UOSL, not VAC4EU. I'm not sure this is a "permanent" soltuion. Tagging @verarumi for future reference, in case something needs to be changed with the CDM tables

GiorgioLimoncella commented 1 year ago

Thank you @LAMaglan , The error in question does not affect the results, so it is OK to comment it as you did at the time.