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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 in step_02_03_T2 #56

Closed karinswart closed 1 year ago

karinswart commented 1 year ago

Hi @GiorgioLimoncella, I have the following error in step_02_03_T2:

Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'S:/DataPrive/SAS-Projecten/VAC4EU/PfizerCovVAC/Data Characterisation/ConcePTIONAlgorithmPregnancies-version_4.0/g_intermediate/LastMestrualPeriodImplyingPregnancy.RData', probable reason 'No such file or directory'

Can you help with this? Thanks!

GiorgioLimoncella commented 1 year ago

Hi @karinswart,

I found the error, you can download the fixed version of the script from the repository (not the release), by clicking on the green button "code", as in the image.

Screenshot 2023-04-28 alle 14 39 03

karinswart commented 1 year ago

Thanks, @GiorgioLimoncella! Should I rerun all? Or just the parameters and continue where I was?

GiorgioLimoncella commented 1 year ago

It would be better to relaunch everything!

karinswart commented 1 year ago

Ok, will do!

karinswart commented 1 year ago

Hi @GiorgioLimoncella, Another issue in step_04_01_T2: Error in .checkTypos(e, names_x) : Object 'pregnancy_with_dates_out_of_range' not found amongst CONCEPTSETS, EUROCAT, PROMPT, ITEMSETS

Could you again assist with this ? Thank you!

GiorgioLimoncella commented 1 year ago

Hi @karinswart,

It seems that the variable "pregnancy_with_dates_out_of_range" was not created.

This variable is constructed in internal consistency checks, basically checking that the date of the pregnancy record is included in the data reliability period.

The data reliability period is retrieved from the INSTANCE table.

Could you please check that the variabial "source_table_name" in the INSTANCE.csv file takes the same value as the origin variables in the others tables? (e.g. mo_origin in MEDICAL_OBSERVATION, origin_of_event in EVENT, so_origin in SUVEY_OBS, ...)