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Flagged correct ICD10-CM as wrong #35

Closed Kuroshiwo closed 2 years ago

Kuroshiwo commented 2 years ago

R> ## ICD to uniform short format R> R> ICD_Short <- icdDxDecimalToShort(dxDataFile = sampleDxFile,

Wrong ICD version: total 3 ICD codes (the number of occurrences is in brackets) c("I25110 (3)", "N10 (1)", "R4182 (1)")

Warning messages: 1: The ICD mentioned above matches to "NA" due to the format or other issues. 2: "Wrong ICD format" means the ICD has wrong format 3: "Wrong ICD version" means the ICD classify to wrong ICD version (cause the "icd10usingDate" or other issues) R>

ISSUES: T814XXA is valid ICD10-CM code short version of T81.4XXA. T81.4XXA is a billable ICD code used to specify a diagnosis of infection following a procedure, initial encounter. A 'billable code' is detailed enough to be used to specify a medical diagnosis.

I25110 is a valid ICD10-CM code short version of I25.110. I25.110 is a billable ICD code used to specify a diagnosis of atherosclerotic heart disease of native coronary artery with unstable angina pectoris. A 'billable code' is detailed enough to be used to specify a medical diagnosis.

It would be better if user is allowed to select the ICD version to be used. The function argument - icd10usingDate appears to be very limiting.

Thanks for your time.

yijutseng commented 2 years ago

Hello @Kuroshiwo,

Thanks for reporting the issues.

For the first T814XXA issue, we need to check the ICD table we used in the package. @ChunJuC could you please check the table and update it to the up-to-date version?

For the second issue, I understand that the "date" might be limiting in some situations. If your data have the "tag" of the ICD version, you can use the attribute "icdVerColName" to set the version of the ICD used for the specific records. Please check the following document for further instruction. https://dhlab-tseng.github.io/dxpr/reference/dxUniform.html
@ChunJuC that would be great if you can add an example of using the "icdVerColName" attribute in the document.

Thank you,

YiJu

mircyam commented 2 years ago

Hi @Kuroshiwo,

Thanks for reporting.

For the T814XXA issue, T814XXA was reassigned to T8140XA on 2019 update of ICD-10. Since dxpr uses 2019 version of ICD-10, T814XXA is not available in our ICD table.

As for the version issue, I re-write the sample datatable with a column recording ICD version (column name = Version), so it allows to manipulate data solely by version "tag" (rather than "date"). https://dhlab-tseng.github.io/dxpr/reference/dxUniform.html Hope the instruction could help.

ICD-10 is still updating annually, so we are currently considering releasing a new version of dxpr which uses newest ICD-10 version and includes CCSR into its function.

Thanks,

Chun-Ju

Kuroshiwo commented 2 years ago

Thank you very much yijutseng and ChunJuC for your prompt response to these issues. I will check your instructions and test the application. I will provide a response later.

Have the best of the day.

Kuroshiwo

Kuroshiwo commented 2 years ago

Hi @yijutseng and @ChunJuC,

R> sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] lab_0.1.0 dxpr_0.3.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8
[6] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5
[11] tidyverse_1.3.1 data.table_1.14.2 lubridate_1.8.0 skimr_2.1.3

I followed the suggestions in your previous response, however, errors were thrown as follows:

SCENARIOS 1: "icdVerColName = 10L" was included as argument to a function as stated in the package reference manual

R> ######### I - 1) DATA INTEGRATION AND FORMAT TRANSFORMATION R> ## ICD to uniform short format R> R> ICD_Short <- icdDxDecimalToShort(dxDataFile = sampleDxFile,

SCENARIOS 2: Instead of "10L", "10" was used as "icdVerColName = 10". But an error was thrown.

R> ######### I - 1) DATA INTEGRATION AND FORMAT TRANSFORMATION R> ## ICD to uniform short format R> R> ICD_Short <- icdDxDecimalToShort(dxDataFile = sampleDxFile,

SCENARIOS 3: The argument "icdVerColName = 10" was commented out and no errors were thrown.

Did I do something wrong?

Thanks for your time.

@Kuroshiwo

mircyam commented 2 years ago

Hi @Kuroshiwo,

According to your data, the icdVerColName is supposed to be Version rather than 10 nor 10L. If there is a column recorded ICD version, then 'icdVerColName' is the column name of that column. (In this case, column name is Version, and 10L is column value.)

Could you please change the argument input, and retry if this function works.

And we will considering revising our instructions to be more clear.

Thanks!

Chun-Ju

Kuroshiwo commented 2 years ago

Hi @ChunJuC

Again, thank you for your prompt response to my request.

Yes, the icdVerColName worked as you explained. And yes, please consider revising the instructions.

Now, I am waiting for switching to current revision of ICD-10 CM so I can use the package on real world data.

Thanks for your efforts.

Kuroshiwo

mircyam commented 2 years ago

Hello @Kuroshiwo,

We have released a new version of dxpr :) In this version, we collect all valid ICD-10-CM codes from 2019 to 2022. And we also include CCSR classification method for ICD-10-CM. May you kindly check the new release, and if there is any suggestion, please contact us anytime :)

Happy coding!

Chun-Ju

Kuroshiwo commented 2 years ago

Fantastic. Thanks for the information. I will check it out and provide a feedback.

Enjoy the rest of your day.

Richard

On Mon, May 16, 2022 at 1:15 AM ChunJuC @.***> wrote:

Hello @Kuroshiwo https://github.com/Kuroshiwo,

We have released a new version of dxpr :) In this version, we collect all valid ICD-10-CM codes from 2019 to 2022. And we also include CCSR classification method for ICD-10-CM. May you kindly check the new release, and if there is any suggestion, please contact us anytime :)

Happy coding!

Chun-Ju

— Reply to this email directly, view it on GitHub https://github.com/DHLab-TSENG/dxpr/issues/35#issuecomment-1127311542, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACXK2AULTQXNRR65G73SKXLVKHYYBANCNFSM5QAUYIYQ . You are receiving this because you were mentioned.Message ID: @.***>