pathologie

Tidy ICD-10-CM Interface

📦 Installation

You can install pathologie from GitHub with:

# install.packages("pak")
pak::pak("andrewallenbruce/pathologie")

🔰 Usage

library(pathologie)
library(fuimus)
library(dplyr)

icd10cm(icd = c("I10", "I15.0")) |> 
  glimpse()
#> Rows: 2
#> Columns: 10
#> $ icd_ch_no       <int> 9, 9
#> $ icd_ch_abb      <chr> "CARDIO", "CARDIO"
#> $ icd_ch_name     <chr> "Diseases of the circulatory system", "Diseases of the…
#> $ icd_ch_range    <chr> "I00 - I99", "I00 - I99"
#> $ icd_sec_name    <chr> "Other rheumatic heart diseases", "Secondary hypertens…
#> $ icd_sec_range   <chr> "I09 - I10", "I15 - I15.9"
#> $ order           <int> 11397, 11411
#> $ valid           <int> 1, 1
#> $ icd_code        <chr> "I10", "I15.0"
#> $ icd_description <chr> "Essential (primary) hypertension", "Renovascular hype…

icd10api(icd_code = "I1")
#> # A tibble: 18 × 2
#>    icd_code icd_description                                                     
#>    <chr>    <chr>                                                               
#>  1 I10      Essential (primary) hypertension                                    
#>  2 I11.0    Hypertensive heart disease with heart failure                       
#>  3 I11.9    Hypertensive heart disease without heart failure                    
#>  4 I12.0    Hypertensive chronic kidney disease with stage 5 chronic kidney dis…
#>  5 I12.9    Hypertensive chronic kidney disease with stage 1 through stage 4 ch…
#>  6 I13.0    Hypertensive heart and chronic kidney disease with heart failure an…
#>  7 I13.10   Hypertensive heart and chronic kidney disease without heart failure…
#>  8 I13.11   Hypertensive heart and chronic kidney disease without heart failure…
#>  9 I13.2    Hypertensive heart and chronic kidney disease with heart failure an…
#> 10 I15.0    Renovascular hypertension                                           
#> 11 I15.1    Hypertension secondary to other renal disorders                     
#> 12 I15.2    Hypertension secondary to endocrine disorders                       
#> 13 I15.8    Other secondary hypertension                                        
#> 14 I15.9    Secondary hypertension, unspecified                                 
#> 15 I16.0    Hypertensive urgency                                                
#> 16 I16.1    Hypertensive emergency                                              
#> 17 I16.9    Hypertensive crisis, unspecified                                    
#> 18 I1A.0    Resistant hypertension

ICD-10-CM Conflict Rules

ex_data() |>
  dplyr::mutate(
    patient_age = years_floor(
      date_of_birth, 
      date_of_service
      )
    ) |>
  dplyr::left_join(
    search_edits(), 
    by = dplyr::join_by(icd_code), 
    relationship = "many-to-many"
    ) |>
  dplyr::filter(
    icd_conflict_group == "Age"
    ) |>
  dplyr::mutate(
    conflict = apply_age_edits(
      rule = icd_conflict_rule,
      age = patient_age
      )
    )
#> # A tibble: 224 × 8
#>    date_of_birth date_of_service icd_code patient_age icd_description           
#>    <date>        <date>          <chr>          <dbl> <chr>                     
#>  1 2015-11-27    2023-01-08      Z00.00             7 Encntr for general adult …
#>  2 1990-11-07    2023-11-13      F53.0             33 Postpartum depression     
#>  3 2006-12-23    2023-09-26      F64.2             16 Gender identity disorder …
#>  4 1986-01-25    2023-08-05      Z91.82            37 Personal history of milit…
#>  5 1992-10-23    2023-06-29      O90.6             30 Postpartum mood disturban…
#>  6 2014-01-25    2023-06-27      Z00.00             9 Encntr for general adult …
#>  7 2011-01-07    2023-04-12      F64.2             12 Gender identity disorder …
#>  8 1992-12-03    2023-03-02      F53.0             30 Postpartum depression     
#>  9 2000-11-12    2023-10-16      F53.0             22 Postpartum depression     
#> 10 1993-10-12    2022-12-13      F53.0             29 Postpartum depression     
#> # ℹ 214 more rows
#> # ℹ 3 more variables: icd_conflict_group <chr>, icd_conflict_rule <chr>,
#> #   conflict <chr>

---

⚖️ Code of Conduct

Please note that the pathologie project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

🏛️ Governance

This project is primarily maintained by Andrew Bruce. Other authors may occasionally assist with some of these duties.