Procedures with ICD-10-PCS

Although I’m not a fan of procedures myself (clinical practice), I am aficionado of ICD-10 procedure codes (ICD-10-PCS). Compared to their predecessor (ICD-9), ICD-10-PCS is much more eloquent and specific, so it’s actually pleasant to work with!

Procedure classification

The most straightforward of the HCUP software tools included in this package are the Procedure Classes. Procedure classes identify procedures as [1] diagnostic or therapeutic and [2] whether they major (expected to be performed in an operating room) or minor.

library(hcup)
classify_pr("0PS443Z") # Spine surgery
#> [1] "Major Therapeutic"
classify_pr("009U3ZX") # Lumbar puncture
#> [1] "Minor Diagnostic"

This function can be vectorized (e.g. using dplyr::mutate) as shown below:

# Using the dplyr workflow
library(dplyr)
tibble(
  Patients = c("A",       "B",       "C"),
  ICD_10   = c("0PS443Z", "3E05305", "F13ZHZZ")) %>%
  mutate(pr_class = classify_pr(ICD_10))
#> # A tibble: 3 × 3
#>   Patients ICD_10  pr_class         
#>   <chr>    <chr>   <chr>            
#> 1 A        0PS443Z Major Therapeutic
#> 2 B        3E05305 Minor Therapeutic
#> 3 C        F13ZHZZ Minor Diagnostic

Although applications using ICD-9 codes aren’t covered here, this function also works the same for ICD-9 procedure codes.

classify_pr("0015") # Infusion of IL-2
#> [1] "Minor Therapeutic"

CCSR for ICD-10-PCS Procedures

Much more powerful is the Clinical Classifications Software Refined (CCSR) categories, which aggregates the expansive number of ICD-10-PCS procedure codes into a smaller number of clinically meaningful categories.

Similar to the procedure classes (and all functions starting with classify_), this categorizes ICD codes into mutually exclusive categories.

classify_ccsr_pr("0016070")
#> [1] "CNS010"

Again, this can be vectorized for use within data frames. The helper function explain_ccsr can convert these categories into human-readable labels.

library(dplyr)
tibble(icd_10 = c("04L04DZ", "009Y40Z", "0F7C7DZ", "GZ2ZZZZ")) %>%
  mutate(CCSR      = classify_ccsr_pr(icd_10),
         explained = explain_ccsr(CCSR))
#> # A tibble: 4 × 3
#>   icd_10  CCSR   explained                                                      
#>   <chr>   <chr>  <chr>                                                          
#> 1 04L04DZ CAR010 Ligation and embolization of vessels                           
#> 2 009Y40Z CNS003 Spinal canal and spinal cord drainage (excluding lumbar punctu…
#> 3 0F7C7DZ HEP008 Common bile duct sphincterotomy and stenting                   
#> 4 GZ2ZZZZ MHT004 Crisis intervention for mental health

You can also use the “detailed” option within explain_ccsr(ccsr, detailed=TRUE) to return additional data about the CCSR category. This returns a named list, which can be helpful in conjunction with the purrr package.

library(purrr)
# NOTE: The results returned when `detailed = TRUE` depends on the
#       type of CCSR category. See the `CCSR_PR_categories` or 
#       `CCSR_DX_categories` in the `hcup.data` package for details
tibble(CCSR_PR = c("URN001", "RES010", "CAR004")) %>%
  mutate(Explained = explain_ccsr(CCSR_PR),
         details   = explain_ccsr(CCSR_PR, detailed = TRUE),
         domain    = map_chr(details, "clinical_domain"))
#> # A tibble: 3 × 4
#>   CCSR_PR Explained                                      details   domain       
#>   <chr>   <chr>                                          <list>    <chr>        
#> 1 URN001  Cystoscopy and ureteroscopy (including biopsy) <chr [7]> Urinary Syst…
#> 2 RES010  Tracheostomy                                   <chr [7]> Respiratory …
#> 3 CAR004  Percutaneous coronary interventions (PCI)      <chr [7]> Cardiovascul…

Bringing it together

icd_pr_codes <- c("0PS443Z", "3E05305", "F13ZHZZ", "04L04DZ", "009Y40Z", "0F7C7DZ", "GZ2ZZZZ")

tibble(icd_pr10 = icd_pr_codes) %>%
  mutate(CCSR      = classify_ccsr_pr(icd_pr_codes),
         PR_cls    = classify_pr(icd_pr_codes),
         explained = explain_ccsr(CCSR))
#> # A tibble: 7 × 4
#>   icd_pr10 CCSR   PR_cls            explained                                   
#>   <chr>    <chr>  <chr>             <chr>                                       
#> 1 0PS443Z  MST012 Major Therapeutic Bone fixation (excluding extremities)       
#> 2 3E05305  ADM012 Minor Therapeutic Chemotherapy                                
#> 3 F13ZHZZ  ENT004 Minor Diagnostic  Diagnostic audiology                        
#> 4 04L04DZ  CAR010 Major Therapeutic Ligation and embolization of vessels        
#> 5 009Y40Z  CNS003 Major Therapeutic Spinal canal and spinal cord drainage (excl…
#> 6 0F7C7DZ  HEP008 Major Therapeutic Common bile duct sphincterotomy and stenting
#> 7 GZ2ZZZZ  MHT004 Minor Therapeutic Crisis intervention for mental health