Introduction

The adult comorbidities defined by authors such as Charlson, Quan and Elixhuaser are not suitable for pediatric research. Feudtner and others produced comorbidity definitions suitable for infants and children, with mappings defined for both ICD-9 and ICD-10 codes (Feinstein et al. 2018; Feudtner et al. 2014). These are now included in the icd package for R, which enables fast calculation of comorbidities for PCCC and other ICD code to comorbidity maps.

Calculating PCCC comorbidities

The PCCC comorbidities may be derived from both diagnostic and procedure codes. The following simulated data has both:

head(dat)
#>      id icd_dx1 icd_dx2
#> 1 10001   C8411   K0849
#> 2 10002 S20451A S52699M
#> 3 10003    I600    Z990
#> 4 10004  T424X6 S42016K
#> 5 10005   M2117  T477X3
#> 6 10006  S60559     H69

The data is in ‘wide’ format. icd no longer needs the data to be in ‘long’ format. The PCCC comorbidity classes can be computed directly from the source data and summarized in a plot. Here we calculate the PCCC from ICD diagnostic codes and ICD procedure codes separately, and logically combine them to get the result.

pccc_dx <- comorbid_pccc_dx(dat)
pccc_pcs <- icd10_comorbid_pccc_pcs(dat,
  icd_name = c("icd_pcs1", "icd_pcs2")
)
res <- pccc_dx | pccc_pcs

res[295:300, ]
#>       Neuromusc   CVD Respiratory Renal    GI HematoImmu Metabolic
#> 10295     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#> 10296     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#> 10297     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#> 10298     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#> 10299     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#> 10300     FALSE FALSE       FALSE FALSE FALSE      FALSE     FALSE
#>       CongeniGenetic Malignancy Neonatal TechDep Transplant
#> 10295          FALSE      FALSE    FALSE   FALSE      FALSE
#> 10296          FALSE      FALSE    FALSE   FALSE      FALSE
#> 10297          FALSE      FALSE    FALSE   FALSE      FALSE
#> 10298          FALSE      FALSE    FALSE   FALSE      FALSE
#> 10299          FALSE      FALSE    FALSE   FALSE      FALSE
#> 10300          FALSE      FALSE    FALSE   FALSE      FALSE

Let’s look at the summary results:

colSums(res)
#>      Neuromusc            CVD    Respiratory          Renal             GI 
#>            236            294             97            101            239 
#>     HematoImmu      Metabolic CongeniGenetic     Malignancy       Neonatal 
#>            121            198            139            152            101 
#>        TechDep     Transplant 
#>            565            165