README.md

In aarmiller/codeBuildr: This package provides functions for loading project codes

codeBuildR

Description

This package contains useful functions for working with ICD Codes (diagnoses and procedures), CCS groupings along with NDC drug codes. It also contains datasets used to generate common code groups such as index diseases (e.g., AMI or CDI), medications (e.g., antibiotics).

This package is intended to replace and expand upon the icdplus package. All prior functions and datasets contained in icdplus have been placed in this package.

Structure

Code used to generate common disease, medication or procedure groupings are located in R/disease_codes, R/drug_codes or R/proc_codes, respectively. These scripts should generate .csv files that reside in inst/extdata. Note: these files will be stored externally to the package and are saved as raw text files to manage code revisions on GitHub, but will be installed with the package.

If code used to generate the common disease, medication and procedure groupings require manually created raw csv files, these should be stored in data-raw/disease_codes, data-raw/drug_codes or data-raw/proc_codes, respectively.

Examples - Exisiting icdplus codes

library(codeBuildr)

Crosswalk ICD-9-CM and ICD-10-CM codes

Covert ICD-9 code for C.diff to ICD-10

icd9_to_icd10("00845")

## [1] "A047"

Use children() from icd package to collect any nested codes

icd9_to_icd10("00845") %>% children()

## [1] "A047"  "A0471" "A0472"

Convert ICD-10 back to ICD-9 for C.diff

icd10_to_icd9("A047")

## [1] "00845"

Working with CCS codes

Find a ccs code from a term:

find_ccs("flu")

## # A tibble: 2 x 2
##   ccs_code ccs_category                   
##      <int> <chr>                          
## 1       55 Fluid and electrolyte disorders
## 2      123 Influenza

find_ccs("influenza")

## # A tibble: 1 x 2
##   ccs_code ccs_category
##      <int> <chr>       
## 1      123 Influenza

Get descriptions for CCS codes:

explain_ccs(c(1,100))

## # A tibble: 2 x 2
##   ccs_code ccs_category               
##      <int> <chr>                      
## 1        1 Tuberculosis               
## 2      100 Acute myocardial infarction

Get ICD-9 codes for a CCS group

get_icd_from_ccs(100)

##  [1] "4100"  "41000" "41001" "41002" "4101"  "41010" "41011" "41012" "4102" 
## [10] "41020" "41021" "41022" "4103"  "41030" "41031" "41032" "4104"  "41040"
## [19] "41041" "41042" "4105"  "41050" "41051" "41052" "4106"  "41060" "41061"
## [28] "41062" "4107"  "41070" "41071" "41072" "4108"  "41080" "41081" "41082"
## [37] "4109"  "41090" "41091" "41092"

Get ICD-10 codes for a CCS group

get_icd_from_ccs(100,icd_version = 10)

##  [1] "I2101" "I2102" "I2109" "I2111" "I2119" "I2121" "I2129" "I213"  "I214" 
## [10] "I219"  "I21A1" "I21A9" "I220"  "I221"  "I222"  "I228"  "I229"

Examples - Loading Code Sets

Loading diagnosis code sets

See the available disease code sets

avail_disease_codes()

## # A tibble: 9 x 2
##   name                 description                       
##   <chr>                <chr>                             
## 1 ami                  Acute Myocardial Infarction       
## 2 asthma               Asthma                            
## 3 cdi                  Clostridioides difficile infection
## 4 cf_carrier           Cystic Fibrosis Carrier           
## 5 cf                   Cystic Fibrosis                   
## 6 covid                COVID-19                          
## 7 pancreatitis_acute   Acute Pancreatitis                
## 8 pancreatitis_chronic Chronic Pancreatitis              
## 9 pancreatitis         Pancreatitis

Load disease codes sets

load_disease_codes(c("ami","cdi"))

## $ami
## $ami$desc
## [1] "Acute Myocardial Infarction"
## 
## $ami$icd9_codes
##  [1] "410"   "4100"  "41000" "41001" "41002" "4101"  "41010" "41011" "41012"
## [10] "4102"  "41020" "41021" "41022" "4103"  "41030" "41031" "41032" "4104" 
## [19] "41040" "41041" "41042" "4105"  "41050" "41051" "41052" "4106"  "41060"
## [28] "41061" "41062" "4107"  "41070" "41071" "41072" "4108"  "41080" "41081"
## [37] "41082" "4109"  "41090" "41091" "41092"
## 
## $ami$icd10_codes
##  [1] "I21"   "I210"  "I2101" "I2102" "I2109" "I211"  "I2111" "I2119" "I212" 
## [10] "I2121" "I2129" "I213"  "I214"  "I219"  "I21A"  "I21A1" "I21A9" "I22"  
## [19] "I220"  "I221"  "I222"  "I228"  "I229" 
## 
## 
## $cdi
## $cdi$desc
## [1] "Clostridioides difficile infection"
## 
## $cdi$icd9_codes
## [1] "00845"
## 
## $cdi$icd10_codes
## [1] "A047"  "A0471" "A0472"

Loading RX (medication) code sets

See the available rx code sets

avail_rx_codes()

## [1] "abx_cdi_risk" "all_abx"

Load an rx code set

all_abx <- load_rx_codes("all_abx")

names(all_abx)

##  [1] "clindamycin"      "fluoroquinolones" "cephalosporins"   "monobactams"     
##  [5] "carbapenems"      "penicillins"      "macrolides"       "sulfonamides"    
##  [9] "other"            "tetracyclines"    "glycopeptides"    "nitroimidazoles"

head(all_abx$clindamycin)

## [1] "00003294210" "00003294211" "00003294220" "00003294221" "00003294222"
## [6] "00009022501"

aarmiller/codeBuildr documentation built on April 14, 2025, 1:59 p.m.