The purpose of the peridefs package is to provide safe and easy access to validated definitions of common characteristics in real world data analysis. It provides code sets (ICD-9, ICD-10, and HCPCS/CPT) to define conditions such as hypertension, diabetes, and atherosclerotic cardiovascular disease, and it also contains generic names for common drug types (e.g., anti-diabetes).
Why peridefs?
- Dynamic and safe: each condition and drug class can be updated over time, but those updates will not break existing code or force that code to use the updated definitions.
- Built by experts: every code set is designed by Dr Ligong Chen and Hong Zhao, who have decades of experience working with claims data and have developed each code set following a standardized, validated procedure.
- Adaptable: codes are stored in pre-built specs for standard conditions, and they can be modified through a built-in API that allows codes to be removed or added. We do not recommend changing our specs, but we do want that to be an option in case it’s needed.
Quick start
A quick look at how you can get relevant information from peridefs family of get_ functions
library(peridefs)
# Retrieve ICD-10 hypertension codes as a tibble
get_hypertension_v1_codes(code_type = "dx_icd10")
#> # A tibble: 23 × 4
#> type code priority version
#> <chr> <chr> <int> <chr>
#> 1 dx_icd10 I10 1 v1
#> 2 dx_icd10 I11 1 v1
#> 3 dx_icd10 I110 1 v1
#> 4 dx_icd10 I119 1 v1
#> 5 dx_icd10 I12 1 v1
#> 6 dx_icd10 I120 1 v1
#> 7 dx_icd10 I129 1 v1
#> 8 dx_icd10 I13 1 v1
#> 9 dx_icd10 I130 1 v1
#> 10 dx_icd10 I131 1 v1
#> # ℹ 13 more rows
# Complement with icd package to look up code explanations
library(icd) # for as.icd9 / as.icd10 / explain_code functions
library(tidyverse) # for mutate / map_chr functions
get_hypertension_v1_codes(code_type = 'dx_icd10') %>%
mutate(explanation = map_chr(code, ~explain_code(as.icd10(.x))))
#> # A tibble: 23 × 5
#> type code priority version explanation
#> <chr> <chr> <int> <chr> <chr>
#> 1 dx_icd10 I10 1 v1 Essential (primary) hypertension
#> 2 dx_icd10 I11 1 v1 Hypertensive heart disease
#> 3 dx_icd10 I110 1 v1 Hypertensive heart disease with heart failure
#> 4 dx_icd10 I119 1 v1 Hypertensive heart disease without heart failure
#> 5 dx_icd10 I12 1 v1 Hypertensive chronic kidney disease
#> 6 dx_icd10 I120 1 v1 Hypertensive chronic kidney disease with stage 5 chronic kidney disease or end stage renal disease
#> 7 dx_icd10 I129 1 v1 Hypertensive chronic kidney disease with stage 1 through stage 4 chronic kidney disease, or unspecified c…
#> 8 dx_icd10 I13 1 v1 Hypertensive heart and chronic kidney disease
#> 9 dx_icd10 I130 1 v1 Hypertensive heart and chronic kidney disease with heart failure and stage 1 through stage 4 chronic kidn…
#> 10 dx_icd10 I131 1 v1 Hypertensive heart and chronic kidney disease without heart failure
#> # ℹ 13 more rows
# Retrieve generic drug names for ACE inhibitors (version 2)
get_hypertension_generics(component = 'acei_v2')
#> # A tibble: 31 × 6
#> generic brand priority condition class version
#> <chr> <list> <int> <chr> <chr> <chr>
#> 1 AMLODIPINE BESYLATE/BENAZEPRIL <chr [0]> 1 <NA> acei v2
#> 2 BENAZEPRIL <chr [0]> 1 <NA> acei v2
#> 3 BENAZEPRIL HCL <chr [0]> 1 <NA> acei v2
#> 4 BENAZEPRIL/HYDROCHLOROTHIAZIDE <chr [0]> 1 <NA> acei v2
#> 5 CAPTOPRIL <chr [0]> 1 <NA> acei v2
#> 6 CAPTOPRIL/HYDROCHLOROTHIAZIDE <chr [0]> 1 <NA> acei v2
#> 7 ENALAPRIL <chr [0]> 1 <NA> acei v2
#> 8 ENALAPRIL MALEATE <chr [0]> 1 <NA> acei v2
#> 9 ENALAPRIL MALEATE/FELODIPINE <chr [0]> 1 <NA> acei v2
#> 10 ENALAPRIL MALEATE/HCTZ <chr [0]> 1 <NA> acei v2
#> # ℹ 21 more rowsSpecs
peridefs is built on an R6 back-end that provides specs for conditions and drug classes. You can work directly with our exported specs if the get_ functions don’t provide exactly what you’re looking for.
# the spec objects all have a built-in print method that
# gives a helpful summary and recommended method for
# defining the given condition.
spec_hypertension_v1
#>
#> ── Hypertension (v1) ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Condition: `hypertension`
#> Condition def:
#> ℹ Any of the following:
#> • ≥1 inpatient claim with an ICD-9 discharge diagnosis of 401.x, 403.0x, 403.1x, or 403.9x, or ICD-10 discharge diagnosis code of I10,
#> I11.x, I12.x, I13.x, I15.x, I12.0, I12.9, I16.x in any discharge diagnosis position.
#> • ≥2 outpatient physician visit claims with the same diagnosis codes, at least 30 days apart.
#> • ≥2 pharmacy fills for an antihypertensive medication (see spec_hypertension)
#>
#> Code sets:
#> `dx_icd9`: 13 condition / 0 outcome codes
#> `dx_icd10`: 23 condition / 0 outcome codes
# just like get_hypertension_v1_codes() above
spec_hypertension_v1$get_codes()
#> # A tibble: 36 × 4
#> type code priority version
#> <chr> <chr> <int> <chr>
#> 1 dx_icd9 401 1 v1
#> 2 dx_icd9 4010 1 v1
#> 3 dx_icd9 4011 1 v1
#> 4 dx_icd9 4019 1 v1
#> 5 dx_icd9 4030 1 v1
#> 6 dx_icd9 40300 1 v1
#> 7 dx_icd9 40301 1 v1
#> 8 dx_icd9 4031 1 v1
#> 9 dx_icd9 40310 1 v1
#> 10 dx_icd9 40311 1 v1
#> # ℹ 26 more rowsSafety
These safety features are a work in progress, but the vision is as follows:
We have tests for each condition that assert the code sets are equal to static vectors. These tests ensure that package updates will never inadvertently overwrite existing code sets, meaning your analyses will never be unexplicably changed by our updates to the package.
When we make updates to a condition, we simply add a new spec (e.g.,
spec_hypertension_v1,spec_hypertension_v2,spec_hypertension_v3, etc. and throw a once-per-session warning if you are using an older version of a definition.