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Getting Started with HCUPtools

Vikrant Dev Rathore

2025-12-05

Source: vignettes/HCUPtools.Rmd
HCUPtools.Rmd

HCUPtools is an R package for accessing and working with resources from the Agency for Healthcare Research and Quality (AHRQ) Healthcare Cost and Utilization Project (HCUP). This vignette provides a comprehensive guide to using the package for common healthcare data analysis tasks.

Installation and Setup 

# Install from CRAN
install.packages("HCUPtools")

# Load the package
library(HCUPtools)
library(dplyr)  # For data manipulation examples

Part 1: Downloading CCSR Mapping Files

The Clinical Classifications Software Refined (CCSR) is a tool developed by AHRQ/HCUP to categorize ICD-10-CM diagnosis codes and ICD-10-PCS procedure codes into clinically meaningful categories. The download_ccsr() function provides direct access to these mapping files.

Download Latest Version 

# Download the latest diagnosis CCSR mapping file
dx_map <- download_ccsr("diagnosis")

# Download the latest procedure CCSR mapping file
pr_map <- download_ccsr("procedure")

Download Specific Version 

# Download a specific version (useful for reproducibility)
dx_map_v2025 <- download_ccsr("diagnosis", version = "v2025.1")
pr_map_v2025 <- download_ccsr("procedure", version = "v2025.1")

List Available Versions 

# List all available versions
all_versions <- list_ccsr_versions()
print(all_versions)

# List only diagnosis versions
dx_versions <- list_ccsr_versions("diagnosis")

# List only procedure versions
pr_versions <- list_ccsr_versions("procedure")

Part 2: Mapping ICD-10 Codes to CCSR Categories

Once you have downloaded a mapping file, you can use ccsr_map() to map ICD-10 codes to CCSR categories. This function supports multiple output formats to accommodate different analytical needs.

Prepare Sample Data 

# Create sample patient data with ICD-10 diagnosis codes
patient_data <- tibble::tibble(
  patient_id = 1:10,
  admission_date = as.Date(c("2024-01-15", "2024-02-20", "2024-03-10", 
                              "2024-04-05", "2024-05-12", "2024-06-18",
                              "2024-07-22", "2024-08-30", "2024-09-14",
                              "2024-10-08")),
  icd10_dx = c("E11.9", "I10", "M79.3", "E78.5", "K21.9", 
               "I50.9", "N18.6", "E78.5", "I25.10", "J44.1")
)

Long Format (Default)

The long format duplicates records for each assigned CCSR category. This is essential for cross-classification analysis where you need to count all assigned categories.

# Map codes using long format (default)
mapped_long <- ccsr_map(
  data = patient_data,
  code_col = "icd10_dx",
  map_df = dx_map,
  output_format = "long"
)

# View the results
head(mapped_long, 20)

# Count occurrences of each CCSR category
ccsr_counts <- mapped_long |>
  count(ccsr_category, sort = TRUE)
print(ccsr_counts)

Use Case: Long format is ideal when you want to: - Count how many times each CCSR category appears - Analyze cross-classifications (one ICD-10 code mapping to multiple CCSR categories) - Create frequency tables of CCSR categories

Wide Format

The wide format creates multiple columns (CCSR_1, CCSR_2, etc.) for multiple categories, keeping one row per ICD-10 code.

# Map codes using wide format
mapped_wide <- ccsr_map(
  data = patient_data,
  code_col = "icd10_dx",
  map_df = dx_map,
  output_format = "wide"
)

# View the results
head(mapped_wide)

Use Case: Wide format is ideal when you want to: - Keep all CCSR categories for each patient in a single row - Perform patient-level analysis - Maintain the original data structure with additional CCSR columns

Default Category Only

For diagnosis codes, CCSR assigns a “default” category that is recommended for principal diagnosis analysis. Use default_only = TRUE to extract only this default category.

# Map codes using default category only
mapped_default <- ccsr_map(
  data = patient_data,
  code_col = "icd10_dx",
  map_df = dx_map,
  default_only = TRUE
)

# View the results
head(mapped_default)

Use Case: Default category is ideal when you want to: - Analyze principal diagnoses only - Follow HCUP recommendations for diagnosis analysis - Maintain one-to-one mapping (one ICD-10 code = one CCSR category)

Part 3: Getting CCSR Descriptions

To understand what CCSR categories mean, use get_ccsr_description():

# Get descriptions for specific CCSR codes
ccsr_codes <- c("ADM010", "NEP003", "CIR019", "END001", "MBD001")
descriptions <- get_ccsr_description(ccsr_codes, map_df = dx_map)
print(descriptions)

# Get descriptions without pre-downloaded mapping (will download automatically)
descriptions_auto <- get_ccsr_description(
  c("ADM010", "NEP003"), 
  type = "diagnosis"
)

Part 4: Working with Procedure Codes

The package also supports ICD-10-PCS procedure codes:

# Download procedure mapping
pr_map <- download_ccsr("procedure")

# Create sample procedure data
procedure_data <- tibble::tibble(
  case_id = 1:5,
  procedure_date = as.Date(c("2024-01-20", "2024-02-15", "2024-03-22",
                              "2024-04-10", "2024-05-18")),
  icd10_pcs = c("0DB60ZZ", "0DT70ZZ", "0WQ3XZ", "0FB00ZZ", "0HB00ZX")
)

# Map procedure codes
mapped_procedures <- ccsr_map(
  data = procedure_data,
  code_col = "icd10_pcs",
  map_df = pr_map
)

# View the results
head(mapped_procedures)

Part 5: Complete Analysis Workflow

Here’s a complete workflow for analyzing CCSR categories in a dataset:

# Step 1: Download mapping file
dx_map <- download_ccsr("diagnosis")

# Step 2: Map diagnosis codes
patient_data_mapped <- ccsr_map(
  data = patient_data,
  code_col = "icd10_dx",
  map_df = dx_map,
  output_format = "long"
)

# Step 3: Count occurrences of each CCSR category
ccsr_counts <- patient_data_mapped |>
  count(ccsr_category, sort = TRUE)

# Step 4: Merge with descriptions for reporting
ccsr_counts_with_desc <- ccsr_counts |>
  left_join(
    get_ccsr_description(
      unique(patient_data_mapped$ccsr_category), 
      map_df = dx_map
    ),
    by = c("ccsr_category" = "ccsr_code")
  )

# Step 5: View the final results
print(ccsr_counts_with_desc)

Part 6: Downloading HCUP Summary Trend Tables

The package also provides access to HCUP Summary Trend Tables, which contain aggregated information on hospital utilization trends:

# List available tables (interactive menu)
available_tables <- download_trend_tables()
print(available_tables)

# Download a specific table by ID
# Table 2a: All Inpatient Encounter Types - Trends in Number of Discharges
table_path <- download_trend_tables("2a")

# Download all tables as a ZIP file (~81 MB)
all_tables_zip <- download_trend_tables("all")

The trend tables include: - Overview of trends in inpatient and emergency department utilization - All inpatient encounter types (discharges, percent, length of stay, mortality, population rates) - Inpatient encounter types (normal newborns, deliveries, elective/non-elective stays) - Inpatient service lines (maternal/neonatal, mental health, injuries, surgeries, medical conditions) - ED treat-and-release visits

For more information, see: HCUP Summary Trend Tables

Reading Trend Tables 

# Read the trend table data
trend_data <- read_trend_table(table_path, sheet = "National")
head(trend_data)

# List available sheets
sheets <- list_trend_table_sheets(table_path)
print(sheets)

# Read specific state data
california_data <- read_trend_table(table_path, sheet = "California")

Part 7: Accessing CCSR Change Logs

View changes between CCSR versions:

# Get change log as data table (default)
changelog <- ccsr_changelog(version = "v2026.1")
print(changelog)

# Get change log URL
changelog_url <- ccsr_changelog(version = "v2026.1", format = "url")

# View change log in default PDF viewer
ccsr_changelog(version = "v2026.1", format = "view")

# Download change log file
changelog_file <- ccsr_changelog(version = "v2026.1", format = "download")

Part 8: Generating Citations

When using HCUP data in publications, always cite the source properly:

# Generate text citation for CCSR
cat(hcup_citation())

# Generate citation for Summary Trend Tables
cat(hcup_citation(resource = "trend_tables"))

# Generate BibTeX citation (for LaTeX documents)
cat(hcup_citation(format = "bibtex"))

# Generate R citation object (for R markdown)
citation_obj <- hcup_citation(format = "r")
print(citation_obj)

Part 9: Reading Downloaded Files

If you’ve already downloaded files, you can read them directly:

# Read CCSR file from various formats
dx_map <- read_ccsr("path/to/DXCCSR-v2026-1.zip")
dx_map <- read_ccsr("path/to/DXCCSR_v2026-1.csv")
dx_map <- read_ccsr("path/to/DXCCSR_v2026-1.xlsx")
dx_map <- read_ccsr("path/to/extracted_directory/")

# Read trend table Excel file
national_data <- read_trend_table(
  "path/to/HCUP_SummaryTrendTables_T2a.xlsx",
  sheet = "National"
)

Important Notes

Data Download

  • The package downloads data directly from HCUP, so an internet connection is required for the first download
  • Downloaded files are cached by default to avoid re-downloading
  • Set cache = FALSE to disable caching

Cross-Classification

  • One ICD-10 code can map to multiple CCSR categories
  • Use long format to see all mappings
  • Use default category for principal diagnosis analysis

Default Categories

  • For diagnosis codes, CCSR assigns a default category recommended for principal diagnosis analysis
  • Use default_only = TRUE to extract only the default category

Performance

Important Disclaimer: This package is an independent, non-commercial tool developed by a third party. It is not affiliated with, endorsed by, or supported by AHRQ or HCUP in any way. This package is not an official AHRQ or HCUP product.

This package facilitates access to publicly available and free HCUP resources:

  • CCSR Mapping Files - Classification software tools (free download)
  • HCUP Summary Trend Tables - Aggregated statistical reports (free download)

Critical: This package does NOT access any HCUP databases (NIS, KID, SID, NEDS, etc.) that require purchase through the HCUP Central Distributor.

User Responsibilities

Users are responsible for: - Ensuring compliance with all applicable HCUP Data Use Agreements (DUAs) - Verifying the accuracy of results - Citing the appropriate AHRQ/HCUP sources in publications - Understanding and adhering to all HCUP data usage restrictions

Essential Resources

Additional Resources