🏥 Compare ICD Code Lists & Generate HTML Report with `knitr`

[dlemas]

📌 Issue Description

We need to compare two lists of ICD codes using R and generate an HTML report using knitr to summarize the differences. The report will identify missing codes that need to be requested from the Integrated Data Repository (IDR) (IDR UF Health).

🔹 Task Overview

1. Input Data:

   • List A: smm_codes_we_have.csv: ICD codes we currently have.
   • List B: smm_codes_oneflorida.csv: ICD codes available from the IDR.

2. Goal:

   • Identify which codes in List A are not present in List B.
   • Output a formatted HTML report summarizing findings.

📊 Expected Output

• A structured HTML report containing:
  • Overview of the analysis.
  • Summary table (total and missing ICD codes).
  • A downloadable CSV file of missing codes.
  • code will be uploaded to the "task_02_2025" directory

🔧 Suggested Approach

1. Load both lists in R (read.csv() or readxl::read_excel()).
2. Use setdiff() to find missing ICD codes:

   missing_codes <- setdiff(list_a$ICD_Code, list_b$ICD_Code)
   

[xKayxx]

missing_icd_codes.csv

Install package

install.packages("dplyr")

Load necessary package

library(dplyr)

Set working directory

setwd('C:/Users/Kay/Downloads')

Import CSVs

data_we_have <- read.csv('smm_codes_we_have.csv', stringsAsFactors = FALSE)
data_from_fl <- read.csv('smm_codes_oneflorida.csv', stringsAsFactors = FALSE)

Extract relevant columns and clean data

codes_we_have <- data_we_have %>%
select(diagnosis_code, diagnosis_description) %>%
mutate(diagnosis_code = trimws(tolower(diagnosis_code)))

codes_from_fl <- data_from_fl %>%
select(icd_decimal) %>%
mutate(icd_decimal = trimws(tolower(icd_decimal)))

Find missing codes

missing_codes <- setdiff(codes_we_have$diagnosis_code, codes_from_fl$icd_decimal)

Filter missing codes with their descriptions

missing_data <- codes_we_have %>%
filter(diagnosis_code %in% missing_codes)

Print summary for debugging

cat("Total codes in 'we have':", nrow(codes_we_have), "\n")
cat("Total codes in 'from_fl':", nrow(codes_from_fl), "\n")
cat("Total missing codes:", nrow(missing_data), "\n")

Save missing codes to a new CSV file

if (nrow(missing_data) > 0) {
write.csv(missing_data, "C:/Users/Kay/Downloads/missing_icd_codes.csv", row.names = FALSE)
cat("Missing codes saved to 'missing_icd_codes.csv'.\n")
} else {
cat("No missing codes found. No file was created.\n")
}

[xKayxx]

Demo video: https://drive.google.com/file/d/1560xS89XNlvnvng6TvTo3D-rMcJikhsg/view?usp=sharing

[xKayxx]

Set working directory

setwd('C:/Users/Kay/Downloads')

Load necessary packages

library(dplyr)
library(knitr)
library(kableExtra)
library(rmarkdown)

Import CSVs

data_we_have <- read.csv("smm_codes_we_have.csv", stringsAsFactors = FALSE)
data_from_fl <- read.csv("smm_codes_oneflorida.csv", stringsAsFactors = FALSE)

Extract relevant columns and clean data

codes_we_have <- data_we_have %>%
select(diagnosis_code, diagnosis_description) %>%
mutate(diagnosis_code = trimws(tolower(diagnosis_code)))

codes_from_fl <- data_from_fl %>%
select(icd_decimal) %>%
mutate(icd_decimal = trimws(tolower(icd_decimal)))

Find missing codes

missing_codes <- setdiff(codes_we_have$diagnosis_code, codes_from_fl$icd_decimal)

Filter missing codes with their descriptions

missing_data <- codes_we_have %>%
filter(diagnosis_code %in% missing_codes)

Create an HTML report manually

html_report <- "icd_comparison_report.html"

html_content <- paste(
"<title>ICD Code Comparison Report</title>",
"

ICD Code Comparison Report

",
"

Summary of Analysis

",
"",
paste(""),
paste(""),
paste(""),
"

Category	Count
Total ICD Codes (We Have)	", nrow(codes_we_have), "
Total ICD Codes (OneFlorida)	", nrow(codes_from_fl), "
Missing ICD Codes	", nrow(missing_data), "

",
"

Missing ICD Codes

",
if (nrow(missing_data) > 0) {
paste("",
paste(apply(missing_data, 1, function(row) paste("")), collapse=""),
"

Diagnosis Code	Description
", row[1], "	", row[2], "

")
} else {
"

No missing codes found.

"
},
if (nrow(missing_data) > 0) {
write.csv(missing_data, "missing_icd_codes.csv", row.names = FALSE)
"

Download Missing ICD Codes

"
} else {
""
},
"",
sep="\n"
)

Write the HTML report to a file

writeLines(html_content, html_report)

cat("HTML report generated: icd_comparison_report.html\n")

[xKayxx]

HTML Report: https://drive.google.com/file/d/1uwCzCcsHfxRo0ai6Gjs60QSJjRUXPix7/view?usp=sharing