## ----setup, include=FALSE-----------------------------------------------------
suppressWarnings({
  suppressPackageStartupMessages({
    loadNamespace("knitr") # for opts_chunk only
    library("icdcomorbid")
    library("magrittr")
    })
  })
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(icdcomorbid)

## ----add-decimal--------------------------------------------------------------
# Example ICD code dataframe
df <- data.frame(
  id = c(1, 2, 3),
  icd_1 = c("C509", "D633", "I210"),
  icd_2 = c("D509", "E788", "N183")
)

# Adding decimal to the ICD codes
formatted_df <- add_decimal(df, icd_cols = c("icd_1", "icd_2"))

# Displaying the updated dataframe
print(formatted_df)

## ----long-to-wide-------------------------------------------------------------
# Example long format data with multiple rows per patient
long_data <- data.frame(
  patient_id = c(1, 1, 2, 2, 3),
  icd_1 = c("A01", "A02", "B01", "B02", "C01"),
  icd_2 = c("D01", "E02", "F01", "G02", "H01")
)

# Reshaping the data to wide format
wide_data <- long_to_wide(long_data, idx = "patient_id", icd_cols = c("icd_1", "icd_2"))

# Displaying the reshaped data
print(wide_data)

## ----icd9-example-------------------------------------------------------------
# Example ICD-9 data
icd9_data <- data.frame(
  patient_id = c(1, 1, 2, 2, 3),
  icd9_code = c("4010", "2500", "4140", "4280", "4930")
)

# Map ICD-9 codes to comorbidities using Charlson index
mapping <- "charlson9"

comorbidities_icd9 <- icd9_to_comorbid(
  df = icd9_data,
  idx = "patient_id",
  icd_cols = "icd9_code",
  mapping = mapping,
  batch_size = 2
)

# Display the comorbidity results
head(comorbidities_icd9)

## ----icd10-example------------------------------------------------------------
# Example data with ICD-10 codes
icd10_data <- data.frame(
  patient_id = c(1, 1, 2, 2, 3),
  icd_code = c("E11", "I10", "E11", "I50", "I21")
)
mapping <- "quan_elixhauser10"

# Calculate comorbidities for ICD-10 data using Elixhauser index
icd10_comorbidities <- icd10_to_comorbid(
  df = icd10_data,
  idx = "patient_id",
  icd_cols = "icd_code",
  mapping = mapping,
  batch_size = 2
)

# Display the comorbidity results
head(icd10_comorbidities)

## ----custom-mapping-----------------------------------------------------------
# Custom mapping
custom_mapping <- list(
  "Hypertension" = c("4010", "4011", "4019"),
  "Diabetes" = c("2500", "2501", "2502")
)

# Map ICD-9 codes to comorbidities using custom mapping
comorbidities_custom <- icd9_to_comorbid(
  df = icd9_data,
  idx = "patient_id",
  icd_cols = "icd9_code",
  mapping = custom_mapping,
  batch_size = 2
)

# Display the comorbidity results
head(comorbidities_custom)

## ----episode-of-care----------------------------------------------------------
# Example data with admit and discharge dates for DAD and NACRS
dad_data <- data.frame(
    patient_id = c(1, 1, 2),
    dad_admit = as.POSIXct(c("2023-01-01 10:00:00", "2023-02-01 09:00:00", 
    												 "2023-01-15 08:00:00"), tz="UTC"),
    dad_dis = as.POSIXct(c("2023-01-10 15:00:00", "2023-02-10 14:00:00", 
    											 "2023-01-20 12:00:00"), tz="UTC")
)

nacrs_data <- data.frame(
    patient_id = c(1, 2, 2),
    nacrs_admit = as.POSIXct(c("2023-01-15 10:00:00", "2023-01-25 09:00:00", 
    													 "2023-03-01 08:00:00"), tz="UTC"),
    nacrs_dis = as.POSIXct(c("2023-01-20 15:00:00", "2023-01-30 14:00:00", 
    												 "2023-03-05 12:00:00"), tz="UTC")
)

# Creating episodes of care
episodes <- episode_of_care(dad_data, nacrs_data, patient_id_col = "patient_id", 
														dad_visit_date_col = "dad_admit", 
														dad_exit_date_col = "dad_dis", 
														nacrs_visit_date_col = "nacrs_admit", 
														nacrs_exit_date_col = "nacrs_dis")
head(episodes)