## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----basic_10y, eval=FALSE----------------------------------------------------
# library(CVrisk)
# 
# # Calculate 10-year risk for a 50-year-old female
# risk_10y <- ascvd_10y_prevent(
#   gender = "female",
#   age = 50,
#   sbp = 160,           # Systolic blood pressure (mm Hg)
#   bp_med = 1,          # On BP medication (1=Yes, 0=No)
#   totchol = 200,       # Total cholesterol (mg/dL)
#   hdl = 45,            # HDL cholesterol (mg/dL)
#   statin = 0,          # On statin (1=Yes, 0=No)
#   diabetes = 1,        # Has diabetes (1=Yes, 0=No)
#   smoker = 0,          # Current smoker (1=Yes, 0=No)
#   egfr = 90,           # Estimated GFR (mL/min/1.73m²)
#   bmi = 35             # Body mass index (kg/m²)
# )
# 
# print(risk_10y)  # Returns risk as percentage

## ----basic_30y, eval=FALSE----------------------------------------------------
# # Calculate 30-year risk for a 45-year-old male
# risk_30y <- ascvd_30y_prevent(
#   gender = "male",
#   age = 45,
#   sbp = 130,
#   bp_med = 0,
#   totchol = 200,
#   hdl = 50,
#   statin = 0,
#   diabetes = 0,
#   smoker = 1,          # Current smoker
#   egfr = 95,
#   bmi = 28
# )
# 
# print(risk_30y)

## ----with_hba1c, eval=FALSE---------------------------------------------------
# # With HbA1c - model will automatically select "hba1c" variant
# risk_with_hba1c <- ascvd_10y_prevent(
#   gender = "male",
#   age = 55,
#   sbp = 140,
#   bp_med = 0,
#   totchol = 213,
#   hdl = 50,
#   statin = 0,
#   diabetes = 1,
#   smoker = 0,
#   egfr = 90,
#   bmi = 30,
#   hba1c = 7.5,         # Glycated hemoglobin (%)
#   model = "auto"       # Automatically uses hba1c model
# )

## ----with_uacr, eval=FALSE----------------------------------------------------
# # With UACR
# risk_with_uacr <- ascvd_10y_prevent(
#   gender = "female",
#   age = 60,
#   sbp = 150,
#   bp_med = 1,
#   totchol = 220,
#   hdl = 55,
#   statin = 1,
#   diabetes = 1,
#   smoker = 0,
#   egfr = 75,
#   bmi = 32,
#   uacr = 150          # UACR in mg/g
# )

## ----with_sdi, eval=FALSE-----------------------------------------------------
# # With ZIP code for SDI
# risk_with_sdi <- ascvd_10y_prevent(
#   gender = "male",
#   age = 52,
#   sbp = 135,
#   bp_med = 0,
#   totchol = 195,
#   hdl = 48,
#   statin = 0,
#   diabetes = 0,
#   smoker = 0,
#   egfr = 88,
#   bmi = 29,
#   zip = "02114"       # Boston, MA
# )

## ----full_model, eval=FALSE---------------------------------------------------
# # Full model with all optional predictors
# risk_full <- ascvd_10y_prevent(
#   gender = "female",
#   age = 58,
#   sbp = 145,
#   bp_med = 1,
#   totchol = 210,
#   hdl = 52,
#   statin = 1,
#   diabetes = 1,
#   smoker = 0,
#   egfr = 80,
#   bmi = 31,
#   hba1c = 7.2,
#   uacr = 100,
#   zip = "10001",
#   model = "auto"      # Will use full model
# )

## ----explicit_model, eval=FALSE-----------------------------------------------
# # Force base model even with optional predictors available
# risk_base_only <- ascvd_10y_prevent(
#   gender = "male",
#   age = 55,
#   sbp = 140,
#   bp_med = 0,
#   totchol = 213,
#   hdl = 50,
#   statin = 0,
#   diabetes = 1,
#   smoker = 0,
#   egfr = 90,
#   bmi = 30,
#   hba1c = 7.5,        # Available but will be ignored
#   model = "base"      # Explicitly use base model
# )

## ----compare_prevent_accaha, eval=FALSE---------------------------------------
# # Create sample patient data
# patient_data <- data.frame(
#   age = c(50, 55, 60),
#   gender = c("female", "male", "female"),
#   race = c("white", "aa", "white"),
#   sbp = c(160, 140, 150),
#   bp_med = c(1, 0, 1),
#   totchol = c(200, 213, 220),
#   hdl = c(45, 50, 55),
#   statin = c(0, 0, 1),
#   diabetes = c(1, 0, 1),
#   smoker = c(0, 0, 0),
#   egfr = c(90, 90, 75),
#   bmi = c(35, 30, 32)
# )
# 
# # Compare PREVENT 10-year with ACC/AHA 2013
# results <- compute_CVrisk(
#   patient_data,
#   scores = c("ascvd_10y_accaha", "ascvd_10y_prevent"),
#   age = "age",
#   gender = "gender",
#   race = "race",
#   sbp = "sbp",
#   bp_med = "bp_med",
#   totchol = "totchol",
#   hdl = "hdl",
#   statin = "statin",
#   diabetes = "diabetes",
#   smoker = "smoker",
#   egfr = "egfr",
#   bmi = "bmi"
# )
# 
# # View results
# print(results[, c("age", "gender", "ascvd_10y_accaha", "ascvd_10y_prevent")])

## ----compare_prevent_frs, eval=FALSE------------------------------------------
# # Compare PREVENT with Framingham Risk Score
# results_frs <- compute_CVrisk(
#   patient_data,
#   scores = c("ascvd_10y_frs", "ascvd_10y_prevent"),
#   age = "age",
#   gender = "gender",
#   sbp = "sbp",
#   bp_med = "bp_med",
#   totchol = "totchol",
#   hdl = "hdl",
#   diabetes = "diabetes",
#   smoker = "smoker",
#   egfr = "egfr",
#   bmi = "bmi"
# )
# 
# print(results_frs)

## ----multiple_scores, eval=FALSE----------------------------------------------
# # Calculate multiple scores including 30-year risk
# comprehensive_results <- compute_CVrisk(
#   patient_data,
#   scores = c("ascvd_10y_accaha", "ascvd_10y_frs",
#              "ascvd_10y_prevent", "ascvd_30y_prevent"),
#   age = "age",
#   gender = "gender",
#   race = "race",
#   sbp = "sbp",
#   bp_med = "bp_med",
#   totchol = "totchol",
#   hdl = "hdl",
#   statin = "statin",
#   diabetes = "diabetes",
#   smoker = "smoker",
#   egfr = "egfr",
#   bmi = "bmi"
# )
# 
# # View side-by-side comparison
# print(comprehensive_results[, c("age", "gender",
#                                 "ascvd_10y_accaha",
#                                 "ascvd_10y_frs",
#                                 "ascvd_10y_prevent",
#                                 "ascvd_30y_prevent")])

## ----model_param_compute, eval=FALSE------------------------------------------
# # Force base model for all PREVENT calculations
# results_base <- compute_CVrisk(
#   patient_data,
#   scores = c("ascvd_10y_prevent", "ascvd_30y_prevent"),
#   age = "age",
#   gender = "gender",
#   sbp = "sbp",
#   bp_med = "bp_med",
#   totchol = "totchol",
#   hdl = "hdl",
#   statin = "statin",
#   diabetes = "diabetes",
#   smoker = "smoker",
#   egfr = "egfr",
#   bmi = "bmi",
#   model = "base"      # Pass model parameter
# )

## ----missing_data, eval=FALSE-------------------------------------------------
# # Patient with missing eGFR
# risk_missing <- ascvd_10y_prevent(
#   gender = "male",
#   age = 55,
#   sbp = 140,
#   bp_med = 0,
#   totchol = 213,
#   hdl = 50,
#   statin = 0,
#   diabetes = 0,
#   smoker = 0,
#   egfr = NA,          # Missing
#   bmi = 30
# )
# 
# print(risk_missing)   # Returns NA

## ----vectorized, eval=FALSE---------------------------------------------------
# # Calculate risks for multiple patients at once
# ages <- c(45, 50, 55, 60)
# genders <- c("male", "female", "male", "female")
# sbps <- c(130, 140, 150, 160)
# 
# risks <- ascvd_10y_prevent(
#   gender = genders,
#   age = ages,
#   sbp = sbps,
#   bp_med = c(0, 0, 1, 1),
#   totchol = c(200, 210, 220, 230),
#   hdl = c(50, 45, 55, 48),
#   statin = c(0, 0, 0, 1),
#   diabetes = c(0, 0, 1, 1),
#   smoker = c(0, 1, 0, 0),
#   egfr = c(95, 90, 85, 80),
#   bmi = c(28, 30, 32, 34)
# )
# 
# print(risks)  # Returns vector of risks