inst/doc/essential8-get-started.R

In essential8: Reproducible Cardiovascular Health Metric Scoring

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

## ----create-data--------------------------------------------------------------
library(essential8)

adult_data <- data.frame(
  id = c("patient_1", "patient_2"),
  age = c(42, 61),
  sex = c("female", "male"),
  # Daily servings
  olive_oil = c(2, 1),
  green_leafy_vegetables = c(1, 0.5),
  other_vegetables = c(2, 1),
  whole_grains = c(2, 1),
  # Weekly servings
  berries = c(3, 1),
  other_fruit = c(5, 2),
  meat = c(2, 5),
  fish = c(3, 1),
  chicken = c(2, 4),
  cheese = c(1, 4),
  butter_cream = c(1, 5),
  beans = c(3, 1),
  sweets_and_pastries = c(1, 5),
  nuts = c(4, 1),
  fast_food = c(0, 2),
  alcohol = c(4, 0),
  moderate_activity_minutes = c(100, 60),
  vigorous_activity_minutes = c(25, 0),
  smoking_status = c("never", "former"),
  years_since_quit = c(0, 6),
  current_inhaled_nds = c(FALSE, FALSE),
  secondhand_smoke_home = c(FALSE, FALSE),
  sleep_hours = c(7.5, 6.5),
  bmi = c(24.2, 24.0),
  bmi_profile = c("general", "asian_pacific"),
  non_hdl_cholesterol = c(125, 145),
  lipid_lowering_treatment = c(FALSE, TRUE),
  diabetes = c(FALSE, FALSE),
  glucose_measure = c("fasting_glucose", "hba1c"),
  glucose_value = c(95, 6.0),
  systolic_bp = c(118, 132),
  diastolic_bp = c(76, 84),
  antihypertensive_treatment = c(FALSE, TRUE)
)

## ----score-data---------------------------------------------------------------
scored <- score_le8(adult_data, diet_method = "mepa")

scored[c(
  "id",
  "mepa_total",
  "le8_diet_score",
  "physical_activity_moderate_equivalent_minutes",
  "le8_composite_score",
  "le8_category"
)]

## ----component-scores---------------------------------------------------------
component_columns <- setdiff(
  grep("^le8_.*_score$", names(scored), value = TRUE),
  "le8_composite_score"
)

scored[c("id", component_columns)]

## ----percentile---------------------------------------------------------------
percentile_data <- adult_data[1, , drop = FALSE]
percentile_data$diet_value <- 95
percentile_scores <- score_le8(
  percentile_data,
  diet_method = "percentile"
)
percentile_scores[
  c("diet_value", "le8_diet_score", "le8_composite_score")
]

## ----incomplete-data----------------------------------------------------------
incomplete_data <- adult_data
incomplete_data$sleep_hours[1] <- NA_real_
incomplete_data$bmi[2] <- NA_real_

incomplete_scores <- score_le8(
  incomplete_data,
  min_components = 7
)

incomplete_scores[c(
  "id",
  "le8_composite_score",
  "le8_n_components",
  "le8_complete"
)]