• Calculate Eugenol Intake
• SCRIPT
  • Merge FooDB-matched Ingredient Codes to FooDB Eugenol Content File.
  • Export Eugenol Intake File for DII Calculation

Calculate Eugenol Intake

This script takes in your disaggregated dietary data and FooDB-linked descriptions to calculate eugenol intake per recall and subject.

INPUTS

• Recall_Disaggregated_mapped.csv.bz2 - Disaggregated dietary data, mapped to FooDB foods, From Step 2 of Polyphenol Estimator
• FooDB_Eugenol_Content_Final.csv - Eugenol Content for foods in FooDB, Provided File

OUTPUTS

• Recall_DII_eugenol_by_recall.csv: Sum eugenol content for each participant recall

SCRIPT

Load packages

suppressMessages(library(dplyr))
suppressMessages(library(vroom))
suppressMessages(library(tidyr))
suppressMessages(library(stringr))

Load data

# Load provided file paths
source("provided_files.R")

# Load Dietary data that has been disaggregated and connected to FooDB
input_mapped = vroom::vroom('outputs/Recall_Disaggregated_mapped.csv.bz2', 
                            show_col_types = FALSE)

# Eugenol Content in FooDB
# Note: Eugenol doesn't have retention factors from Phenol Explorer
eugenol = vroom::vroom(FooDB_eugenol, show_col_types = FALSE) %>%
  select(-c(source_type, food_name:orig_source_name))

Merge FooDB-matched Ingredient Codes to FooDB Eugenol Content File.

• Link between FooDB Polyphenol Content and code-matched data is food_id.

input_mapped_content = input_mapped %>%
  # Bring in the Polyphenol Content
  dplyr::left_join(eugenol, by = 'food_id') %>%
  # Remove content that is NA
  filter(!is.na(orig_content_avg)) %>%
  # Calculate eugenol amount consumed in milligrams
  mutate(eugenol_mg = (orig_content_avg * 0.01) * FoodAmt_Ing_g) %>%
  # Sum eugenol content by subject and recall
  group_by(subject, RecallNo) %>%
  # Calculate EUGENOL summed per recall, and rename for dietaryindex function
  mutate(EUGENOL= sum(eugenol_mg)) %>%
  ungroup() %>%
  select(c(subject, RecallNo, EUGENOL)) %>%
  # Keep distinct entries
  distinct(subject, RecallNo, .keep_all = TRUE)

Export Eugenol Intake File for DII Calculation

vroom::vroom_write(input_mapped_content, 'outputs/Recall_DII_eugenol_by_recall.csv', delim = ",")