• Calculate DII Polyphenol Subclasses
• SCRIPT
  • Filter in relevant DII subclass polyphenols
  • Specify grouping variables
  • SUM subclass intake
  • Export Polyphenol Subclass Intakes for DII Calculation

Calculate DII Polyphenol Subclasses

This script takes your data that has been mapped to FooDB polyphenol content, extracts compounds categorized under the six required DII subclasses (flavan-3-ols, Flavones, Flavonols, Flavonones, Anthocyanidins, Isoflavones), and calculates the total intake of these subclasses per participant recall or record.

INPUTS

• Diet_FooDB_polyphenol_content.csv.bz2: Disaggregated dietary data, mapped to FooDB polyphenol content, at the compound-level
• FooDB_DII_polyphenol_list.csv - Polyphenols under the six polyphenol subclasses required for DII-2014, Provided File

OUTPUTS

• Diet_DII_subclass_by_entry.csv: Sum DII polyphenol subclass content for each participant recall or record

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 mapped to polyphenol content
input_polyphenol_content = vroom::vroom('outputs/Diet_FooDB_polyphenol_content.csv.bz2',
                                        show_col_types = FALSE)

# Polyphenol classifications
subclasses = vroom::vroom(FooDB_DII_subclasses, show_col_types = FALSE)

Filter in relevant DII subclass polyphenols

input_polyphenol_content_filtered = input_polyphenol_content %>%
  dplyr::filter(compound_public_id %in% subclasses$compound_public_id) %>%
  # Merge the class information so subclasses are grouped correctly
  dplyr::left_join(subclasses)

## Joining with `by = join_by(compound_public_id, compound_name)`

Specify grouping variables

Column grouping depends on whether output is from a record or recall.

if ("RecallNo" %in% names(input_polyphenol_content_filtered)) {
  group_vars = c("subject", "RecallNo", "component")
  
} else if ("RecordNo" %in% names(input_polyphenol_content_filtered)) {
  group_vars = c("subject", "RecordNo", "RecordDayNo", "component")
  
} else {
  stop("Data must contain RecallNo or RecordNo.")
}

SUM subclass intake

The column component contains the DII category.

subclass_intakes = input_polyphenol_content_filtered %>%
  dplyr::group_by(across(all_of(group_vars))) %>%
  # Sum polyphenol category intake, mg by recall
  dplyr::mutate(component_sum = sum(pp_consumed)) %>%
  dplyr::ungroup() %>%
  # Keep distinct entries
  dplyr::distinct(across(all_of(group_vars)), .keep_all = TRUE) %>%
  # Minimize the number of columns for pivoting to wide format
  dplyr::select(c(subject,
                  any_of(c("RecallNo", "RecordNo", "RecordDayNo")),
                  component, component_sum)) %>%
  # pivot to wide version
  tidyr::pivot_wider(names_from = component, values_from = component_sum) %>%
  # Rename the columns to match the DII category names in the DietaryIndex function
  dplyr::rename(
    ISOFLAVONES = Isoflavones,
    "FLA3OL" = "Flavan-3-ols",
    "FLAVONES" = "Flavones",
    "FLAVONOLS" =  "Flavonols",
    "FLAVONONES" = "Flavanones",
    "ANTHOC" = "Anthocyanidins")

Export Polyphenol Subclass Intakes for DII Calculation

vroom::vroom_write(subclass_intakes, 'outputs/Diet_DII_subclass_by_entry.csv', delim = ",")