Calculate Total Polypenol Intakes

This script calculates total polyphenol intake (mg, mg/1000kcal) for provided dietary data.

INPUTS

  • Recall_FooDB_polyphenol_content.csv.bz2: Disaggregated dietary data, mapped to FooDB polyphenol content, at the compound-level
  • Recall_total_nutrients.csv - total daily nutrient data to go with dietary data.

OUTPUTS

  • summary_total_intake_by_subject.csv
  • summary_total_intake_by_recall.csv

SCRIPTS 

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

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

# Load dietary data mapped to polyphenol content
input_polyphenol_content = vroom::vroom('outputs/Recall_FooDB_polyphenol_content.csv.bz2',
                                        show_col_types = FALSE)

input_kcal = vroom::vroom('outputs/Recall_total_nutrients.csv', show_col_types = FALSE) %>%
  # Ensure consistent KCAL naming whether ASA24 or NHANES
  rename_with(~ "Total_KCAL", .cols = any_of(c("Total_KCAL", # Specific to ASA24
                                               "Total_DRXIKCAL"))) %>%  # Specific to NHANES
  select(c(subject, RecallNo, Total_KCAL))

# Merge the two files
input_polyphenol_kcal = left_join(input_polyphenol_content, input_kcal)

## Joining with `by = join_by(subject, RecallNo)`

Total daily Polyphenol Intake Numbers BY RECALL 

content_by_recall = input_polyphenol_kcal %>%
  
  # Sum by Recall and Participant
  group_by(subject, RecallNo) %>%
  mutate(pp_recallsum_mg = sum(pp_consumed, na.rm = TRUE),
         pp_recallsum_mg1000kcal = pp_recallsum_mg/(Total_KCAL/1000)) %>%
  ungroup() %>%
  distinct(subject, RecallNo, .keep_all = TRUE) %>%
  select(c(subject, RecallNo, pp_recallsum_mg, Total_KCAL, pp_recallsum_mg1000kcal))

# Write Output
vroom::vroom_write(content_by_recall, "outputs/summary_total_intake_by_recall.csv", delim = ",")

Total daily Polyphenol Intake Numbers AVERAGE FOR SUBJECT 

content_by_subject = content_by_recall %>%
  
  # Average by Participant
  group_by(subject) %>%
  mutate(pp_average_mg = mean(pp_recallsum_mg, na.rm = TRUE),
         kcal_average = mean(Total_KCAL, na.rm = TRUE),
         pp_average_mg_1000kcal = pp_average_mg/(kcal_average/1000)) %>%
  ungroup() %>%
  distinct(subject, .keep_all = TRUE) %>%
  select(c(subject, pp_average_mg, kcal_average, pp_average_mg_1000kcal))

# Write Output
vroom::vroom_write(content_by_subject, "outputs/summary_total_intake_by_subject.csv", delim = ",")