R/diet.R

In Big-Life-Lab/cchsflow: Transforming and Harmonizing CCHS Variables

#' @title Diet score
#'
#' @description This function creates a derived diet variable (diet_score)
#'  based on consumption of fruit, salad, potatoes, carrots, other vegetables
#'  and juice. 2 baseline points plus summation of total points for diet
#'  attributes. Negative overall scores are recoded to 0, resulting in a range
#'  from 0 to 10.
#' 
#' \itemize{
#'   \item 1 point per daily fruit and vegetable consumption, excluding fruit 
#'   juice (maximum 8 points).
#'   \item -2 points for high potato intake (>=7 (males),
#'    >=5 (females) times/week)
#'   \item -2 points for no carrot intake
#'   \item -2 points per daily frequency of fruit juice consumption greater than 
#'   once/day (maximum -10 points)
#'  }
#'
#' @details 
#'  While diet score can be calculated for all survey respondents, in
#'  the 2005 CCHS survey cycle, fruit and vegetable consumption was an optional
#'  section in which certain provinces had opted in to be asked to respondents.
#'  In this survey cycle, fruit and vegetable consumption was asked to
#'  respondents in British Columbia, Ontario, Alberta, and Prince Edward Island.
#'  As such, diet score has a large number of missing respondents for this 
#'  cycle.
#'
#' @param FVCDFRU daily consumption of fruit
#'
#' @param FVCDSAL daily consumption of green salad
#'
#' @param FVCDPOT daily consumption of potatoes
#'
#' @param FVCDCAR daily consumption of carrots
#'
#' @param FVCDVEG daily consumption of other vegetables
#'
#' @param FVCDJUI daily consumption of fruit juice
#' 
#' @param DHH_SEX sex; 1 = male, 2 = female
#'
#' @examples 
#' # Using the diet_score_fun function to create the derived diet variable  
#' # across CCHS cycles.
#' # diet_score_fun() is specified in the variable_details.csv.
#'
#' # To create a harmonized diet_score variable across CCHS cycles, use 
#' # rec_with_table() for each CCHS cycle and specify diet_score_fun and the
#' # required base variables.
#' # Using merge_rec_data(), you can combine diet_score across cycles.
#'
#' library(cchsflow)
#'
#' diet_score2009_2010 <- rec_with_table(
#'   cchs2009_2010_p, c(
#'     "FVCDFRU", "FVCDSAL", "FVCDPOT", "FVCDCAR", "FVCDVEG", "FVCDJUI", 
#'     "DHH_SEX", "diet_score"
#'   )
#' )
#'
#' head(diet_score2009_2010)
#'
#' diet_score2011_2012 <- rec_with_table(
#'   cchs2011_2012_p,c(
#'     "FVCDFRU", "FVCDSAL", "FVCDPOT", "FVCDCAR", "FVCDVEG", "FVCDJUI", 
#'     "DHH_SEX", "diet_score"
#'   )
#' )
#'
#' tail(diet_score2011_2012)
#'
#' combined_diet_score <- suppressWarnings(merge_rec_data(diet_score2009_2010,
#'  diet_score2011_2012))
#'
#' head(combined_diet_score)
#' tail(combined_diet_score)
#' @export
diet_score_fun <-
  function(FVCDFRU, FVCDSAL, FVCDPOT, FVCDCAR, FVCDVEG, FVCDJUI, DHH_SEX) {
    all_diet_score_parameters <- c(
      FVCDFRU, FVCDSAL, FVCDPOT, FVCDCAR, FVCDVEG, FVCDJUI
    )
    if(sum(haven::is_tagged_na(all_diet_score_parameters, "a")) > 0) {
      return(haven::tagged_na("a"))
    }
    if(sum(haven::is_tagged_na(all_diet_score_parameters, "b")) > 0) {
      return(haven::tagged_na("b"))
    }
    
    if("NA(b)" %in% c(FVCDFRU, FVCDSAL, FVCDPOT, FVCDCAR, FVCDVEG, FVCDJUI)) {
      return("NA(b)")
    }
    
    # Total fruit and vegetables, excluding fruit juice
      total_fruitveg <- 
        if_else2(!is.na(FVCDFRU) & !is.na(FVCDSAL) & !is.na(FVCDPOT) & 
                   !is.na(FVCDCAR)  & !is.na(FVCDVEG), FVCDFRU + FVCDSAL + 
                   FVCDPOT + FVCDCAR + FVCDVEG, NA)
    
    # Maximum total fruit and vegetables = 8
      max_fruitveg <-
        if_else2(is.na(total_fruitveg), NA,
                 if_else2(total_fruitveg>8, 8, total_fruitveg))
    
    # High potato intake flag
      daily_pot_limit <-
        if_else2(DHH_SEX==1, 1,
                 if_else2(DHH_SEX==2, 5/7, NA))
      FVCDPOT_high <-
        if_else2(is.na(FVCDPOT), NA,
                 if_else2(FVCDPOT>=(daily_pot_limit), 1, 0))

    # No carrot intake flag
      FVCDCAR_nil <-
        if_else2(is.na(FVCDCAR), NA,
                 if_else2(FVCDCAR==0, 1, 0))

    # High juice intake flag
      FVCDJUI_high <-
        if_else2(is.na(FVCDJUI), NA,
                 if_else2(FVCDJUI <=1, 0, FVCDJUI - 1))

   diet_raw_score <- if_else2(!is.na(max_fruitveg) & !is.na(FVCDPOT_high) & 
                     !is.na(FVCDCAR_nil) & !is.na(FVCDJUI_high),  2 +
                       max_fruitveg - (2*FVCDPOT_high) - (2*FVCDCAR_nil) - 
                       (2*FVCDJUI_high), NA)
   
  diet_score <- if_else2(diet_raw_score <0, 0,
            if_else2(diet_raw_score >10, 10,
                    if_else2(!is.na(diet_raw_score), diet_raw_score,
                             tagged_na("b"))))
   return(diet_score)
  }


#' @title Categorized diet score
#' 
#' @description This function creates a categorical derived diet variable 
#' (diet_score_cat3) that categorizes derived diet score (diet_score).
#' 
#' @details The diet score is based on consumption of fruit, salad, potatoes, 
#' carrots, other vegetables and juice. 2 baseline points plus summation of 
#' total points for diet attributes. Negative overall scores are recoded to 0, 
#' resulting in a range from 0 to 10.The categories were based on the 
#' Mortality Population Risk Tool (Douglas Manuel et al. 2016). 
#' 
#' diet_score_cat3 uses the derived variable diet_score. diet_score uses 
#' sex, and fruit and vegetable variables that have been transformed by 
#' cchsflow (see documentation on diet_score). In order to categorize diet 
#' across CCHS cycles, sex, and fruit and vegetable variables must be 
#' transformed and harmonized.
#' 
#' @param diet_score derived variable that calculates diet score.
#' See \code{\link{diet_score_fun}} for documentation on how variable 
#' was derived.
#' 
#' @return value for diet score categories using diet_score_cat3 variable.
#' 
#' @examples 
#' # Using the diet_score_fun_cat function to categorize the derived diet 
#' # variable across CCHS cycles.
#' # diet_score_fun_cat() is specified in the variable_details.csv.
#'
#' # To create a harmonized diet_score_cat3 variable across CCHS cycles, use 
#' # rec_with_table() for each CCHS cycle.
#' # Since diet_score is also a derived variable, you will have to specify 
#' # the variables that are derived from it.
#' # Using merge_rec_data(), you can combine diet_score_cat3 across cycles.
#'
#' library(cchsflow)
#'
#' diet_score_cat2009_2010 <- rec_with_table(
#'   cchs2009_2010_p, c(
#'     "FVCDFRU", "FVCDSAL", "FVCDPOT", "FVCDCAR", "FVCDVEG", "FVCDJUI", 
#'     "DHH_SEX", "diet_score", "diet_score_cat3"
#'   )
#' )
#'
#' head(diet_score_cat2009_2010)
#'
#' diet_score_cat2011_2012 <- rec_with_table(
#'   cchs2011_2012_p,c(
#'     "FVCDFRU", "FVCDSAL", "FVCDPOT", "FVCDCAR", "FVCDVEG", "FVCDJUI", 
#'     "DHH_SEX", "diet_score", "diet_score_cat3"
#'   )
#' )
#'
#' tail(diet_score_cat2011_2012)
#'
#' combined_diet_score_cat <- suppressWarnings(merge_rec_data(
#' diet_score_cat2009_2010, diet_score_cat2011_2012))
#'
#' head(combined_diet_score_cat)
#' tail(combined_diet_score_cat)
#' @export

diet_score_fun_cat <-
  function(diet_score){
    # Poor diet
    if_else2(diet_score >=0 & diet_score < 2, 1,
    # Fair diet 
    if_else2(diet_score >=2 & diet_score < 8, 2,
    # Adequate diet 
    if_else2(diet_score >=8 & diet_score <= 10, 3,
    # No response
    if_else2(haven::is_tagged_na(diet_score, "a"), "NA(a)", "NA(b)"))))
  }