#------------------------------------------------------------------------------#

#	                        WFP RAM Standardized Scripts
#             Calculating Food Consumption Score - Nutrition (FCSN)

#------------------------------------------------------------------------------#

rm(list = ls())

## Load Packages --------------------------------------------------------------#

library(tidyverse)
library(labelled)
library(expss)

# Load Sample Data ------------------------------------------------------------#

data <- read_csv("~/GitHub/RAMResourcesScripts/Static/FCSN_Sample_Survey.csv")

# Label FCSN relevant variables -----------------------------------------------#

var_label(data$FCSNPrMeatF) <- "Consumption in past 7 days: Flesh meat"
var_label(data$FCSNPrMeatO) <- "Consumption in past 7 days: Organ meat"
var_label(data$FCSNPrFish)  <- "Consumption in past 7 days: Fish/shellfish"
var_label(data$FCSNPrEggs)  <- "Consumption in past 7 days: Eggs"
var_label(data$FCSNVegOrg)  <- "Consumption in past 7 days: Orange vegetables (vegetables rich in Vitamin A)"
var_label(data$FCSNVegGre)  <- "Consumption in past 7 days: Green leafy vegetables"
var_label(data$FCSNFruiOrg) <- "Consumption in past 7 days: Orange fruits (Fruits rich in Vitamin A)"
	
#recode "n/a" values to 0 and change to numeric
vars2recode <- c("FCSNPrMeatF","FCSNPrMeatO","FCSNPrFish","FCSNPrEggs",
                 "FCSNVegOrg","FCSNVegGre","FCSNFruiOrg")

data <- data %>% mutate_at(vars2recode, ~replace(., . == "n/a", "0"))
data <- data %>% mutate_at(vars2recode, as.numeric)

# Compute aggregates of key micronutrient consumption -------------------------#

## Vitamin A-Rich Foods -------------------------------------------------------#

data <- data %>% mutate(FGVitA = FCSDairy +FCSNPrMeatO +FCSNPrEggs +
                                 FCSNVegOrg +FCSNVegGre +FCSNFruiOrg)
var_label(data$FGVitA) <- "Consumption of vitamin A-rich foods"

## Protein-Rich Foods ---------------------------------------------------------#

data <- data %>% mutate(FGProtein = FCSPulse +FCSDairy +FCSNPrMeatF +
                                    FCSNPrMeatO +FCSNPrFish +FCSNPrEggs)
var_label(data$FGProtein) <- "Consumption of protein-rich foods"

## Iron-Rich Foods ------------------------------------------------------------#

data <- data %>% mutate(FGHIron = FCSNPrMeatF +FCSNPrMeatO +FCSNPrFish)
var_label(data$FGHIron) <- "Consumption of heme iron-rich foods"

## recode into nutritious groups  ---------------------------------------------#

data <- data %>% mutate(FGVitACat = case_when(FGVitA == 0 ~ 1,
                                    between(FGVitA,1,6)   ~ 2, 
                                    FGVitA >= 7           ~ 3),
                        FGProteinCat = case_when(FGProtein == 0 ~ 1, 
                                       between(FGProtein,1,6)   ~ 2,
                                       FGProtein >= 7           ~ 3),
                        FGHIronCat = case_when(FGHIron == 0 ~ 1,
                                     between(FGHIron,1,6)   ~ 2,
                                     FGHIron >= 7           ~ 3))

# define variables labels and properties for FGVitACat FGProteinCat FGHIronCat
data <- data %>%
  mutate(across(c(FGVitACat, FGProteinCat, FGHIronCat), 
                ~labelled(., labels = c(
                  "Never consumed" = 1,
                  "Consumed sometimes" = 2,
                  "Consumed at least 7 times" = 3
                ))))

data <- data %>%
  mutate(across(c(FGVitACat, FGProteinCat, FGHIronCat),
                ~factor(., levels = c(1, 2, 3),
                           labels = c("Never consumed", "Consumed sometimes", 
                                   "Consumed at least 7 times"))))

var_label(data$FGVitACat)    <- "Consumption group of vitamin A-rich foods"
var_label(data$FGProteinCat) <- "Consumption group of protein-rich foods"
var_label(data$FGHIronCat)   <- "Consumption group of heme iron-rich foods"

# End of Scripts