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create_index_version2.R
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########################################################################################
# Project : AHAH Index - Version 2
# Program name : create_index_v2.R
# Author : Konstantinos Daras - [email protected]
# Date created : 26 Feb 2019
# Purpose : Calculates the domains and the overall AHAH index.
#
# Revision History --------------------------------------------------------------------
# Date Author Ref Revision (Date in YYYYMMDD format)
# 26 Feb 2019 KD 1 Original code.
########################################################################################
library(nFactors)
# Quantile calcs
idr <- function(x){((x-quantile(x, 0.5, na.rm=TRUE)))/
((quantile(x, 0.95, na.rm=TRUE))-(quantile(x, 0.05, na.rm=TRUE)))}
# Exponential transformation ~> X=-23 ln(1-R(1-exp(-100/23)))
exp_trans <- function(x,y){-23*log(1-(x/nrow(y))*(1-exp(-100/23)), base = exp(1))}
# Use of Rankit rank-based normalisation
exp_default <- function(x,y){(x-0.5)/nrow(y)}
# Dataset
data <- read.csv("/ahahinputs.csv", sep = ",")
# Ranking
data$gpp_dist <- rank(data$gpp_dist,ties.method= "min")
data$ed_dist <- rank(data$ed_dist,ties.method= "min")
data$dent_dist <- rank(data$dent_dist,ties.method= "min")
data$pharm_dist <- rank(data$pharm_dist,ties.method= "min")
data$gamb_dist <- rank(data$gamb_dist,ties.method= "min")
data$gamb_dist <- rank(-data$gamb_dist) # Invert ranking
data$ffood_dist <- rank(data$ffood_dist,ties.method= "min")
data$ffood_dist <- rank(-data$ffood_dist) # Invert ranking
data$pubs_dist <- rank(data$pubs_dist,ties.method= "min")
data$pubs_dist <- rank(-data$pubs_dist) # Invert ranking
data$off_dist <- rank(data$off_dist,ties.method= "min")
data$off_dist <- rank(-data$off_dist) # Invert ranking
data$tobac_dist<- rank(data$tobac_dist,ties.method= "min")
data$tobac_dist <- rank(-data$tobac_dist) # Invert ranking
data$leis_dist <- rank(data$leis_dist,ties.method= "min")
data$blue_dist <- rank(data$blue_dist,ties.method= "min")
data$green_act <- rank(data$green_act,ties.method= "min")
data$green_pas <- rank(data$green_pas,ties.method= "min")
data$green_pas <- rank(-data$green_pas) # Invert ranking
data$no2_mean <- rank(data$no2_mean,ties.method= "min")
data$pm10_mean <- rank(data$pm10_mean,ties.method= "min")
data$so2_mean <- rank(data$so2_mean,ties.method= "min")
# Rankit rank-based normalisation / Normal transformation
data$gpp_dist <- exp_default(data$gpp_dist, data)
data$gpp_dist <- qnorm(data$gpp_dist, mean = 0, sd = 1)
data$ed_dist <- exp_default(data$ed_dist, data)
data$ed_dist <- qnorm(data$ed_dist, mean = 0, sd = 1)
data$dent_dist <- exp_default(data$dent_dist, data)
data$dent_dist <- qnorm(data$dent_dist, mean = 0, sd = 1)
data$pharm_dist <- exp_default(data$pharm_dist, data)
data$pharm_dist <- qnorm(data$pharm_dist, mean = 0, sd = 1)
data$gamb_dist <- exp_default(data$gamb_dist, data)
data$gamb_dist <- qnorm(data$gamb_dist, mean = 0, sd = 1)
data$ffood_dist <- exp_default(data$ffood_dist, data)
data$ffood_dist <- qnorm(data$ffood_dist, mean = 0, sd = 1)
data$pubs_dist <- exp_default(data$pubs_dist, data)
data$pubs_dist <- qnorm(data$pubs_dist, mean = 0, sd = 1)
data$leis_dist <- exp_default(data$leis_dist, data)
data$leis_dist <- qnorm(data$leis_dist, mean = 0, sd = 1)
data$blue_dist <- exp_default(data$blue_dist, data)
data$blue_dist <- qnorm(data$blue_dist, mean = 0, sd = 1)
data$green_act <- exp_default(data$green_act, data)
data$green_act <- qnorm(data$green_act, mean = 0, sd = 1)
data$green_pas <- exp_default(data$green_pas, data)
data$green_pas <- qnorm(data$green_pas, mean = 0, sd = 1)
data$off_dist <- exp_default(data$off_dist, data)
data$off_dist <- qnorm(data$off_dist, mean = 0, sd = 1)
data$tobac_dist <- exp_default(data$tobac_dist, data)
data$tobac_dist <- qnorm(data$tobac_dist, mean = 0, sd = 1)
data$no2_mean <- exp_default(data$no2_mean, data)
data$no2_mean <- qnorm(data$no2_mean, mean = 0, sd = 1)
data$pm10_mean <- exp_default(data$pm10_mean, data)
data$pm10_mean <- qnorm(data$pm10_mean, mean = 0, sd = 1)
data$so2_mean <- exp_default(data$so2_mean, data)
data$so2_mean <- qnorm(data$so2_mean, mean = 0, sd = 1)
##
# Write data
saveRDS(data,"norm_data_all_variables.rds")
# Load data
data <- readRDS("norm_data_all_variables.rds")
# Domain scores
data$r_domain <- (0.20 * data$gamb_dist +
0.20 * data$ffood_dist +
0.20 * data$pubs_dist +
0.20 * data$off_dist +
0.20 * data$tobac_dist)
data$h_domain <- (0.20 * data$gpp_dist +
0.20 * data$ed_dist +
0.20 * data$dent_dist +
0.20 * data$pharm_dist +
0.20 * data$leis_dist)
data$g_domain <- ((1/3) * data$green_act +
(1/3) * data$green_pas +
(1/3) * data$blue_dist)
data$e_domain <- ((1/3) * data$no2_mean +
(1/3) * data$pm10_mean +
(1/3) * data$so2_mean)
# Domain ranks
data$r_rank <- rank(data$r_domain,ties.method= "min")
data$h_rank <- rank(data$h_domain,ties.method= "min")
data$g_rank <- rank(data$g_domain,ties.method= "min")
data$e_rank <- rank(data$e_domain,ties.method= "min")
#
# Exp domains
data$r_exp <- exp_trans(data$r_rank,data)
data$h_exp <- exp_trans(data$h_rank,data)
data$g_exp <- exp_trans(data$g_rank,data)
data$e_exp <- exp_trans(data$e_rank,data)
# AHAH score
data$ahah <- (0.25 * data$r_exp +
0.25 * data$h_exp +
0.25 * data$g_exp +
0.25 * data$e_exp)
write.csv(data,"ahahdomainsindex.csv",quote = FALSE, row.names = FALSE)