Hi I am trying to run the following code please
# Clean DHS Data
# Clean DHS survey data. Create Household Level
# dataframe with relevant socioeconomic variables.
renv::restore()
pacman::p_load(tidyverse,
rgdal,
viridis,
readstata13,
dplyr,
data.table,
raster,
stargazer,
stringdist,
tmaptools,
stringr,
geosphere,
rgeos,
haven,
ggmap,
sf,
sp,
glmnet,
rgeos,
caret,
mltest,
RANN,
lubridate,
jsonlite,
httr,
curl,
ggpmisc,
haven,
sjmisc,
dbscan,
ggplot2,
spatialEco,
geosphere,
radiant.data,
readxl,
mclust,
missMDA,
DescTools,
furrr,
countrycode,
FactoMineR,
progressr,
ggmap,
ggridges,
ggpubr,
xgboost,
WDI,
scales,
ggExtra,
ggrepel,
ggcorrplot,
rnaturalearth,
ggthemes,
gghalves,
ggtext,
ggsignif,
LiblineaR,
caret,
exactextractr)
github_dir = "/ocean/projects/soc230008p/ramzan/Big Data Poverty Estimation/"
source(file.path(github_dir, "Functions", "functions.R"))
install.packages("rgdal")
if (!require(dplyr)) {
install.packages("dplyr")
library(dplyr)
}
if (!require(stringr)) {
install.packages("stringr")
library(stringr)
}
if (!require(magrittr)) {
install.packages("magrittr")
library(magrittr)
}
if (!require(purrr)) {
install.packages("purrr")
library(purrr)
}
if (!require(haven)) {
install.packages("haven")
library(haven)
}
library(sf)
library(rgdal)
dhs_dir = "/ocean/projects/soc230008p/ramzan/Big Data Poverty Estimation/Data/DHS"
# Functions to Clean Data ------------------------------------------------------
clean_hh <- function(df,
hh_vars){
#### Country specific fixes
if(grepl("KH_2014|KH_2010", df$hv000[1])){
# DH doesn't record anything for hv201 (water source); however, has water source
# during dry and wet times. Use dry (sh102)
df <- df %>%
dplyr::select(-hv201) %>%
dplyr::rename(hv201 = sh102)
}
if(grepl("KH_2005", df$hv000[1])){
# DH doesn't record anything for hv201 (water source); however, has water source
# during dry and wet times. Use dry (sh102)
df <- df %>%
dplyr::select(-hv201) %>%
dplyr::rename(hv201 = hv201d)
}
#### Education variables
## Functions
to_na_if_30above <- function(x){
x[x >= 30] <- NA
return(x)
}
to_na_if_4above <- function(x){
x[x >= 4] <- NA
return(x)
}
max_ig_na <- function(x){
x <- max(x, na.rm = T)
x[x %in% c(Inf,-Inf)] <- NA
return(x)
}
count_0 <- function(x){
sum(x == 0, na.rm = T)
}
count_1 <- function(x){
sum(x == 1, na.rm = T)
}
count_2 <- function(x){
sum(x == 2, na.rm = T)
}
count_3 <- function(x){
sum(x == 3, na.rm = T)
}
count_3g <- function(x){
sum(x > 3, na.rm = T)
}
mean_ig_na <- function(x){
x <- mean(x, na.rm = T)
x[x %in% c(Inf,-Inf)] <- NA
return(x)
}
median_ig_na <- function(x){
x <- median(x, na.rm = T)
x[x %in% c(Inf,-Inf)] <- NA
return(x)
}
## Education Completed in Single Years
educ_years <- df %>%
dplyr::select(contains("hv108")) %>%
mutate_all(to_numeric) %>%
mutate_all(as.numeric) %>%
mutate_all(to_na_if_30above)
df$educ_years_hh_max <- apply(educ_years, 1, max_ig_na)
df$educ_years_hh_mean <- apply(educ_years, 1, mean_ig_na)
## Highest Education Level Obtained
# 0 = Early childhoon education program
# 1 = Primary
# 2 = Secondary
# 3 = Higher
# 8 = Don't Know
# 00 = Less than 1 year completed
# 98 = Don't know
educ_levels <- df %>%
dplyr::select(contains("hv106")) %>%
mutate_all(to_numeric) %>%
mutate_all(as.numeric) %>%
mutate_all(to_na_if_4above)
df$educ_levels_hh_max <- apply(educ_levels, 1, max_ig_na)
df$educ_levels_hh_n0 <- apply(educ_levels, 1, count_0)
df$educ_levels_hh_n1 <- apply(educ_levels, 1, count_1)
df$educ_levels_hh_n2 <- apply(educ_levels, 1, count_2)
df$educ_levels_hh_n3 <- apply(educ_levels, 1, count_3)
df$educ_levels_hh_n3g <- apply(educ_levels, 1, count_3g)
# Make sure has all variables, which is needed for renaming
for(var_i in hh_vars){
if(is.null(df[[var_i]])){
df[[var_i]] <- NA
}
}
df_out <- df %>%
dplyr::rename(cluster_id = hv001,
water_source = hv201,
water_time_to_get = hv204,
floor_material = hv213,
toilet_type = hv205,
has_electricity = hv206,
has_radio = hv207,
has_tv = hv208,
has_fridge = hv209,
has_motorbike = hv211,
has_car = hv212,
n_hh_members = hv009,
#kitchen_is_sep_room = hv242,
#has_bank_account = hv247,
wall_material = hv214,
roof_material = hv215,
n_rooms_sleeping = hv216,
wealth_index = hv270,
wealth_index_score = hv271) %>%
dplyr::select(hhid,
cluster_id,
educ_levels_hh_max,
educ_levels_hh_n0,
educ_levels_hh_n1,
educ_levels_hh_n2,
educ_levels_hh_n3,
educ_levels_hh_n3g,
educ_years_hh_max,
educ_years_hh_mean,
water_source,
water_time_to_get,
floor_material,
toilet_type,
has_electricity,
has_radio,
has_tv,
has_fridge,
has_motorbike,
has_car,
n_hh_members,
#kitchen_is_sep_room,
#has_bank_account,
wall_material,
roof_material,
n_rooms_sleeping,
wealth_index, wealth_index_score) %>%
# value labels sometime different. For example, in some surveys, for floor
# material, cement is 34 and in others cement is 35.
mutate(floor_material = floor_material %>% as_factor() %>% as.character(),
wall_material = wall_material %>% as_factor() %>% as.character(),
roof_material = roof_material %>% as_factor() %>% as.character(),
water_source = water_source %>% as_factor() %>% as.character(),
toilet_type = toilet_type %>% as_factor() %>% as.character(),
water_time_to_get = water_time_to_get %>% as.numeric()) %>%
dplyr::mutate(cluster_id = cluster_id %>% as.character())
return(df_out)
}
clean_geo <- function(df){
df <- df@data %>%
dplyr::filter(SOURCE != "MIS") %>% # Missing lat/lon
dplyr::rename(cluster_id = DHSCLUST,
uid = DHSID,
latitude = LATNUM,
longitude = LONGNUM,
urban_rural = URBAN_RURA,
year = DHSYEAR,
country_code = DHSCC) %>%
dplyr::select(cluster_id, uid, latitude, longitude, urban_rural, year, country_code) %>%
dplyr::mutate(cluster_id = cluster_id %>% as.character())
return(df)
}
merge_clean <- function(hh_df, geo_df){
df_out <- hh_df %>%
left_join(geo_df, by = "cluster_id") %>%
mutate_at(vars(urban_rural), as.character) %>%
dplyr::select(uid, cluster_id, everything()) %>%
dplyr::mutate(year = year %>% as.character())
return(df_out)
}
process_dhs <- function(dir){
# DESCRIPTION: Cleans and merges dhs dataseets
# ARGs:
# dir: Directory that countains DHS survey modules for a specific country and year
print(dir)
# List of all files for that country & year
files_all <- file.path(dir) %>% list.files(recursive=T, full.names = T)
files_all <- files_all[!grepl("archive", files_all)]
# Grab HH and geo file paths
hh_path <- files_all %>% str_subset("[A-Z]{2}HR") %>% str_subset(".dta$|.DTA$")
geo_path <- files_all %>% str_subset("[A-Z]{2}GE") %>% str_subset(".shp$")
# Load and clean data
num_to_string <- function(x){
if(x <= 9){
x <- paste0("0", x)
} else{
x <- as.character(x)
}
return(x)
}
num_to_string <- Vectorize(num_to_string)
## Load variable names; needed for hv108 (education), which includes a value
# for each household
df_onerow_names <- read_dta(hh_path, n_max = 1) %>% names()
# Years of education
if(TRUE %in% (df_onerow_names %>% str_detect("hv108"))){
hh108_names <- df_onerow_names %>%
str_subset("hv108")
} else{
hh108_names <- NULL
}
# Levels of education
if(TRUE %in% (df_onerow_names %>% str_detect("hv106"))){
hh106_names <- df_onerow_names %>%
str_subset("hv106")
} else{
hh106_names <- NULL
}
hh_vars <- c("hhid",
"hv000",
hh108_names,
hh106_names,
"hv216",
"sh110j",
"sh110k",
"hv001",
"hv201",
"hv204",
"hv205",
"hv213",
"hv206",
"hv207",
"hv208",
"hv209",
"hv211",
"hv212",
"hv214",
"hv215",
"hv221",
"hv009",
"hv270",
"hv271")
if(grepl("RawData/KH", dir)){
hh_vars <- c(hh_vars, "sh102")
}
# Sometimes not all variables are in the dataset
hh_vars_import <- hh_vars[hh_vars %in% df_onerow_names]
hh_df <- read_dta(hh_path, col_select = all_of(hh_vars_import)) %>% clean_hh(hh_vars = hh_vars)
geo_sdf <- readOGR(geo_path) %>% clean_geo()
# Merge data
survey_df <- merge_clean(hh_df, geo_sdf)
survey_df$country_year <- dir %>% str_replace_all(".*/", "")
# If wealth index in separate dataset, merge in. In earlier DHS rounds, WI
# was in a separate dataset and not in the Household Record dataset.
wi_path <- files_all %>% str_subset("[A-Z]{2}WI") %>% str_subset(".dta$|.DTA$")
if(length(wi_path) > 0){
wi_df <- read_dta(wi_path)
# For Egypt in 2000, hhids didn't match; needed to remove extra while space
if(dir %>% str_detect("EG_2000")){
wi_df$whhid <- wi_df$whhid %>% str_squish()
survey_df$hhid <- survey_df$hhid %>% str_squish()
}
survey_df <- survey_df %>%
left_join(wi_df, c("hhid" = "whhid")) %>%
dplyr::mutate(wi_from_diff_dataset = T)
}
return(survey_df)
}
# Process Data -----------------------------------------------------------------
## Create vector of paths to country-year folders
countries <- file.path(dhs_dir, "RawData") %>% list.files()
country_year_dirs <- lapply(countries, function(country_i){
country_year_dir <- file.path(dhs_dir, "RawData", country_i) %>% list.files(full.names = T)
}) %>%
unlist()
## Remove archive folders
country_year_dirs <- country_year_dirs[!grepl("archive", country_year_dirs)]
dhs_all_df <- map_df(country_year_dirs, process_dhs)
## Fix country code
# In some cases, India uses IN country code (when IN is Indonesia, and should be IA)
dhs_all_df$country_code <- dhs_all_df$country_year %>% substring(1,2)
dhs_all_df$year <- dhs_all_df$country_year %>% substring(4,7) %>% as.numeric()
# Export HH Level Data ---------------------------------------------------------
saveRDS(dhs_all_df, file.path(dhs_dir, "FinalData", "Individual Datasets",
"survey_socioeconomic_hhlevel.Rds"))
**and getting the following issues please**
> dhs_all_df <- map_df(country_year_dirs, process_dhs)
[1] "/ocean/projects/soc230008p/ramzan/Big Data Poverty Estimation/Data/DHS/RawData/AL/AL_2008-09_DHS_03292022_1959_82518"
Error in `map()`:
ℹ In index: 1.
Caused by error in `readOGR()`:
! could not find function "readOGR"
Run `rlang::last_trace()` to see where the error occurred.
Warning messages:
1: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
2: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
3: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
4: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
5: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
6: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
7: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
8: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
9: In max(x, na.rm = T) : no non-missing arguments to max; returning -Inf
>
> ## Fix country code
> # In some cases, India uses IN country code (when IN is Indonesia, and should be IA)
> dhs_all_df$country_code <- dhs_all_df$country_year %>% substring(1,2)
Error: object 'dhs_all_df' not found
> dhs_all_df$year <- dhs_all_df$country_year %>% substring(4,7) %>% as.numeric()
Error: object 'dhs_all_df' not found
>
> # Export HH Level Data ---------------------------------------------------------
> saveRDS(dhs_all_df, file.path(dhs_dir, "FinalData", "Individual Datasets",
+ "survey_socioeconomic_hhlevel.Rds"))
Error: object 'dhs_all_df' not found
>