olympus/data/spew_1.3.0_fixes/prep_sierra_leone.R

In leerichardson/spew: SPEW Framework for Generating Synthetic Ecosystems

# Lee Richardson
# 1/22/2016
# Purpose: This file is meant to prepare the 
# ipums shapefiles and counts for use by 
# spew on Olympus

# Prepare the data and R Session ---
rm(list = ls())
devtools::load_all("/mnt/beegfs1/data/shared_group_data/syneco/spew")
library(stringdist)
library(maptools)

# # Read in the shapefile and counts 
input_path <- "/mnt/beegfs1/data/shared_group_data/syneco/spew_input/africa/western_africa/sle/input"

out_pt <- paste0(input_path, "/counts/geohive/2015/2/sierraleone_revised.csv")
out_shape <- paste0(input_path, "/shapefiles/ipums/2004/1/sierra_leone_revised")

data_group <- "ipums"
folders <- list(pop_table = "counts", 
                    pums = "PUMS", 
                    shapefiles = "shapefiles")

pop_table <- spew:::read_pop_table(input_path, folders, data_group)
pop_table <- spew:::standardize_pop_table(pop_table, data_group)
pop_table$n_house <- as.numeric(gsub(",", "", pop_table$n_house))

shapefile <- spew:::read_shapefiles(input_path, folders, data_group)
shapefile <- spew:::standardize_shapefiles(shapefile, data_group)

# Obtain the shapefile and count names
shapefile_names <- shapefile$place_id
level <- spew:::get_level(shapefile_names, pop_table)
count_indices <- which(pop_table$level == level)
count_names <- pop_table$place_id[count_indices]

# Clean the names of their non ascii character, uppercases, and spaces 
count_names <- spew:::clean_names(count_names)
shapefile_names <- spew:::clean_names(shapefile_names)

# ----------------------------------------------
# MAKE CHANGES HERE ----------------------------
# ----------------------------------------------
count_names <- gsub(pattern = "district", replacement = "", x = count_names)


# Verify the changes work and write the edited files  ---
shapefile_indices <- amatch(count_names, shapefile_names, 
							method = "jw", maxDist = .3)

stopifnot(!any(is.na(shapefile_indices)))
stopifnot(!any(duplicated(shapefile_indices)))

# Write the "revised" version of the pop_table AND shapefile if necessary 
pop_table[count_indices, "place_id"] <- shapefile_names[shapefile_indices]
write.table(pop_table, 
 			file = out_pt, 
 			sep = ",", 
 			row.names = FALSE, 
 			qmethod = "double")

shapefile$place_id <- shapefile_names
writeSpatialShape(shapefile, out_shape)