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##################################################################
#### El Salvador - Land Reform - Prop Level Geographical Covs ####
##################################################################
rm(list = ls()) # Clear variables
require(foreign)
require(ggplot2)
require(rgdal)
require(rgeos)
require(RColorBrewer) # creates nice color schemes
require(maptools) # loads sp library too
require(scales) # customize scales
require(gridExtra) # mutiple plots
require(plyr) # join function
require(dplyr)
require(mapproj) # projection tools
require(raster) # raster tools
require(animation) # Saving GIFs
require(tidyr)
require(readstata13)
require(haven)
require(gstat) # interpolation tools
require(ncdf4)
require(Hmisc)
require(lubridate)
library(lmtest)
library(sandwich)
library(dotwhisker) # coef plots
library(broom)
require(stringr)
require(readxl)
require(rmapshaper)
require(extrafont)
require(ggmap)
require(exactextractr) # faster extract
require(sf) # faster extract
require(elevatr) # elevation data
require(rdrobust)
require(stringdist)
############## LOAD DATA ################
## Read in Data:
# Load the Property-Level Data:
prop_data <- read.dta(file="./Data/prop_data.dta")
# dta file Created in R, ESLR_CleanPropertyData.R
prop_data <- mutate(prop_data, norm_dist = Total_Propretario - 500.00,
Above500 = ifelse(norm_dist>0,1,0))
# Load the Canton Shapefile:
cantons <- readOGR(dsn="./Data/", layer="cantons_wCodigos")
############## CALCULATE GEO COVS ###############
# Projections:
wgs84_proj <- "+proj=longlat +ellps=WGS84 +datum=WGS84" # WGS 1984
mercator <- "+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +no_defs" # Project to mercator to calculate distance in meters
## GEOGRAPHIC BALANCE:
# BUFFER SIZE:
buffer_size <- 2500
# PREP SHAPEFILES:
cantons_wCovariates <- as(cantons,"sf")
cantons_wCovariates <- st_transform(cantons_wCovariates, st_crs(mercator))
# SUITABILITY FOR DIFFERENT CROPS
# Export Crops: Coffee, Sugar Cane and Cotton (though cotton no longer produced there)
# Internal Crops: Maiz, Beans, Sorghum, maybe Rice
# COFFEE:
# Read in Rasters:
path_to_suit_coffee <- "./Data/crop_suit/coffeelo.tif"
coffee_suit <- raster(paste(path_to_suit_coffee,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$canton_coffee_suit <- exact_extract(coffee_suit,
cantons_wCovariates,
'median')
# SUGAR CANE:
# Read in Rasters:
path_to_suit_sugarcane <- "./Data/crop_suit/sugarcanelo.tif"
sugarcane_suit <- raster(paste(path_to_suit_sugarcane,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$sugarcane_suit <- exact_extract(sugarcane_suit,
cantons_wCovariates,
'median')
# COTTON:
# Read in Rasters:
path_to_suit_cotton <- "./Data/crop_suit/cottonlo.tif"
cotton_suit <- raster(paste(path_to_suit_cotton,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$cotton_suit <- exact_extract(cotton_suit,
cantons_wCovariates,
'median')
# Non-Export:
# Maize:
# Read in Rasters:
path_to_suit_maiz <- "./Data/crop_suit/maizelo.tif"
miaze_suit <- raster(paste(path_to_suit_maiz,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$miaze_suit <- exact_extract(miaze_suit,
cantons_wCovariates,
'median')
# Beans:
# Read in Rasters:
path_to_suit_beans <- "./Data/crop_suit/phaseolusbeanlo.tif"
bean_suit <- raster(paste(path_to_suit_beans,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$bean_suit <- exact_extract(bean_suit,
cantons_wCovariates,
'median')
# Sorghum:
# Read in Rasters:
path_to_suit_sorghum <- "./Data/crop_suit/sorghumlo.tif"
sorghum_suit <- raster(paste(path_to_suit_sorghum,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$sorghum_suit <- exact_extract(sorghum_suit,
cantons_wCovariates,
'median')
# Rice:
# Read in Rasters:
path_to_suit_rice <- "./Data/crop_suit/wetricelo.tif" # indricelo.tif
rice_suit <- raster(paste(path_to_suit_rice,"",sep=""))
# Merge to CANTONS:
cantons_wCovariates$rice_suit <- exact_extract(rice_suit,
cantons_wCovariates,
'median')
# Precipitation:
path_rain <- "./Data/wc2.1_2.5m_prec_2000-2009/"
# Loop over 12 months and calculate mean rainfall (mm):
for (month in 1:12) {
# Convert from .adf to raster for analysis:
print(month)
x <- raster(paste(path_rain,"wc2.1_2.5m_prec_2007-",
ifelse(month%/%10==0,paste0("0",month),month),
".tif",sep=""))
rainfall <- (x)
proj4string(rainfall) <- CRS(wgs84_proj) # assign projection since empty
assign(paste("rain","_",month,sep=""), rainfall)
}
sum_rain <- (rain_1 + rain_2 + rain_3 + rain_4 + rain_5 + rain_6 + rain_7 + rain_8 + rain_9 + rain_10 + rain_11 + rain_12)
# Extract:
cantons_wCovariates$canton_mean_rain <- exact_extract(sum_rain,
cantons_wCovariates,
'median')
# Land Suitability:
# http://nelson.wisc.edu/sage/data-and-models/atlas/maps.php?datasetid=19&includerelatedlinks=1&dataset=19
path_land_suit <- "Data/suit/suit/w001001.adf"
# Convert from .adf to raster for analysis:
x <- new("GDALReadOnlyDataset", path_land_suit)
xx<-asSGDF_GROD(x)
land_suit <- raster(xx)
proj4string(land_suit) <- CRS(proj4string(cantons)) # assign projection since empty
# Extract:
cantons_wCovariates$canton_land_suit <- exact_extract(land_suit,
cantons_wCovariates,
'median')
## Elevation: ##
elev <- get_elev_raster(locations = cantons, z= 1)
# Extract:
cantons_wCovariates$canton_elev_dem_30sec <- exact_extract(elev, cantons_wCovariates,'median')
write_dta(st_drop_geometry(cantons_wCovariates), "./Output/cantons_wGeoCovariates.dta")
################# STD FUNCTIONS ###################
# STD FUNCTIONS:
lm.beta <- function (MOD, dta,y="ln_agprod")
{
b <- MOD$coef[1]
model.dta <- filter(dta, norm_dist > -1*MOD$bws["h","left"] & norm_dist < MOD$bws["h","right"] )
sx <- sd(model.dta[,c("Above500")])
sy <- sd((model.dta[,c(y)]),na.rm=TRUE)
beta <- b * sx/sy
return(beta)
}
lm.beta.ses <- function (MOD, dta,y="ln_agprod")
{
b <- MOD$se[1]
model.dta <- filter(dta, norm_dist > -1*MOD$bws["h","left"] & norm_dist < MOD$bws["h","right"] )
sx <- sd(model.dta[,c("Above500")])
sy <- sd((model.dta[,c(y)]),na.rm=TRUE)
beta <- b * sx/sy
return(beta)
}
winsor <- function (x, fraction=.01)
{
if(length(fraction) != 1 || fraction < 0 ||
fraction > 0.5) {
stop("bad value for 'fraction'")
}
lim <- quantile(x, probs=c(fraction, 1-fraction),na.rm = TRUE)
x[ x < lim[1] ] <- NA
x[ x > lim[2] ] <- NA
x
}
################# AESTHETICS ##################
aesthetics <- list(
theme_bw(),
theme(legend.title=element_blank(),
text=element_text(family="Palatino"),
plot.background=element_rect(colour="white",fill="white"),
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),
axis.title=element_text(size=12,face="bold"),
))
################### BALANCE PLOT ####################
## Coef Plots:
alpha<- 0.05
Multiplier <- qnorm(1 - alpha / 2)
prop_data_wgeo <- left_join(prop_data, st_drop_geometry(cantons_wCovariates),by=c("CODIGO"))
b0 <- rdrobust(y = (prop_data_wgeo$miaze_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b1 <- rdrobust(y = (prop_data_wgeo$sorghum_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b2 <- rdrobust(y = (prop_data_wgeo$bean_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b3 <- rdrobust(y = (prop_data_wgeo$rice_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b4 <- rdrobust(y = (prop_data_wgeo$cotton_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b5 <- rdrobust(y = (prop_data_wgeo$sugarcane_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b6 <- rdrobust(y = (prop_data_wgeo$canton_coffee_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b7 <- rdrobust(y = (prop_data_wgeo$canton_elev_dem_30sec), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b8 <- rdrobust(y = (prop_data_wgeo$canton_mean_rain), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
b9 <- rdrobust(y = (prop_data_wgeo$canton_land_suit), x=prop_data_wgeo$norm_dist,c = 0,p = 1,q=2, bwselect = "mserd", cluster=prop_data_wgeo$Expropretario_ISTA, vce="hc0")
beta_coefs <- c(lm.beta(MOD=b0, dta=prop_data_wgeo, y="miaze_suit"),
lm.beta(MOD=b1, dta=prop_data_wgeo, y="sorghum_suit"),
lm.beta(MOD=b2, dta=prop_data_wgeo, y="bean_suit"),
lm.beta(MOD=b3, dta=prop_data_wgeo, y="rice_suit"),
lm.beta(MOD=b4, dta=prop_data_wgeo, y="cotton_suit"),
lm.beta(MOD=b5, dta=prop_data_wgeo, y="sugarcane_suit"),
lm.beta(MOD=b6, dta=prop_data_wgeo, y="canton_coffee_suit"),
lm.beta(MOD=b7, dta=prop_data_wgeo, y="canton_elev_dem_30sec"),
lm.beta(MOD=b8, dta=prop_data_wgeo, y="canton_mean_rain"),
lm.beta(MOD=b9, dta=prop_data_wgeo, y="canton_land_suit"))
beta_ses <- c(lm.beta.ses(MOD=b0, dta=prop_data_wgeo, y="miaze_suit"),
lm.beta.ses(MOD=b1, dta=prop_data_wgeo, y="sorghum_suit"),
lm.beta.ses(MOD=b2, dta=prop_data_wgeo, y="bean_suit"),
lm.beta.ses(MOD=b3, dta=prop_data_wgeo, y="rice_suit"),
lm.beta.ses(MOD=b4, dta=prop_data_wgeo, y="cotton_suit"),
lm.beta.ses(MOD=b5, dta=prop_data_wgeo, y="sugarcane_suit"),
lm.beta.ses(MOD=b6, dta=prop_data_wgeo, y="canton_coffee_suit"),
lm.beta.ses(MOD=b7, dta=prop_data_wgeo, y="canton_elev_dem_30sec"),
lm.beta.ses(MOD=b8, dta=prop_data_wgeo, y="canton_mean_rain"),
lm.beta.ses(MOD=b9, dta=prop_data_wgeo, y="canton_land_suit"))
yvars<-c("Maize Suitability","Sorghum Suitability","Bean Suitability","Rice Suitability","Cotton Suitability","Sugar Cane Suitability","Coffee Suitability","Elevation","Precipitation","Land Suitability")
geo_vars <- c("miaze_suit","sorghum_suit","bean_suit","rice_suit","cotton_suit",
"sugarcane_suit", "canton_coffee_suit", "canton_elev_dem_30sec",
"canton_mean_rain","canton_land_suit")
betas <- cbind(yvars,beta_coefs,beta_ses)
ests <- cbind(geo_vars, c(b0$coef[1],b1$coef[1],b2$coef[1],b3$coef[1],b4$coef[1],b5$coef[1],b6$coef[1],b7$coef[1],b8$coef[1],b9$coef[1]),
c(b0$se[1],b1$se[1],b2$se[1],b3$se[1],b4$se[1],b5$se[1],b6$se[1],b7$coef[1],b8$se[1],b9$se[1]))
# Save estimates for un-balancedness exercise:
write_dta(as.data.frame(ests),path="./Output/balance_ests.dta")
row.names(betas)<-NULL
MatrixofModels <- as.data.frame(as.matrix(betas))
colnames(MatrixofModels) <- c("IV", "Estimate", "StandardError")
MatrixofModels$IV <- factor(MatrixofModels$IV, levels = rev(c("Land Suitability", "Precipitation", "Elevation", "Coffee Suitability", "Sugar Cane Suitability", "Cotton Suitability", "Maize Suitability", "Bean Suitability", "Rice Suitability", "Sorghum Suitability")))# MatrixofModels$IV)
MatrixofModels[, -c(1, 6)] <- apply(MatrixofModels[, -c(1, 6)], 2, function(x){as.numeric(as.character(x))})
###################
## BALANCE FIGURE:
##################
# Plot:
OutputPlot <- qplot(IV, Estimate, ymin = Estimate - Multiplier * StandardError,
ymax = Estimate + Multiplier * StandardError, data = MatrixofModels, geom = "pointrange",
ylab = NULL, xlab = NULL)
OutputPlot <- OutputPlot + geom_hline(yintercept = 0, lwd = I(7/12), colour = I(hsv(0/12, 7/12, 7/12)), alpha = I(5/12))
# Stupid fix to fix the scales overlapping on the bottom:
OutputPlot <- OutputPlot + geom_hline(yintercept = 0.0, alpha = 0.05)
#OutputPlot <- OutputPlot + facet_grid(~ ModelName) + coord_flip() + theme_bw() + ylab("\nStandardized Effect")
OutputPlot <- OutputPlot + coord_flip() + theme_classic() + ylab("\nStandardized Effect") +
xlab("")
# Save:
OutputPlot + scale_y_continuous(breaks = seq(-0.4, 0.4,0.1)) + aesthetics
ggsave(filename="./Output/CoefPlot_Balance_PropLevel1980.pdf",width = 6, height=4)
############################
## SELECTIVE SORTING FIGURE:
############################
require(rdd)
### FIXING X LIM & FONT:
DCdensity2 <- function (runvar, cutpoint, bin = NULL, bw = NULL, verbose = FALSE,
plot = TRUE, ext.out = FALSE, htest = FALSE, my_xlim = c(-0.5,0.5)) # my_xlim param added
{
runvar <- runvar[complete.cases(runvar)]
rn <- length(runvar)
rsd <- sd(runvar)
rmin <- min(runvar)
rmax <- max(runvar)
if (missing(cutpoint)) {
if (verbose)
cat("Assuming cutpoint of zero.\n")
cutpoint <- 0
}
if (cutpoint <= rmin | cutpoint >= rmax) {
stop("Cutpoint must lie within range of runvar")
}
if (is.null(bin)) {
bin <- 2 * rsd * rn^(-1/2)
if (verbose)
cat("Using calculated bin size: ", sprintf("%.3f",
bin), "\n")
}
l <- floor((rmin - cutpoint)/bin) * bin + bin/2 + cutpoint
r <- floor((rmax - cutpoint)/bin) * bin + bin/2 + cutpoint
lc <- cutpoint - (bin/2)
rc <- cutpoint + (bin/2)
j <- floor((rmax - rmin)/bin) + 2
binnum <- round((((floor((runvar - cutpoint)/bin) * bin +
bin/2 + cutpoint) - l)/bin) + 1)
cellval <- rep(0, j)
for (i in seq(1, rn)) {
cnum <- binnum[i]
cellval[cnum] <- cellval[cnum] + 1
}
cellval <- (cellval/rn)/bin
cellmp <- seq(from = 1, to = j, by = 1)
cellmp <- floor(((l + (cellmp - 1) * bin) - cutpoint)/bin) *
bin + bin/2 + cutpoint
if (is.null(bw)) {
leftofc <- round((((floor((lc - cutpoint)/bin) * bin +
bin/2 + cutpoint) - l)/bin) + 1)
rightofc <- round((((floor((rc - cutpoint)/bin) * bin +
bin/2 + cutpoint) - l)/bin) + 1)
if (rightofc - leftofc != 1) {
stop("Error occurred in bandwidth calculation")
}
cellmpleft <- cellmp[1:leftofc]
cellmpright <- cellmp[rightofc:j]
P.lm <- lm(cellval ~ poly(cellmp, degree = 4, raw = T),
subset = cellmp < cutpoint)
mse4 <- summary(P.lm)$sigma^2
lcoef <- coef(P.lm)
fppleft <- 2 * lcoef[3] + 6 * lcoef[4] * cellmpleft +
12 * lcoef[5] * cellmpleft * cellmpleft
hleft <- 3.348 * (mse4 * (cutpoint - l)/sum(fppleft *
fppleft))^(1/5)
P.lm <- lm(cellval ~ poly(cellmp, degree = 4, raw = T),
subset = cellmp >= cutpoint)
mse4 <- summary(P.lm)$sigma^2
rcoef <- coef(P.lm)
fppright <- 2 * rcoef[3] + 6 * rcoef[4] * cellmpright +
12 * rcoef[5] * cellmpright * cellmpright
hright <- 3.348 * (mse4 * (r - cutpoint)/sum(fppright *
fppright))^(1/5)
bw = 0.5 * (hleft + hright)
if (verbose)
cat("Using calculated bandwidth: ", sprintf("%.3f",
bw), "\n")
}
if (sum(runvar > cutpoint - bw & runvar < cutpoint) == 0 |
sum(runvar < cutpoint + bw & runvar >= cutpoint) == 0)
stop("Insufficient data within the bandwidth.")
if (plot) {
d.l <- data.frame(cellmp = cellmp[cellmp < cutpoint],
cellval = cellval[cellmp < cutpoint], dist = NA,
est = NA, lwr = NA, upr = NA)
pmin <- cutpoint - 2 * rsd
pmax <- cutpoint + 2 * rsd
for (i in 1:nrow(d.l)) {
d.l$dist <- d.l$cellmp - d.l[i, "cellmp"]
w <- kernelwts(d.l$dist, 0, bw, kernel = "triangular")
newd <- data.frame(dist = 0)
pred <- predict(lm(cellval ~ dist, weights = w, data = d.l),
interval = "confidence", newdata = newd)
d.l$est[i] <- pred[1]
d.l$lwr[i] <- pred[2]
d.l$upr[i] <- pred[3]
}
d.r <- data.frame(cellmp = cellmp[cellmp >= cutpoint],
cellval = cellval[cellmp >= cutpoint], dist = NA,
est = NA, lwr = NA, upr = NA)
for (i in 1:nrow(d.r)) {
d.r$dist <- d.r$cellmp - d.r[i, "cellmp"]
w <- kernelwts(d.r$dist, 0, bw, kernel = "triangular")
newd <- data.frame(dist = 0)
pred <- predict(lm(cellval ~ dist, weights = w, data = d.r),
interval = "confidence", newdata = newd)
d.r$est[i] <- pred[1]
d.r$lwr[i] <- pred[2]
d.r$upr[i] <- pred[3]
}
plot(d.l$cellmp, d.l$est, lty = 1, lwd = 2, col = "black", # xlim set here based on the parameter
type = "l", xlim = my_xlim, ylim = c(min(cellval[cellmp <=
pmax & cellmp >= pmin]), max(cellval[cellmp <=
pmax & cellmp >= pmin])), xlab = NA, ylab = NA,
main = NA)
lines(d.l$cellmp, d.l$lwr, lty = 2, lwd = 1, col = "black",
type = "l")
lines(d.l$cellmp, d.l$upr, lty = 2, lwd = 1, col = "black",
type = "l")
lines(d.r$cellmp, d.r$est, lty = 1, lwd = 2, col = "black",
type = "l")
lines(d.r$cellmp, d.r$lwr, lty = 2, lwd = 1, col = "black",
type = "l")
lines(d.r$cellmp, d.r$upr, lty = 2, lwd = 1, col = "black",
type = "l")
points(cellmp, cellval, type = "p", pch = 20)
}
cmp <- cellmp
cval <- cellval
padzeros <- ceiling(bw/bin)
jp <- j + 2 * padzeros
if (padzeros >= 1) {
cval <- c(rep(0, padzeros), cellval, rep(0, padzeros))
cmp <- c(seq(l - padzeros * bin, l - bin, bin), cellmp,
seq(r + bin, r + padzeros * bin, bin))
}
dist <- cmp - cutpoint
w <- 1 - abs(dist/bw)
w <- ifelse(w > 0, w * (cmp < cutpoint), 0)
w <- (w/sum(w)) * jp
fhatl <- predict(lm(cval ~ dist, weights = w), newdata = data.frame(dist = 0))[[1]]
w <- 1 - abs(dist/bw)
w <- ifelse(w > 0, w * (cmp >= cutpoint), 0)
w <- (w/sum(w)) * jp
fhatr <- predict(lm(cval ~ dist, weights = w), newdata = data.frame(dist = 0))[[1]]
thetahat <- log(fhatr) - log(fhatl)
sethetahat <- sqrt((1/(rn * bw)) * (24/5) * ((1/fhatr) +
(1/fhatl)))
z <- thetahat/sethetahat
p <- 2 * pnorm(abs(z), lower.tail = FALSE)
if (verbose) {
cat("Log difference in heights is ", sprintf("%.3f",
thetahat), " with SE ", sprintf("%.3f", sethetahat),
"\n")
cat(" this gives a z-stat of ", sprintf("%.3f", z),
"\n")
cat(" and a p value of ", sprintf("%.3f", p), "\n")
}
if (ext.out)
return(list(theta = thetahat, se = sethetahat, z = z,
p = p, binsize = bin, bw = bw, cutpoint = cutpoint,
data = data.frame(cellmp, cellval)))
else if (htest) {
structure(list(statistic = c(z = z), p.value = p, method = "McCrary (2008) sorting test",
parameter = c(binwidth = bin, bandwidth = bw, cutpoint = cutpoint),
alternative = "no apparent sorting"), class = "htest")
}
else return(p)
}
prop_subset <- prop_data[which(prop_data$Total_Propretario < 1500 & prop_data$Total_Propretario >180),]
pdf(file="./Output/McCrarySorting_PropLevel.pdf", height=6, width=9, paper = "USr", family = "Palatino")
DCdensity2(runvar = prop_subset$Total_Propretario,cutpoint = 500,plot = TRUE,verbose = TRUE, ext.out = FALSE, bw=350, my_xlim = c(200,1000))
abline(v=500,col=c("red"))
#par(family = 'sans') # the default of R
title(xlab="Cumulative Landholdings (ha)", ylab="Density")
dev.off()