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44_plot_coverage.R
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44_plot_coverage.R
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# author: Fernando Aramburu Merlos
# date: 2022-10-07
# setup ---------
host <- system("hostname", TRUE)
if (host == "LAPTOP-ST129J47") {
setwd("C:/Users/ferar/OneDrive - University of Nebraska-Lincoln/GYGA")
} else if (host == "LRDAH-DX5B0R3") {
setwd("C:/Users/faramburumerlos2/OneDrive - University of Nebraska-Lincoln/GYGA")
}
library(data.table)
library(stringr)
# prepare data
mm_cvg <- fread("extrap_method/tables/models_coverage.csv")
mm_cvg[, crop_sp:= str_extract(crop, "(?<= ).+")]
mm_cvg <- dcast(mm_cvg, crop + crop_sp ~ cv_method, value.var = "coverage")
gg_cvg <- fread("data/API/GYGA_total_area_coverage_R_I.csv")
cvg <- gg_cvg[mm_cvg, on = .NATURAL]
cvg[, global:= global/100 * world]
cvg[, interp:= interp/100 * world]
cvg <- cvg[, lapply(.SD, sum), by = .(crop_sp), .SDcols = c("world", "ctry_spam", "global", "interp", "cz_spam", "cz_ctry_spam")]
cvg <- cvg[, .(crop = crop_sp, meta_global = global/world,
gyga_global = cz_spam/world, cz_global = cz_ctry_spam/world,
meta_interp = interp/ctry_spam, gyga_interp = cz_ctry_spam/ctry_spam)]
cvg_global <- cvg[, t(cbind(cz_global, gyga_global, meta_global))]
rownames(cvg_global) <- c("CZ inter", "CZ extra", "Metamodel")
colnames(cvg_global) <- cvg$crop
cvg_interp <- cvg[, t(cbind(gyga_interp, meta_interp))]
rownames(cvg_interp) <- c("CZ inter", "Metamodel")
colnames(cvg_interp) <- cvg$crop
# Individual Plot ------------------------------
#cols <- RColorBrewer::brewer.pal(3, "Set1")
cols <- viridis::plasma(3, end = 0.8)
### Global ---------------
cvg_global <- cvg_global[, c("maize", "wheat", "rice")]
cvg_global <- cvg_global[-grep("inter", row.names(cvg_global)),]
png("extrap_method/plots/global_coverage.png", 4, 3, "in", res = 300)
par(mar = c(3,4,1, 1), cex.axis = .8, mgp = c(2,.7,0))
barplot(
cvg_global * 100,
beside = TRUE,
col = cols[c(1,3)],
axes = FALSE,
ylim = c(0,100),
las = 1,
cex.names = 1.1
)
axis(1, at = c(0.6, 6 * 1.2), pos = 0, labels = c("", ""), lwd.ticks = 0, xpd = NA)
axis(2, at = seq(0,100,20), pos = 0.6, las = 1)
mtext("Global crop area coverage (%)", 2, line = 2.5)
legend("bottomright", legend = c("Climate Zones", "Metamodel"),
inset = c(0, -0.3), xpd = NA, cex = 0.9, horiz = TRUE, x.intersp = 0.5, text.width = 3,
fill = cols[c(1,3)], bty = "n" )
dev.off()
### interp --------------------
cvg_interp <- cvg_interp[, c("maize", "wheat", "rice")]
png("extrap_method/plots/interp_coverage.png", 4, 3, "in", res = 300)
par(mar = c(3,4,1, 5), cex.axis = .8, mgp = c(2,.7,0))
barplot(
cvg_interp * 100,
beside = TRUE,
col = cols[c(1,3)],
axes = FALSE,
ylim = c(0,100),
las = 1,
cex.names = 1.1
)
axis(1, at = c(0.5, 8 * 1.2), pos = 0, labels = c("", ""), lwd.ticks = 0, xpd = NA)
axis(2, at = seq(0,100,20), pos = 0.5, las = 1)
mtext("Country Coverage (%)", 2, line = 2.5)
legend(x = par("usr")[2]*.98, y = 50, legend = c("CZ interp.", "Metamodel"), fill = cols[c(1,3)],
xpd = NA, cex = 0.8, bty = "n", xjust = 0, yjust = 0.5)
dev.off()
# Two panel plot ------------------------------
cvg_global <- cvg_global[rownames(cvg_global) != "CZ inter",]
#cols <- RColorBrewer::brewer.pal(3, "Set1")
cols <- viridis::plasma(2, end = 0.8)
png("extrap_method/plots/coverage.png", 7, 3, "in", res = 300)
par(mfrow = c(1,2), oma = c(0,0,0,5), mar = c(4,4,1,1), cex.axis = .8, mgp = c(2,.7,0), xpd = NA)
barplot(
cvg_interp * 100,
beside = TRUE,
col = cols,
axes = FALSE,
ylim = c(0,100),
las = 1,
cex.names = 1.1
)
axis(1, at = c(0.5, 8 * 1.2), pos = 0, labels = c("", ""), lwd.ticks = 0, xpd = NA)
axis(2, at = seq(0,100,20), pos = 0.5, las = 1)
mtext("Average national coverage (%)", 2, line = 2)
mtext("INTERPOLATION", 1, line = 2.5, font = 2)
barplot(
cvg_global * 100,
beside = TRUE,
col = cols,
axes = FALSE,
ylim = c(0,100),
las = 1,
cex.names = 1.1
)
axis(1, at = c(0.5, 8 * 1.2), pos = 0, labels = c("", ""), lwd.ticks = 0, xpd = NA)
axis(2, at = seq(0,100,20), pos = 0.6, las = 1)
mtext("Global coverage (%)", 2, line = 2)
legend("right", legend = c("GYGA-CZ", "metamodel"), inset = c(-0.55),
fill = cols, xpd = NA, bty = "n", x.intersp = 0.5, cex = .9)
mtext("EXTRAPOLATION", 1, line = 2.5, font = 2)
dev.off()
# TABLE ----------------
round(cvg_global*100)
round(cvg_interp*100)
# CZ-Country global
gg_cvg[
crop_sp %in% c("wheat", "maize", "rice")
, round(100 * sum(cz_ctry_spam)/sum(world))
, by = .(crop_sp)]
# CZ extrap in GYGA countries