RCode/60_dib_DataDescription.R
In markusfritsch/smoothLUR: Functions and data for smooth Land Use Regression Modeling
#######################################################
### Figures and tables for exploratory data analysis
#######################################################
## Load packages
library(data.table)
library(ggplot2)
library(RColorBrewer)
library(sp)
library(cowplot)
library(smoothLUR)
library(ggmap)
###
### Table 3: Descriptives of continuous variables in monSitesDE ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
MEAN <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
mean), 2)
SD <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
sd), 2)
FIVENUM <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
fivenum), 2)
###
### Fig.1: Boxplots of continuous variables in monSitesDE depending AQeType ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
dat.long <- melt(dat[,c(2,7,10:19,21:25)])
dat.long$AQeType <- dat$AQeType
p.box <- ggplot(data = dat.long, aes(x = variable, y = value, fill = AQeType, color = AQeType)) +
theme_bw() +
xlab("") +
ylab("") +
geom_boxplot(fill=NA,lwd=0.75) +
facet_wrap(~variable,scale="free",nrow = 6)+
scale_color_manual(values = brewer.pal(9, "BrBG")[c(1,2,3)],
aesthetics = c("fill", "colour"))+
theme(axis.text.y = element_text(size = 14),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
strip.text = element_text(size = 14),
legend.title = element_text(size = 16),
legend.text = element_text(size = 16),
legend.position = c(0.8, 0.075))
#pdf("../img/BoxplotsVariablesMonSitesDE.pdf",width = 12, height = 9)
p.box
#dev.off()
dat.long2 <- rbind(dat.long[,c(1:2)],dat.long[,c(1:2)])
dat.long2$AQeType <- NA
dat.long2$AQeType[1:6851] <- dat.long[,3]
dat.long2$AQeType[6852:13702] <- "all"
p.box2 <- ggplot(data = dat.long2, aes(x = variable, y = value, fill = AQeType, color = AQeType)) +
theme_bw() +
xlab("") +
ylab("") +
geom_boxplot(fill=NA,lwd=0.75) +
facet_wrap(~variable,scale="free",nrow = 6)+
scale_color_manual(values = brewer.pal(9, "BrBG")[c(9,1,2,3)],
aesthetics = c("fill", "colour"))+
theme(axis.text.y = element_text(size = 14),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
strip.text = element_text(size = 14),
legend.title = element_blank(),
legend.text = element_text(size = 14),
legend.position = c(0.8, 0.075))
#pdf("../img/BoxplotsVariablesMonSitesDE2.pdf",width = 12, height = 9)
#postscript("../img/BoxplotsVariablesMonSitesDE2.eps",width = 12, height = 9, horizontal = FALSE)
p.box2
#dev.off()
###
### Fig.2: Locations of monitoring sites and concentration levels in monSitesDE ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
datB <- dat[dat$AQeType == "background", ]
datT <- dat[dat$AQeType == "traffic", ]
datI <- dat[dat$AQeType == "industrial",]
dat$AQeType <- factor(dat$AQeType)
p.MonSites <- ggplot(data=dat,aes(x=Lon,y=Lat,color=Y))+
geom_point(aes(shape=AQeType), size = 2)+
coord_equal()+
theme_bw()+
xlab("Lon (in WGS84)")+
ylab("Lat (in WGS84)")+
scale_fill_gradientn(name = "Y",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(15, 75, 15),
labels = seq(15, 75, 15),
limits = c(min(dat$Y),max(dat$Y)),
aesthetics = "colour")+
theme(legend.title = element_text(size = 16),
legend.text = element_text(size = 16),
legend.background = element_blank(),
axis.text = element_text(size = 16),
axis.title = element_text(size = 16)) +
guides(color = guide_colourbar(barheight = 14, barwidth = 2))
#pdf("../img/MonSitesTypeNO2Level.pdf", width = 12, height = 8)
#postscript("../img/MonSitesTypeNO2Level.eps", width = 12, height = 8, horizontal = FALSE)
p.MonSites
#dev.off()
###
### Fig.3: Interpolation maps of variables in gridDE ----
###
rm(list = ls())
data(gridDE)
df.grid.DE <- gridDE
# Derive SpatialPointsDataFrame from 'df.grid.DE'
spdf.DE <- SpatialPointsDataFrame(coords = cbind(df.grid.DE$Lon.WGS84, df.grid.DE$Lat.WGS84),
data = df.grid.DE,
proj4string = CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))
GK3 <- CRS("+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs")
proj4string(spdf.DE)
spdf.DE2 <- spTransform(spdf.DE, GK3)
proj4string(spdf.DE2)
dat.tmp <- spdf.DE2@data
dat.tmp$long <- coordinates(spdf.DE2)[,1]
dat.tmp$lat <- coordinates(spdf.DE2)[,2]
(p.DE.Alt <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Alt), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Alt",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,2500,500),
labels = seq(0,2500,500),
limits = c(min(dat.tmp$Alt),max(dat.tmp$Alt)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.LowDens <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = LowDens), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "LowDens",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$LowDens),max(dat.tmp$LowDens)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.Agri <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Agri), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Agri",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$Agri),max(dat.tmp$Agri)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.Forest <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Forest), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Forest",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$Forest),max(dat.tmp$Forest)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.PriRoad <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = PriRoad), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "PriRoad",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,7000,1400),
labels = seq(0,7000,1400),
limits = c(min(dat.tmp$PriRoad),max(dat.tmp$PriRoad)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.FedAuto <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = FedAuto), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "FedAuto",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,5000,1000),
labels = seq(0,5000,1000),
limits = c(min(dat.tmp$FedAuto),max(dat.tmp$FedAuto)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
#png("../img/GridVariables.png",width = 900, height = 1500)
#pdf("../img/GridVariables.pdf",width = 12, height = 20)
ggdraw() +
draw_plot(p.DE.Alt, 0, 0.66, 0.5, 0.33) +
draw_plot(p.DE.LowDens, 0.5, 0.66, 0.5, 0.33) +
draw_plot(p.DE.Agri, 0,0.33,0.5,0.33) +
draw_plot(p.DE.Forest, 0.5,0.33,0.5,0.33) +
draw_plot(p.DE.PriRoad, 0,0,0.5,0.33) +
draw_plot(p.DE.FedAuto, 0.5,0,0.5,0.33)
#dev.off()
markusfritsch/smoothLUR documentation built on Nov. 5, 2022, 3:42 p.m.
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#######################################################
### Figures and tables for exploratory data analysis
#######################################################
## Load packages
library(data.table)
library(ggplot2)
library(RColorBrewer)
library(sp)
library(cowplot)
library(smoothLUR)
library(ggmap)
###
### Table 3: Descriptives of continuous variables in monSitesDE ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
MEAN <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
mean), 2)
SD <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
sd), 2)
FIVENUM <- round(apply(dat[,c(2,7,10:19,21:25)],
MARGIN = 2,
fivenum), 2)
###
### Fig.1: Boxplots of continuous variables in monSitesDE depending AQeType ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
dat.long <- melt(dat[,c(2,7,10:19,21:25)])
dat.long$AQeType <- dat$AQeType
p.box <- ggplot(data = dat.long, aes(x = variable, y = value, fill = AQeType, color = AQeType)) +
theme_bw() +
xlab("") +
ylab("") +
geom_boxplot(fill=NA,lwd=0.75) +
facet_wrap(~variable,scale="free",nrow = 6)+
scale_color_manual(values = brewer.pal(9, "BrBG")[c(1,2,3)],
aesthetics = c("fill", "colour"))+
theme(axis.text.y = element_text(size = 14),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
strip.text = element_text(size = 14),
legend.title = element_text(size = 16),
legend.text = element_text(size = 16),
legend.position = c(0.8, 0.075))
#pdf("../img/BoxplotsVariablesMonSitesDE.pdf",width = 12, height = 9)
p.box
#dev.off()
dat.long2 <- rbind(dat.long[,c(1:2)],dat.long[,c(1:2)])
dat.long2$AQeType <- NA
dat.long2$AQeType[1:6851] <- dat.long[,3]
dat.long2$AQeType[6852:13702] <- "all"
p.box2 <- ggplot(data = dat.long2, aes(x = variable, y = value, fill = AQeType, color = AQeType)) +
theme_bw() +
xlab("") +
ylab("") +
geom_boxplot(fill=NA,lwd=0.75) +
facet_wrap(~variable,scale="free",nrow = 6)+
scale_color_manual(values = brewer.pal(9, "BrBG")[c(9,1,2,3)],
aesthetics = c("fill", "colour"))+
theme(axis.text.y = element_text(size = 14),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
strip.text = element_text(size = 14),
legend.title = element_blank(),
legend.text = element_text(size = 14),
legend.position = c(0.8, 0.075))
#pdf("../img/BoxplotsVariablesMonSitesDE2.pdf",width = 12, height = 9)
#postscript("../img/BoxplotsVariablesMonSitesDE2.eps",width = 12, height = 9, horizontal = FALSE)
p.box2
#dev.off()
###
### Fig.2: Locations of monitoring sites and concentration levels in monSitesDE ----
###
rm(list = ls())
data(monSitesDE)
dat <- monSitesDE
datB <- dat[dat$AQeType == "background", ]
datT <- dat[dat$AQeType == "traffic", ]
datI <- dat[dat$AQeType == "industrial",]
dat$AQeType <- factor(dat$AQeType)
p.MonSites <- ggplot(data=dat,aes(x=Lon,y=Lat,color=Y))+
geom_point(aes(shape=AQeType), size = 2)+
coord_equal()+
theme_bw()+
xlab("Lon (in WGS84)")+
ylab("Lat (in WGS84)")+
scale_fill_gradientn(name = "Y",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(15, 75, 15),
labels = seq(15, 75, 15),
limits = c(min(dat$Y),max(dat$Y)),
aesthetics = "colour")+
theme(legend.title = element_text(size = 16),
legend.text = element_text(size = 16),
legend.background = element_blank(),
axis.text = element_text(size = 16),
axis.title = element_text(size = 16)) +
guides(color = guide_colourbar(barheight = 14, barwidth = 2))
#pdf("../img/MonSitesTypeNO2Level.pdf", width = 12, height = 8)
#postscript("../img/MonSitesTypeNO2Level.eps", width = 12, height = 8, horizontal = FALSE)
p.MonSites
#dev.off()
###
### Fig.3: Interpolation maps of variables in gridDE ----
###
rm(list = ls())
data(gridDE)
df.grid.DE <- gridDE
# Derive SpatialPointsDataFrame from 'df.grid.DE'
spdf.DE <- SpatialPointsDataFrame(coords = cbind(df.grid.DE$Lon.WGS84, df.grid.DE$Lat.WGS84),
data = df.grid.DE,
proj4string = CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))
GK3 <- CRS("+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs")
proj4string(spdf.DE)
spdf.DE2 <- spTransform(spdf.DE, GK3)
proj4string(spdf.DE2)
dat.tmp <- spdf.DE2@data
dat.tmp$long <- coordinates(spdf.DE2)[,1]
dat.tmp$lat <- coordinates(spdf.DE2)[,2]
(p.DE.Alt <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Alt), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Alt",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,2500,500),
labels = seq(0,2500,500),
limits = c(min(dat.tmp$Alt),max(dat.tmp$Alt)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.LowDens <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = LowDens), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "LowDens",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$LowDens),max(dat.tmp$LowDens)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.Agri <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Agri), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Agri",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$Agri),max(dat.tmp$Agri)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.Forest <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = Forest), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "Forest",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,1,0.2),
labels = seq(0,1,0.2),
limits = c(min(dat.tmp$Forest),max(dat.tmp$Forest)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.PriRoad <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = PriRoad), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "PriRoad",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,7000,1400),
labels = seq(0,7000,1400),
limits = c(min(dat.tmp$PriRoad),max(dat.tmp$PriRoad)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
(p.DE.FedAuto <- ggplot(dat.tmp, aes(x = long, y = lat)) +
ggmap::theme_nothing(legend = TRUE) +
xlab("") +
ylab("") +
coord_fixed(1) +
geom_tile(aes(fill = FedAuto), width = 1000, height = 1000, na.rm = TRUE)+
scale_fill_gradientn(name = "FedAuto",
colours = rev(brewer.pal(11, "BrBG")[c(1:5)]),
breaks = seq(0,5000,1000),
labels = seq(0,5000,1000),
limits = c(min(dat.tmp$FedAuto),max(dat.tmp$FedAuto)),
na.value = "white") +
theme(legend.text = element_text(size = 17),
legend.title = element_text(size = 17),
legend.background = element_blank(),
legend.position = "bottom",
legend.box = "vertical",
axis.ticks = element_blank()) +
guides(fill = guide_colourbar(barwidth = 20)))
#png("../img/GridVariables.png",width = 900, height = 1500)
#pdf("../img/GridVariables.pdf",width = 12, height = 20)
ggdraw() +
draw_plot(p.DE.Alt, 0, 0.66, 0.5, 0.33) +
draw_plot(p.DE.LowDens, 0.5, 0.66, 0.5, 0.33) +
draw_plot(p.DE.Agri, 0,0.33,0.5,0.33) +
draw_plot(p.DE.Forest, 0.5,0.33,0.5,0.33) +
draw_plot(p.DE.PriRoad, 0,0,0.5,0.33) +
draw_plot(p.DE.FedAuto, 0.5,0,0.5,0.33)
#dev.off()
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