## ---- echo = FALSE, message = FALSE-------------------------------------------
knitr::opts_chunk$set(collapse = T, fig.width=6, fig.height=3)

## ---- eval = FALSE------------------------------------------------------------
#  ###########################################################################
#  ## This script will replicate the figures (except the screenshots)
#  ## and write them to files.
#  ## The working directory should be set the the parent folder of this script.
#  ###########################################################################
#  
#  ## install.packages(c("tmap", "tmaptools"))
#  library("tmap") # required version 2.0 or later
#  library("tmaptools") # required version 2.0 or later
#  
#  data("World", "metro", package = "tmap")
#  metro$growth <- (metro$pop2020 - metro$pop2010) / (metro$pop2010 * 10) * 100

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 1
#  #############################
#  
#  m1 <- tm_shape(World) +
#      tm_polygons("income_grp", palette = "-Blues",
#        title = "Income class", contrast = 0.7, border.col = "grey30", id = "name") +
#      tm_text("iso_a3", size = "AREA", col = "grey30", root = 3) +
#    tm_shape(metro) +
#      tm_bubbles("pop2010", col = "growth", border.col = "black",
#        border.alpha = 0.5,
#        breaks = c(-Inf, 0, 2, 4, 6, Inf) ,
#        palette = "-RdYlGn",
#        title.size = "Metro population (2010)",
#        title.col = "Annual growth rate (%)",
#        id = "name",
#        popup.vars = c("pop2010", "pop2020", "growth")) +
#    tm_style("gray") +
#    tm_format("World", frame.lwd = 2)
#  tmap_save(m1, "bubble.png", width = 6.125, height = 3, scale = .75, dpi = 300, asp = 0, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 2
#  #############################
#  
#  m0 <- tm_shape(metro) +
#    tm_bubbles(size = "pop2030") +
#    tm_style("cobalt") +
#    tm_format("World")
#  tmap_save(m0, "metro2030.png", width = 6.125, scale = .5, dpi = 300, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 3
#  #############################
#  m21 <- tm_shape(World) + tm_polygons(c("blue", "red")) + tm_layout(frame.lwd = 1.5)
#  tmap_save(m21, "facets1.png", width = 6.125, height = 1.54, scale = .75, dpi = 300, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 4
#  #############################
#  m22 <- tm_shape(World) + tm_polygons("red") + tm_facets(by = "continent", free.coords = FALSE)
#  tmap_save(m22, "facets2.png", width = 6.125, height = 1.8, scale = .75, dpi = 300, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 5
#  #############################
#  tm1 <- tm_shape(World) + tm_polygons()
#  tm2 <- tm_shape(metro) + tm_dots()
#  png("facets3.png", width = 6.125, height = 1.54, units = "in", res = 300)
#    tmap_arrange(tm1, tm2, outer.margins = .01)
#  dev.off()

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 6
#  #############################
#  
#  tmap_mode("view")
#  m1

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 7
#  #############################
#  data("land", "rivers", package = "tmap")
#  m2 <- tm_shape(land) +
#    tm_raster("elevation", breaks = c(-Inf, 250, 500, 1000, 1500, 2000, 2500, 3000, 4000, Inf),
#              palette = terrain.colors(9), title = "Elevation (m)") +
#    tm_shape(rivers) +
#    tm_lines("lightblue", lwd = "strokelwd", scale = 1.5, legend.lwd.show = FALSE) +
#    tm_shape(World, is.master = TRUE) +
#    tm_borders("grey20", lwd = .5) +
#    tm_grid(projection = "longlat", labels.size = 0.4, lwd = 0.25) +
#    tm_text("name", size = "AREA") +
#    tm_compass(position = c(0.08, 0.45), color.light = "grey90", size = 3) +
#    tm_credits("Eckert IV projection", position = c("RIGHT", "BOTTOM")) +
#    tm_style("classic",
#    		 bg.color = "lightblue",
#           space.color = "grey90",
#    		 inner.margins = c(0.04, 0.04, 0.03, 0.02),
#    		 earth.boundary = TRUE) +
#    tm_legend(position = c("left", "bottom"),
#              frame = TRUE,
#              bg.color = "lightblue")
#  tmap_save(m2, "classic.png", width = 6.125, scale = .7, dpi = 300, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 8
#  #############################
#  m3 <- tm_shape(World, projection = "robin") +
#    tm_polygons(c("HPI", "gdp_cap_est"),
#                palette = list("RdYlGn", "Purples"),
#                style = c("pretty", "fixed"), n = 7,
#                breaks = list(NULL, c(0, 500, 2000, 5000, 10000, 25000, 50000, Inf)),
#                title = c("Happy Planet Index", "GDP per capita")) +
#    tm_style("natural", earth.boundary = c(-180, -87, 180, 87))  +
#    tm_format("World", inner.margins = 0.02, frame = FALSE) +
#    tm_legend(position = c("left", "bottom"), bg.color = "gray95", frame = TRUE) +
#    tm_credits(c("", "Robinson projection"), position = c("RIGHT", "BOTTOM"))
#  
#  tmap_save(m3, "world_facets2.png", width = 5, scale = .7, dpi = 300, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 9
#  #############################
#  library("readxl")
#  library("grid")
#  
#  # function to obtain Food Environment Atlas data (2014)
#  get_food_envir_data <- function() {
#    dir <- tempdir()
#    if (!file.exists(file.path(dir, "DataDownload.xls"))) {
#    	download.file("https://www.ers.usda.gov/webdocs/DataFiles/48731/February2014.xls?v=41688", destfile = file.path(dir, "DataDownload.xls"), mode = "wb")
#    }
#    res <- tryCatch({
#    	read_excel(file.path(dir, "DataDownload.xls"), sheet = "HEALTH")	
#    }, error = function(e) {
#    	stop("The excel file cannot be read. Please open it, and remove all sheets except HEALTH. The location of the file is: ", normalizePath(file.path(dir, "DataDownload.xls")))
#    })
#  }
#  
#  # function to obtain US county shape
#  get_US_county_2010_shape <- function() {
#    dir <- tempdir()
#    download.file("http://www2.census.gov/geo/tiger/GENZ2010/gz_2010_us_050_00_20m.zip", destfile = file.path(dir, "gz_2010_us_050_00_20m.zip"))
#    unzip(file.path(dir, "gz_2010_us_050_00_20m.zip"), exdir = dir)
#    US <- sf::read_sf(file.path(dir, "gz_2010_us_050_00_20m.shp"))
#    levels(US$NAME) <- iconv(levels(US$NAME), from = "latin1", to = "utf8")
#    US
#  }
#  
#  # obtain Food Environment Atlas data
#  FEA <- get_food_envir_data()
#  
#  # obtain US county shape
#  US <- get_US_county_2010_shape()
#  
#  us1 <- qtm(US)
#  
#  tmap_save(us1, "US1.png", scale = .5, width = 6.125, asp = 0, outer.margins = 0)
#  
#  #############################
#  ## Figure 10
#  #############################
#  library(dplyr)
#  library(sf)
#  
#  US$FIPS <- paste0(US$STATE, US$COUNTY)
#  
#  # append data to shape
#  #US <- append_data(US, FEA, key.shp = "FIPS", key.data = "FIPS", ignore.duplicates = TRUE)
#  US <- left_join(US, FEA, by = c("FIPS", "FIPS"))
#  
#  
#  unmatched_data <- FEA %>% filter(!(FIPS %in% US$FIPS))
#  
#  tmap_mode("view")
#  qtm(US, fill = "PCT_OBESE_ADULTS10")

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 11
#  #############################
#  US_cont <- US %>%
#    subset(!STATE %in% c("02", "15", "72")) %>%
#    simplify_shape(0.2)
#  
#  US_AK <- US %>%
#    subset(STATE == "02") %>%
#    simplify_shape(0.2)
#  
#  US_HI <- US %>%
#    subset(STATE == "15") %>%
#    simplify_shape(0.2)
#  
#  # create state boundaries
#  US_states <- US_cont %>%
#  	dplyr::select(geometry) %>%
#  	aggregate(by = list(US_cont$STATE), FUN = mean)
#  
#  
#  # contiguous US
#  m_cont <- tm_shape(US_cont, projection = 2163) +
#    tm_polygons("PCT_OBESE_ADULTS10", border.col = "gray50", border.alpha = .5, title = "", showNA = TRUE) +
#    tm_shape(US_states) +
#    tm_borders(lwd = 1, col = "black", alpha = .5) +
#    tm_credits("Data @ Unites States Department of Agriculture\nShape @ Unites States Census Bureau", position = c("right", "bottom")) +
#    tm_layout(title = "2010 Adult Obesity by County, percent",
#              title.position = c("center", "top"),
#              legend.position = c("right", "bottom"),
#              frame = FALSE,
#              inner.margins = c(0.1, 0.1, 0.05, 0.05))
#  
#  # Alaska inset
#  m_AK <- tm_shape(US_AK, projection = 3338) +
#    tm_polygons("PCT_OBESE_ADULTS10", border.col = "gray50", border.alpha = .5, breaks = seq(10, 50, by = 5)) +
#    tm_layout("Alaska", legend.show = FALSE, bg.color = NA, title.size = 0.8, frame = FALSE)
#  
#  # Hawaii inset
#  m_HI <- tm_shape(US_HI, projection = 3759) +
#    tm_polygons("PCT_OBESE_ADULTS10", border.col = "gray50", border.alpha = .5, breaks = seq(10, 50, by = 5)) +
#    tm_layout("Hawaii", legend.show = FALSE, bg.color = NA, title.position = c("LEFT", "BOTTOM"), title.size = 0.8, frame = FALSE)
#  
#  # specify viewports for Alaska and Hawaii
#  vp_AK <- viewport(x = 0.15, y = 0.15, width = 0.3, height = 0.3)
#  vp_HI <- viewport(x = 0.4, y = 0.1, width = 0.2, height = 0.1)
#  
#  # save map
#  tmap_mode("plot")
#  tmap_save(m_cont, "USchoro.png", scale = 0.7, width = 6.125, outer.margins = 0,
#            insets_tm = list(m_AK, m_HI),
#            insets_vp = list(vp_AK, vp_HI))

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 12a
#  #############################
#  library("sf")
#  library("rnaturalearth")
#  
#  # functions to obtain crimes data
#  get_crimes_data <- function(path) {
#    stopifnot(file.exists(path), ("crimes_in_Greater_London_2015-10.zip" %in% list.files(path)))
#    tmp_dir <- tempdir()
#    unzip(file.path(path, "crimes_in_Greater_London_2015-10.zip"), exdir = tmp_dir)
#    rbind(read.csv(file.path(tmp_dir, "2015-10-city-of-london-street.csv")),
#          read.csv(file.path(tmp_dir, "2015-10-metropolitan-street.csv")))
#  }
#  
#  # please download the file "crimes_in_Greater_London_2015-10.zip" (available on https://www.jstatsoft.org as a supplement of this paper), and change the path argument below to the location of the downloaded file:
#  crimes <- get_crimes_data(path = "./")
#  
#  # create sf of known locations
#  crimes <- crimes[!is.na(crimes$Longitude) & !is.na(crimes$Latitude), ]
#  crimes <- st_as_sf(crimes, coords = c("Longitude", "Latitude"), crs = 4326)
#  
#  # set map projection to British National Grid
#  crimes <- st_transform(crimes, crs = 27700)
#  
#  c1 <- qtm(crimes)
#  tmap_save(c1, "crimes1.png", scale = .6, width = 3, units = "in", outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 12b
#  #############################
#  crimes_osm <- read_osm(crimes)
#  c2 <- qtm(crimes_osm) + qtm(crimes, symbols.col = "red", symbols.size = 0.5)
#  tmap_save(c2, "crimes2.jpg", scale = .6, width = 3, units = "in", outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 13
#  #############################
#  c3 <- qtm(crimes_osm, raster.saturation = 0, raster.alpha = 1) +
#    qtm(crimes, symbols.col = "Crime.type", symbols.size = 0.5) +
#    tm_legend(outside = TRUE)
#  tmap_save(c3, "crimes3.png", scale = .8, width = 5, height = 4, units = "in", outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 14
#  #############################
#  regions <- ne_download(scale = "large", type = "states", category = "cultural", returnclass = "sf")
#  london <- regions[which(regions$region == "Greater London"),]
#  london <- st_transform(london, crs = 27700)
#  
#  # remove crimes outside Greater London
#  crimes_london <- crop_shape(crimes, london, polygon =  TRUE)
#  
#  c3b <- qtm(crimes_london, dots.alpha = 0.1) +
#    tm_shape(london) +
#    tm_borders()
#  tmap_save(c3b, "crimes3b.png", scale = .7, width = 6.125, units = "in", outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 15
#  #############################
#  library("devtools")
#  install_github("mtennekes/oldtmaptools")
#  library(oldtmaptools)
#  
#  crime_densities <- smooth_map(crimes_london, bandwidth = 0.5, breaks = c(0, 50, 100, 250, 500, 1000), cover = london)
#  
#  # download rivers, and get Thames shape
#  rivers <- ne_download(scale = "large", type = "rivers_lake_centerlines", category = "physical")
#  thames <- crop_shape(rivers, london)
#  
#  c4 <- tm_shape(crime_densities$polygons) +
#    tm_fill(col = "level", palette = "YlOrRd", title = expression("Crimes per " * km^2)) +
#    tm_shape(london) + tm_borders() +
#    tm_shape(thames) + tm_lines(col = "steelblue", lwd = 4) +
#    tm_compass(position = c("left", "bottom")) +
#    tm_scale_bar(position = c("left", "bottom")) +
#    tm_style("gray", title = "Crimes in Greater London\nOctober 2015")
#  tmap_save(c4, "crimes4.png", scale = .7, width = 6.125, units = "in", outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 16
#  #############################
#  london_city <- london[london$name == "City",]
#  crimes_city <- crop_shape(crimes_london, london_city, polygon = TRUE)
#  london_osm <- read_osm(london_city, type = "stamen-watercolor", zoom = 13)
#  
#  c5 <- qtm(london_osm) +
#    tm_shape(crimes_city) +
#    tm_dots(size = .2) +
#    tm_facets("Crime.type", free.coords = FALSE)
#  tmap_save(c5, "crimes5.png", scale = 1, width = 6.125, asp = NA, outer.margins = 0)

## ---- eval = FALSE------------------------------------------------------------
#  #############################
#  ## Figure 17
#  #############################
#  crime_lookup <- c("Anti-social behaviour" = 2,
#                    "Bicycle theft" = 1,
#                    "Burglary" = 1,
#                    "Criminal damage and arson" = 2,
#                    "Drugs" = 6,
#                    "Other crime" = 7,
#                    "Other theft" = 1,
#                    "Possession of weapons" = 3,
#                    "Public order" = 2,
#                    "Robbery" = 1,
#                    "Shoplifting" = 1,
#                    "Theft from the person" = 1,
#                    "Vehicle crime" = 4,
#                    "Violence and sexual offences" = 5)
#  crime_categories <- c("Property Crime",
#                        "Criminal damage and anti-social behaviour",
#                        "Possession of weapons",
#                        "Vehicle crime",
#                        "Violence and sexual offences",
#                        "Drugs",
#                        "Other crime")
#  crimes_city$Crime.group <- factor(crime_lookup[crimes_city$Crime.type], labels = crime_categories)
#  
#  tmap_mode("view")
#  tm_shape(crimes_city) +
#    tm_dots(jitter = 0.2, col = "Crime.group", palette = "Dark2", popup.vars = TRUE) +
#    tm_view(alpha = 1,
#      basemaps = "Esri.WorldTopoMap")