inst/scripts/figures_etc/pubcrawler_plots.R

In ecohealthalliance/hotspots2: Analysis of the Hotspots dataset on disease emergence

load_all()

current_out_dir <- file.path(out_dir(), "additional_figures")
dir.create(current_out_dir, showWarnings = FALSE)

library(ggplot2)
library(GGally)
library(dplyr)
library(viridis)


library(pubcrawler2hotspots)

data(pubs_hires)
data(pubs_superhires)

prettypubs <- pubs_superhires %>%
  select(x = lon, y = lat, z = w1b) %>%
  rasterFromXYZ(crs = crs(template_raster())) %>%
  raster::disaggregate(2, method = "bilinear") %>%
  mask(mask = country_outlines) %>%
  as.data.frame(xy = TRUE) %>%
  na.omit()

numcolors <- length(unique(prettypubs[["z"]]))

clip_at_sd <- function(x, multiple = 1) {
  m <- mean(x, na.rm = TRUE)
  s <- sd(x, na.rm = TRUE) * multiple
  y <- x %>%
    pmin(m + s) %>%
    pmax(m - s)
  return(y)
}

ggplot() +
  geom_polygon(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, fill = "#440154FF") +
  geom_raster(aes(x = x, y = y, fill = quantvar(z)), data = prettypubs) + 
  geom_path(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, color = "white", size = 0.15) +
  coord_fixed() +
  scale_fill_gradientn(colours = viridis(numcolors),
                       guide = guide_colorbar(title = "Publications")) +
  theme_black_legend() +
  labs(x = NULL, y = NULL)

ggsave(file.path(current_out_dir, "pubcrawler_hires_quantvar.pdf"), height = 4.5, width = 9)
ggsave(file.path(current_out_dir, "pubcrawler_hires_quantvar.png"), height = 4.5, width = 9)

ggplot() +
  geom_polygon(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, fill = "#440154FF") +
  geom_raster(aes(x = x, y = y, fill = winsorize(z, 0.75)), data = prettypubs) + 
  geom_path(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, color = "white", size = 0.15) +
  coord_fixed() +
  scale_fill_gradientn(colours = viridis(numcolors),
                       guide = guide_colorbar(title = "Publications")) +
  theme_black_legend() +
  labs(x = NULL, y = NULL)

ggplot() +
  geom_polygon(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, fill = "#440154FF") +
  geom_raster(aes(x = x, y = y, fill = pmin(z, quantile(z, probs = 0.9))), data = prettypubs) + 
  geom_path(aes(x = lon, y = lat, group = group), data = map.world(), inherit.aes = FALSE, color = "white", size = 0.15) +
  coord_fixed() +
  scale_fill_gradientn(colours = viridis(numcolors),
                       guide = guide_colorbar(title = "Publications")) +
  theme_black_legend() +
  labs(x = NULL, y = NULL)

ggsave(file.path(current_out_dir, "pubcrawler_hires_truncated.pdf"), height = 4.5, width = 9)
ggsave(file.path(current_out_dir, "pubcrawler_hires_truncated.png"), height = 4.5, width = 9)

quickmap(prettypubs, quantvar(z), pal_fun = "viridis") +
  geom_polygon(aes(x = long, y = lat, group = group), data = map_data("world"), inherit.aes = FALSE, color = "white", fill = "#440154FF", size = 0.1) +
  theme_black_nothing()

  viridis(1)