scripts/15_make_FigS2.R

In ecohealthalliance/sars_cov_risk: What the Package Does (One Line, Title Case)

# Fig S1: comparison of species IUCN ranges to AOH

load(here("data/countsHT.rda"))
load(here("data/IUCNareas.rda"))

areaComp <- countsHT %>% 
  group_by(species) %>% 
  dplyr::summarise(areaAOH = sum(areakm2)) %>% 
  left_join(., IUCNareas) %>% 
  rename(AOH = areaAOH, IUCN = IUCNareas) %>% 
  pivot_longer(cols = -c(species), names_to = "type", 
               values_to = "area") %>% 
  # reverse so that ordering will be by IUCN area
  mutate(type = fct_rev(type)) %>% 
  group_by(type) %>% 
  mutate(species = fct_reorder(species, area)) %>% 
  # reverse again so that IUCN gets plotted first
  mutate(type = fct_rev(type))

ggplot(areaComp, aes(x = species, y = area/1000000, group = type, fill = type)) +
  geom_bar(stat = "identity", position = "dodge") +
  scale_fill_manual(values = c("gray70", "gray30"), 
                    guide = guide_legend(reverse = T),
                    name = "") +
  ylab(expression(paste("Total area (million km"^2, ")"))) + xlab("Species") +
  coord_flip() +
  theme_bw() +
  theme(panel.grid.major.y = element_blank(),
        legend.position = c(0.85, 0.2),
        axis.text.y = element_text(face = "italic"),
        axis.text = element_text(color = "black"))

ggsave("figures/FigS2.png", width = 6, height = 5, units = "in", dpi = 300)

# calculate the % difference from IUCN to AOH (for the main text)
# areaDiff <- countsHT %>% 
#   group_by(species) %>% 
#   dplyr::summarise(areaAOH = sum(areakm2)) %>% 
#   left_join(., IUCNareas) %>% 
#   rename(AOH = areaAOH, IUCN = IUCNareas) %>% 
#   mutate(diff = IUCN - AOH, pDiff = diff/IUCN) %>% 
#   arrange(desc(pDiff))
# 
# median(areaDiff$pDiff)