R/plot_allspeciesprob.R

In sustainablefarms/farm_biodiversity_app: An App Predicting Bird Biodiversity on Farms

#plot fun

plot_allspeciesprob <- function(species_prob_current){
  species_prob_current <- data.frame(species = rownames(species_prob_current), species_prob_current)
  traits <- get("traits", envir = globalenv())
  species_prob_current <- dplyr::left_join(species_prob_current, traits, by = c(species = "Common Name")) %>%
    dplyr::rename(`Common Name` = species)
  
  species_prob_current %>%
    dplyr::mutate(`Common Name` = paste(`Common Name`, formatC(median, digits = 2, format = "f"))) %>%
    ordfactby(`Common Name`, `Body Length`) %>%
    ggplot(aes(x = `Common Name`, y = median, fill = median)) +
    geom_bar(stat = "identity", show.legend = FALSE) +
    geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.5) +
    coord_flip(clip = "off") +
    scale_fill_gradient(aesthetics = "fill",
                        low = appcolors[["Green 10"]],
                        high = appcolors[["Dark Green"]]) +
    scale_x_discrete(name = "Increasing Body Length ---->") +
    scale_y_continuous(name = "Occupancy Probability", limits = c(0, 1), expand = expansion(),
                       breaks = seq(0, 1, by = 0.25),
                       labels = c("0", "0.25", "0.5", "0.75", "1")) +
    ggtitle("Probability of Occupying at Least One Patch") +
    theme_minimal() +
    theme(legend.position = "none",
          panel.border = element_rect(fill = NA, color = "grey"),
          panel.grid.major.y = element_blank())
}