Get number of GBIF occurrences per kingdom per year in Belgium with geographic coordinates.

get_n_occ_per_kingdom.r

library(tidyverse)
library(lubridate)
library(rgbif)

start_year <- 2000
years <- seq(start_year, lubridate::year(Sys.Date()))
facet <- "kingdomKey"
# get counts per year for each kingdomKey
n_occ_kingdom <- map_dfr(
  years,
  function(t) {
    rgbif::occ_search(
      country = "BE", 
      year = t, 
      hasCoordinate = TRUE, 
      return = "facets", 
      facet = facet,
      limit = 0)$facets[[facet]] %>%
      rename(kingdomKey = name) %>%
      mutate(year = t)
  }
)

# retrrieve kingdom names
kingdom_names <- 
  n_occ_kingdom %>%
  distinct(kingdomKey) %>%
  group_by(kingdomKey) %>%
  mutate(
    kingdom = rgbif::name_usage(key = kingdomKey, return = "data")$kingdom)

# add kingdom names to counts df
n_occ_kingdom <- 
  n_occ_kingdom %>%
  left_join(
    kingdom_names, 
    by = "kingdomKey") %>%
  select(kingdomKey, kingdom, dplyr::everything())

# save plot in root
map(unique(kingdom_names$kingdom), 
    function(k) {
      ggplot(n_occ_kingdom %>%
               filter(kingdom == k),
             aes(x = year, y = count)) +
        geom_line() +
        geom_point(size=4, fill = "red") +
        ggtitle(k) +
        ggsave(paste0("n_occ_",k,".png"), device = "png")
    }
)