MigratoryBird.R

pacman::p_load( 
  tidyverse,
  rvest,
  xlsx,
  sf)


YEAR = 2009

if(YEAR < 2009 | YEAR > 2023){
  stop("'YEAR' not appropriate!")
}
if(YEAR %in% 2021:2023) {
  ColName1 <- rlang::sym("調査年月日")} else {
    if(YEAR %in% 2013:2020) {
      ColName1 <- rlang::sym("年月日")
    }
}

URL_base0 = "https://www.env.go.jp/nature/dobutsu/bird_flu/migratory/ap_wr_transit"
URL_base <- paste0(URL_base0, substr(as.character(YEAR), 3, 4), "/")

URL_loclatlon = "https://raw.githubusercontent.com/igproj-fusion/BirdMigratory/main/LocLatLon.csv"
jp_pref_geo = "https://github.com/igproj-fusion/R-gis/raw/main/japan_ver2.geojson"
Border = data.frame(lon <- c(127, 130, 138, 138),
                     lat <- c( 40, 40, 44, 46))



#####################################################

JP_PREF <- read_sf(jp_pref_geo)

#####################################################

bird_df <- read_html(paste0(URL_base, "index.html"))|> 
  html_nodes("a") %>% 
  html_attr("href") |> 
  as_tibble() |> 
  filter(grepl(pattern = "sp_csv", x = value)) |> 
  mutate(fname = gsub("sp_csv/", "", value)) |>
  mutate(link = paste0(URL_base, value)) |> 
  select(fname, link)


tmp_dir <- tempdir()
Birds <- NULL
for(i in 1:nrow(bird_df))
{
  file <- file.path(tmp_dir, bird_df$fname[i])
  download.file(bird_df$link[i], destfile = file, mode = "wb")
  d <- read.xlsx(file, sheetIndex = 1) 
  if(YEAR < 2013){
    dt <- d |> 
      filter(!is.na(年)) |> 
      mutate(date = ymd(paste0(年, "-", 月, "-", 日))) |> 
  } else {
    dt <- d |> 
      filter(!is.na(!!ColName1)) |> 
      mutate(date = ymd(!!ColName1)) 
  }
  
  Birds <- dt |> 
    select(date, loc = 調査地名, type = 種名, number = 数) |>
    mutate(number = as.integer(number)) |> 
    rbind(Birds)
}


BIRDS_LOC  <- left_join(Birds, read.csv(URL_loclatlon), by = c("loc" = "loc")) |> 
  st_as_sf(coords = c('lon', 'lat'), crs = st_crs(JP_PREF))



#####################################################
# Example
#####################################################


TYPE <- "カルガモ"


ggplot() +
  geom_sf(data = JP_PREF) +
  geom_path(data = Border, aes(x = lon, y = lat)) +
  geom_sf(data = BIRDS_LOC |> 
            filter(type == TYPE) |> 
            group_by(loc) |> 
            summarize(total = sum(number)), 
          aes(size = total),
          alpha = 0.8, color = "cornflowerblue") +
  ylim(c(27.5, 46)) +
  labs(title = paste0(TYPE, "飛来地 ", YEAR - 1, "秋～", YEAR, "春")) +
  theme_void() +
  theme(plot.margin= unit(c(1, 1, 1, 1), "lines"),
        plot.title = element_text(size = rel(1.4)),
        legend.position = "bottom")


BIRDS_LOC |> 
  filter(type == TYPE) |>
  mutate(year = year(date)) |> 
  mutate(month = month(date)) |> 
  group_by(year, month, area) |> 
  summarize(total = sum(number)) |> 
  mutate(date = ymd(paste0(year, "-", month, "-15"))) |>
  ggplot(aes(x = date, y = total)) +
  geom_line(aes(color = area),
            linewidth = 1) +
  geom_point(aes(shape = area, color = area), size = 3) +
  theme_light() +
  labs(title = paste0(TYPE, "飛来数 ", YEAR - 1, "秋～", YEAR, "春"),
       x = "",
       y = "No. of Observations") +
  theme(plot.margin= unit(c(1, 1, 1, 1), "lines"),
        plot.title = element_text(size = rel(1.5)),
        axis.title = element_text(size = rel(1.3), 
                                  lineheight = 0.3),
        legend.title = element_text(size = rel(0)),
        legend.position = "bottom")