Seaweed, fishing and beautiful creatures

library(raster)
library(leaflet)
library(sf)
library(viridis)
library(tidyverse)
library(arrow)
# remotes::install_github("einarhjorleifsson/omar")
library(omar)
con <- connect_mar()
depth <- 
  "/u3/haf/gisland/data/depth/sjomaelingar_dypislinur.gpkg" |> 
  read_sf() |> 
  filter(depth %in% c(20, 50))
latur_landselir <- 
  "/u3/haf/gisland/data/adhoc/ni_d25v_landselir_1980_2018_selalatur_fl.gpkg" |> 
  read_sf() |> 
  select(nafn = nafnFitju:ar2018, area = Shape_Area) |> 
  st_cast("MULTIPOLYGON") |> 
  st_transform(crs = 4326)
latur_landselir_2sjm <-
  latur_landselir |> 
  st_transform(crs = 3857) |> 
  st_buffer(dist = 1852 * 2, nQuadSegs = 100) |> 
  st_transform(crs = 4326) |> 
  st_cast("MULTILINESTRING")
latur_utselir <- 
  "/u3/haf/gisland/data/adhoc/ni_d25v_utselir_1982_2017_selalatur_fl.gpkg" |> 
  read_sf() |> 
  select(nafn = nafnFitju:ar2017, area = Shape_Area) |> 
  st_cast("MULTIPOLYGON") |> 
  st_transform(crs = 4326)
latur_utselir_2sjm <-
  latur_utselir |> 
  st_transform(crs = 3857) |> 
  st_buffer(dist = 1852 * 2, nQuadSegs = 100) |> 
  st_transform(crs = 4326) |> 
  st_cast("MULTILINESTRING")
fuglar <- 
  "/u3/haf/gisland/data/adhoc/ni_f25v_mikilvaegFuglasvaedi_fl.gpkg" |> 
  read_sf() |> 
  st_cast("MULTIPOLYGON") |> 
  st_make_valid() |> 
  select(nafn = nafnFitju,
         flokkur = flokkurSva,
         area = Shape_Area) |> 
  st_transform(crs = 4326) |> 
  drop_na() |> 
  filter(flokkur %in% c("FG", "SF"))

landings_date_nets <- 
  ln_agf(con) |>
  filter(gid %in% c(2, 3, 4)) |> 
  collect() |> 
  mutate(date = as_date(date),
         gid = case_when(gid == 2 ~ "gadoids",
                         .default = "lumpsucker")) |> 
  select(vid, date, gid) |> 
  distinct() |> 
  arrow::as_arrow_table() |> 
  to_duckdb()
thari <- 
  read_sf("/u3/haf/gisland/data/adhoc/predicted_kelp.gpkg") |> 
  st_transform(crs = 4326)

dx <- 0.005
dy <- dx / 2
g <- 
  open_dataset("~/stasi/fishydata/data/ais/trail") |>
  filter(between(speed, 0.1, 2),
         between(lon, -30, -10),
         between(lat, 63, 68)) |> 
  select(vid, date, time, dt, lon, lat, speed) |> 
  to_duckdb() |> 
  inner_join(landings_date_nets,
             by = join_by(vid, date)) |> 
  mutate(x = lon %/% dx * dx + dx/2,
         y = lat %/% dy * dy + dy/2) |> 
  group_by(x, y, gid) |> 
  summarise(dt = sum(dt, na.rm = TRUE),
            n.years = n_distinct(year(date)),
            .groups = "drop") |> 
  collect()

lumpsucker <- 
  g |> 
  filter(gid == "lumpsucker",
         !is.na(dt)) |> 
  mutate(dt = ifelse(dt > quantile(dt, 0.95), quantile(dt, 0.95), dt)) |>  
  # only grid cells if reported in more than one year
  filter(n.years > 1) |> 
  select(x, y, dt) |> 
  raster::rasterFromXYZ()
raster::crs(lumpsucker) <- "epsg:4326"
inf <- inferno(12, alpha = 1, begin = 0, end = 1, direction = -1)
pal_lumpsucker <- colorNumeric(inf, raster::values(lumpsucker), na.color = "transparent")
gadoids <- 
  g |> 
  filter(gid == "gadoids",
         !is.na(dt)) |> 
  mutate(dt = ifelse(dt > quantile(dt, 0.95), quantile(dt, 0.95), dt)) |>  
  # only grid cells if reported in more than one year
  filter(n.years > 1) |> 
  select(x, y, dt) |> 
  raster::rasterFromXYZ()
raster::crs(gadoids) <- "epsg:4326"
pal_gadoids <- colorNumeric(inf, raster::values(gadoids), na.color = "transparent")


l <-
  leaflet(options = leafletOptions(minZoom = 4, maxZoom = 12)) %>%
  addTiles(urlTemplate = "https://server.arcgisonline.com/ArcGIS/rest/services/World_Imagery/MapServer/tile/{z}/{y}/{x}",
           group = "Image",
           attribution = 'Data source: <a href="https://www.hafogvatn.is">Marine Rearch Institute</a>') %>%
  setView(-15, 66.3, zoom = 8) %>%
  addPolygons(data = thari, weight = 1, fillColor = "green", fillOpacity = 0.75, group = "Þaraskógur") |> 
  addRasterImage(lumpsucker, colors = pal_lumpsucker, opacity = 1, group = "Grásleppuveiðar",
                 maxBytes = Inf,
                 project = TRUE) |> 
  addRasterImage(gadoids, colors = pal_gadoids, opacity = 1, group = "Þorsknetaveiðar",
                 maxBytes = Inf,
                 project = TRUE) |> 
  addPolygons(data = latur_landselir, weight = 1, fillColor = "cyan", fillOpacity = 1, group = "Landsselslátur") |> 
  addPolylines(data = depth, weight = 1, opacity = 1, color = "grey", group = "Dýpi [20 & 50 m]") |> 
  addPolylines(data = latur_landselir_2sjm, weight = 2, color = "cyan", opacity = 1, group = "Landsselslátur 2 sjómílur") |> 
  addPolygons(data = latur_utselir, weight = 1, fillColor = "red", fillOpacity = 1, group = "Útselslátur") |> 
  addPolylines(data = latur_utselir_2sjm, weight = 2, color = "red", opacity = 1, group = "Útselslátur 2 sjómílur") |> 
  addPolylines(data = fuglar |> filter(flokkur == "SF"),
               weight = 2,
               color = "pink", opacity = 1, group = "Sjófuglar") |> 
  addPolylines(data = fuglar |> filter(flokkur == "FG"),
               weight = 2,
               color = "orange", opacity = 1, group = "Fjörufuglar") |> 
  addLayersControl(
    overlayGroups = c("Grásleppuveiðar", "Þorsknetaveiðar", "Þaraskógur", 
                      "Dýpi [20 & 50 m]",
                      "Landsselslátur", "Landsselslátur 2 sjómílur", 
                      "Útselslátur", "Útselslátur 2 sjómílur",
                      "Sjófuglar", "Fjörufuglar"),
    options = layersControlOptions(collapsed = FALSE)) |> 
  hideGroup(group = c("Landsselslátur", "Landsselslátur 2 sjómílur", 
                      "Útselslátur", "Útselslátur 2 sjómílur",
                      "Sjófuglar", "Fjörufuglar"))
l