add data and code for intertidal CHIMMP figure

R/tidal_wetlands.R

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+library(tidyverse)
+library(sf)
+library(tbeptools)
+library(mapview)
+library(here)
+library(patchwork)
+
+# get tidal wetland spatial data --------------------------------------------------------------
+
+dat1950raw <- st_read('T:/05_GIS/HISTORICAL/1950_LULC_Emergents/1950_emergent_habitat.shp')
+dat1950 <- dat1950raw |> 
+  select(FLUCCSCODE = HABITAT) |> 
+  mutate(
+    FLUCCSCODE = case_when(
+      FLUCCSCODE == 'Mangrove/Spartina Marsh' ~ 6120, 
+      FLUCCSCODE == 'Juncus Marsh' ~ 6420, 
+      FLUCCSCODE == 'Salt Barren' ~ 6600
+    )
+  ) |> 
+  st_transform(crs = st_crs(tbshed)) |> 
+  st_intersection(tbshed) |>
+  select(-Acres) |> 
+  st_intersection(tbsegshed)
+
+fls <- list.files('T:/05_GIS/SWFWMD/zipped_all_years/', pattern = 'zip', full.names = T)
+
+out <- vector('list', length(fls))
+names(out) <- basename(fls)
+for(fl in fls){
+
+  cat(fl, '\n')
+  tmpdr <- tempdir()
+
+  unzip(fl, exdir = tmpdr)
+
+  shppth <- list.files(tmpdr, pattern = 'shp$', full.names = T, recursive = T)
+
+  shp <- st_read(shppth, quiet = T)
+
+  shpfilt <- shp |> 
+    filter(FLUCCSCODE %in% c(6120, 6420, 6600)) |> # mangrove, salt marsh, salt barren
+    st_transform(crs = st_crs(tbshed)) |> 
+    select(FLUCCSCODE) |> 
+    st_make_valid() |> 
+    st_intersection(tbshed) |>
+    select(-Acres) |> 
+    st_intersection(tbsegshed)
+
+  out[[basename(fl)]] <- shpfilt
+
+  unlink(tmpdr, recursive = T)
+
+}
+
+swfwmdintertidal <- out
+swfwmdintertidal <- c(list(`1950` = dat1950), swfwmdintertidal)
+names(swfwmdintertidal) <- gsub('lulc|\\.zip', '', names(swfwmdintertidal))
+save(swfwmdintertidal, file = 'data/swfwmdintertidal.RData', compress = 'xz')
+
+# make plot -----------------------------------------------------------------------------------
+
+load(file = here('data/swfwmdintertidal.RData'))
+
+ests <- swfwmdintertidal |> 
+  enframe(name = 'yr') |>
+  mutate(
+    value = map(value, function(x){
+
+      x |>
+        mutate(
+          area = st_area(x)
+        ) |> 
+        st_set_geometry(NULL) |> 
+        summarize(
+          area = sum(area), 
+          .by = c(FLUCCSCODE, bay_segment)
+        )
+
+    })
+  ) |> 
+  unnest('value')
+
+toplo <- ests |> 
+  mutate(
+    yr = as.numeric(yr),
+    yr = case_when(
+      yr == 1950 ~ 1980, 
+      TRUE ~ yr
+    ),
+    habitat = case_when(
+      FLUCCSCODE == 6120 ~ 'Mangrove', 
+      FLUCCSCODE == 6420 ~ 'Salt Marsh', 
+      FLUCCSCODE == 6600 ~ 'Salt Barren'
+    ), 
+    habitat = factor(habitat, levels = c('Salt Barren', 'Salt Marsh', 'Mangrove')),
+    area = units::set_units(area, 'acres'),
+    area = as.numeric(area) / 1000, 
+    bay_segment = factor(bay_segment, levels = c('OTB', 'HB', 'MTB', 'LTB', 'BCB', 'TCB', 'MR'), 
+                         labels = c('Old Tampa Bay (OTB)', 'Hillsborough Bay (HB)', 'Middle Tampa Bay (MTB)', 'Lower Tampa Bay (LTB)', 
+                                    'Boca Ciega Bay (BCB)', 'Terra Ceia Bay (TCB)', 'Manatee River (MR)'))
+
+  )
+
+p1 <- ggplot(toplo, aes(x = yr, y = area, fill = habitat)) +
+  geom_col(color = 'darkgrey') + 
+  scale_fill_manual(values = c('#FFFF14', '#1C99C7', '#83832E')) +
+  scale_x_continuous(breaks = seq(1980, 2020, 10), labels = c(1950,  seq(1990, 2020, 10))) +
+  facet_wrap(~bay_segment, scales = 'free_y', ncol = 2) + 
+  geom_vline(xintercept = 1985, linetype = 'dashed') +
+  theme_minimal() +
+  theme(
+    legend.position = c(0.75, 0.1)
+  ) +
+  labs(
+    x = NULL, 
+    y = 'Acres (x1000)', 
+    fill = NULL
+  )
+
+# base tiles
+bbx <- tbsegshed %>% 
+  st_bbox() %>% 
+  st_as_sfc() %>% 
+  st_buffer(dist = units::set_units(1, kilometer)) %>%
+  st_transform(crs = 4326) %>% 
+  st_bbox()
+
+tls <- maptiles::get_tiles(bbx, provider = "CartoDB.PositronNoLabels", zoom = 10)
+dat_ext <- sf::st_as_sfc(bbx) %>% 
+  st_transform(crs = 4326) %>% 
+  st_bbox()
+
+curex <- swfwmdintertidal[['2020']] |> 
+  mutate(
+    habitat = case_when(
+      FLUCCSCODE == 6120 ~ 'Mangrove', 
+      FLUCCSCODE == 6420 ~ 'Salt Marsh', 
+      FLUCCSCODE == 6600 ~ 'Salt Barren'
+    ),
+    habitat = factor(habitat, levels = c('Salt Barren', 'Salt Marsh', 'Mangrove'))
+  )
+
+labs1 <- tbsegshed |> 
+  filter(!bay_segment %in% c('OTB', 'HB', 'MTB', 'LTB')) |>
+  st_centroid()
+labs2 <- tbseg |> 
+  st_centroid()
+labs <- rbind(labs1, labs2)
+
+m1 <- ggplot() + 
+  tidyterra::geom_spatraster_rgb(data = tls, maxcell = 1e8) +
+  geom_sf(data = tbsegshed, inherit.aes = F, linewidth = 1, fill = NA, color = 'darkgrey') +
+  geom_sf(data = curex, aes(fill = habitat, color = habitat), show.legend = F) +
+  geom_sf_text(data = labs, aes(label = bay_segment), inherit.aes = F) +
+  annotate('text', x = -82.85, y = 27.37, label = 'Current extent (2020)', size = 5, fontface = 'bold', hjust = 0) +
+  scale_fill_manual(values = c('#FFFF14', '#1C99C7', '#83832E')) +
+  scale_color_manual(values = c('#FFFF14', '#1C99C7', '#83832E')) +
+  theme(
+    axis.title = element_blank(),
+    axis.text = element_text(size = 7),
+    legend.position = 'inside',
+    legend.position.inside = c(0.15, 0.15),
+    legend.background = element_blank(),
+    legend.title = element_blank()
+  ) +
+  ggspatial::annotation_scale(location = 'tr', unit_category = 'metric') +
+  coord_sf(xlim = c(dat_ext[1], -82.3), ylim = c(dat_ext[2], 28.1), expand = FALSE, crs = 4326)
+
+p <- p1 + m1 + plot_layout(widths = c(1, 0.8))
+
+png(here('figs/tidal_wetlands.png'), width = 9, height = 6, units = 'in', res = 300, family = 'serif')
+print(p)
+dev.off()