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2024_cold_pool_index.Rmd
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---
title: "Summer Bottom and Surface Temperatures, and the Cold Pool Index"
author:
- affiliation: RACE
description: Research Fish Biologist
email: [email protected]
name: Sean Rohan
output: word_document
fontsize: 12pt
bibliography: coldpool_refs.bib
csl: fish-and-fisheries.csl
addr:
l1: 7600 Sand Point Way NE
l2: NMFS RACE Division, Groundfish Assessment Program
l3: Seattle, WA 98115
---
```{r setup, message=FALSE, warning=FALSE, include=FALSE}
library(coldpool)
library(akgfmaps)
if(!dir.exists("plots")) {dir.create("plots")}
fig_res <- 600
cpa_palette <- c("#21dae7", "#0071ff", "#0000e3", "#000040")
max_year <- 2024
min_year <- max_year - 19 # Default for 20 panel cold pool maps
coldpool:::cold_pool_index$YEAR[order(coldpool:::cold_pool_index$AREA_LTE2_KM2)]
coldpool:::cold_pool_index$YEAR[order(-1*coldpool:::cold_pool_index$MEAN_GEAR_TEMPERATURE)]
coldpool:::cold_pool_index$YEAR[order(-1*coldpool:::cold_pool_index$MEAN_SURFACE_TEMPERATURE)]
```
```{r fig1_cold_pool_index, message=FALSE, warning=FALSE, include=FALSE}
cpi_df <- coldpool:::cold_pool_index |>
dplyr::filter(YEAR <= max_year) |>
dplyr::mutate(group = YEAR < 2020,
var = "Cold Pool Index",
cpi_rank = rank(AREA_LTE2_KM2))
cpi_sd <- sd(cpi_df$AREA_LTE2_KM2/1000)
cpi_mean <- mean(cpi_df$AREA_LTE2_KM2/1000)
plot_cpi_timeseries <- ggplot(data = cpi_df,
mapping = aes(x = YEAR,
y = AREA_LTE2_KM2/1000,
group = group,
label = cpi_rank)) +
geom_point(size = rel(2),
color = "#000040") +
geom_line(color = "#000040") +
geom_hline(yintercept = cpi_mean,
linetype = 2,
color = "#000040") +
geom_hline(yintercept = cpi_mean + c(cpi_sd, -1*cpi_sd),
linetype = 3,
color = "#000040") +
scale_y_continuous(name = expression(bold("Cold Pool Extent"~("thousand"~km^2)))) +
scale_x_continuous(name = "Year",
breaks = seq(1980,2020,4)) +
facet_wrap(~var) +
theme_bw() +
theme(axis.title = element_text(color = "black", face = "bold"),
axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.grid = element_blank(),
legend.title = element_blank(),
legend.position = "bottom",
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA))
ragg::agg_png(filename = here::here("plots", paste0(max_year, "_cold_pool_index.png")),
width = 6,
height = 3,
units = "in",
res = 300)
print(plot_cpi_timeseries)
dev.off()
```
```{r fig2_cpa_stacked_area, message=FALSE, warning=FALSE, include=FALSE}
sebs_layers <- akgfmaps::get_base_layers(select.region = "sebs",
set.crs = coldpool:::ebs_proj_crs)
area_df <- coldpool:::cold_pool_index |>
dplyr::filter(YEAR <= max_year) |>
dplyr::mutate(lteminus1 = AREA_LTEMINUS1_KM2,
lte0 = AREA_LTE0_KM2 - AREA_LTEMINUS1_KM2,
lte1 = AREA_LTE1_KM2 - AREA_LTE0_KM2,
lte2 = AREA_LTE2_KM2 - AREA_LTE1_KM2) |>
dplyr::select(YEAR, lteminus1, lte0, lte1, lte2) |>
reshape2::melt(id.vars = "YEAR") |>
dplyr::mutate(variable = factor(variable,
levels = c( "lte2", "lte1", "lte0", "lteminus1"),
labels = c("\u22642 \u00b0C", "\u22641 \u00b0C", "\u22640 \u00b0C", "\u2264-1 \u00b0C")),
proportion = value/sebs_layers$survey.area$AREA_KM2)
stacked_area_plot <- ggplot() +
geom_area(data = filter(area_df, YEAR < 2020),
mapping = aes(x = YEAR,
y = proportion,
fill = variable)) +
geom_area(data = filter(area_df, YEAR > 2020),
mapping = aes(x = YEAR,
y = proportion,
fill = variable)) +
scale_fill_manual(name = "Temperature",
values = cpa_palette) +
scale_y_continuous(name = "Proportion of EBS Shelf (Plus NW) Survey Area",
limits = c(0, 1),
expand = c(0, 0),
breaks = seq(0,1,0.1)) +
scale_x_continuous(name = "Year",
limits = c(1982, max_year + 0.25),
expand = c(0, 0),
breaks = seq(1982, max_year, 4)) +
theme_bw() +
theme(panel.grid.minor = element_blank(),
axis.title = element_text(face = "bold"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
legend.position = c(0.2, 0.8),
legend.title = element_blank())
ragg::agg_png(file = here::here("plots", paste0(max_year, "_stacked_temperature.png")), height = 4, width = 6, units = "in", res = 600)
print(stacked_area_plot)
dev.off()
stacked_area_simple_label_plot <- ggplot() +
geom_area(data = filter(area_df, YEAR < 2020),
mapping = aes(x = YEAR,
y = proportion,
fill = variable)) +
geom_area(data = filter(area_df, YEAR > 2020),
mapping = aes(x = YEAR,
y = proportion,
fill = variable)) +
scale_fill_manual(name = "Temperature",
values = viridis::mako(5, direction = -1, end = .8)) +
scale_y_continuous(name = "Proportion of EBS Shelf Survey Area",
limits = c(0, 1),
expand = c(0, 0),
breaks = seq(0,1,0.1)) +
scale_x_continuous(name = "Year",
limits = c(1982, max_year + 0.25),
expand = c(0, 0),
breaks = seq(1982, max_year,4)) +
theme_bw() +
theme(panel.grid.minor = element_blank(),
axis.title = element_text(face = "bold"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
legend.position = c(0.1, 0.8),
legend.title = element_blank())
ragg::agg_png(file = here::here("plots", paste0(max_year, "_stacked_temperature_simple_label.png")), height = 4, width = 6, units = "in", res = 600)
print(stacked_area_simple_label_plot)
dev.off()
year_vec <- as.numeric(gsub("[^0-9.-]", "", names(terra::rast(coldpool:::ebs_bottom_temperature))))
start_year <- which(year_vec == min_year)
end_year <- which(year_vec == max_year)
for(i in start_year:end_year) {
sel_layer_df <- as.data.frame(terra::rast(coldpool:::ebs_bottom_temperature)[[i]],
na.rm = FALSE,
xy = TRUE) |>
tidyr::pivot_longer(cols = 3) |>
sf::st_as_sf(coords = c("x", "y"),
crs = coldpool:::ebs_proj_crs) |>
dplyr::rename(year = name,
temperature = value) |>
stars::st_rasterize()
sel_layer_df$temperature <- cut(sel_layer_df$temperature,
breaks = c(-2, -1, 0, 1, 2))
sel_layer_df <- sel_layer_df |>
sf::st_as_sf() |>
dplyr::group_by(temperature) |>
dplyr::summarise(n = n()) |>
dplyr::select(-n) |>
dplyr::ungroup() |>
sf::st_intersection(sebs_layers$survey.area)
sel_layer_df$year <- year_vec[i]
if(i == start_year) {
bt_year_df <- sel_layer_df
} else{
bt_year_df <- dplyr::bind_rows(bt_year_df, sel_layer_df)
}
}
cpa_palette <- c("#21dae7", "#0071ff", "#0000e3", "#000040")
panel_extent <- data.frame(y = c(52, 64),
x = c(-175, -156)) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs)
label_2020 <- data.frame(x = mean(panel_extent$x),
y = mean(panel_extent$y),
label = "No\nSurvey",
year = 2020) |>
dplyr::filter(year <= max_year)
cold_pool_cbar <- coldpool::legend_discrete_cbar(breaks = c(-Inf, -1, 0, 1, 2),
colors = rev(cpa_palette),
legend_direction = "vertical",
font_size = 3.5,
width = 0.1,
expand_size.x = 0.3,
expand_size.y = 0.3,
expand.x = 0.2,
expand.y = 0.9,
spacing_scaling = 1,
text.hjust = 0,
font.family = "sans",
neat.labels = FALSE) +
annotate("text",
x = 1.1,
y = 2.05,
label = expression(bold("Bottom\nTemperature"~(degree*C))),
size = rel(3.2)) +
theme(plot.margin = unit(c(-25, 0,0,-10), units = "pt"))
cold_pool_panels <- ggplot() +
geom_sf(data = sebs_layers$akland, fill = "black",
color = NA) +
geom_sf(data = sebs_layers$survey.area, fill = "grey75") +
geom_sf(data = bt_year_df,
mapping = aes(fill = temperature),
color = NA) +
geom_sf(data = sebs_layers$survey.area,
fill = NA,
color = "black") +
geom_sf(data = sebs_layers$bathymetry) +
geom_polygon(data = data.frame(x = panel_extent$x[c(1,2,2,1,1)],
y = panel_extent$y[c(1,1,2,2,1)],
year = 2020) |> dplyr::filter(year <= max_year),
aes(x = x,
y = y),
fill = "white") +
geom_label(data = label_2020,
aes(x = x,
y = y,
label = label),
label.size = NA) +
coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y,
expand = FALSE) +
scale_x_continuous(name = "Longitude",
breaks = c(-180, -170, -160)) +
scale_y_continuous(name = "Latitude",
breaks = c(54, 58, 62)) +
scale_fill_manual(name = expression("T"~(degree*C)),
values = rev(cpa_palette),
drop = FALSE,
na.value = NA) +
theme_bw() +
theme(axis.title = element_blank(),
axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA),
legend.position = "none") +
facet_wrap(~year, ncol = 4)
cold_pool_grid <- cowplot::plot_grid(
cold_pool_panels,
cowplot::plot_grid(NA, cold_pool_cbar, NA,
nrow = 3),
rel_widths = c(0.9,0.2)
)
coldpool_with_area <-
cowplot::plot_grid(
cowplot::plot_grid(
cold_pool_panels,
stacked_area_plot +
facet_wrap(~"Proportion of EBS Shelf Survey Area") +
scale_y_continuous(name = "Proportion",
limits = c(0, 1),
expand = c(0, 0),
breaks = seq(0,1,0.1)) +
theme(legend.position = "none",
plot.margin = unit(c(-5,5,5,5), units = "pt"),
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA)),
rel_heights = c(0.75, 0.25),
align = "h",
nrow = 2),
cowplot::plot_grid(NA, cold_pool_cbar, NA,
nrow = 3,
rel_heights = c(0.2, 0.6, 0.2)),
rel_widths = c(0.9,0.2)
)
ragg::agg_png(file = here::here("plots", paste0(max_year, "_coldpool_with_area.png")), height = 8, width = 6, units = "in", res = fig_res)
print(coldpool_with_area)
dev.off()
ragg::agg_png(file = here::here("plots", paste0(max_year, "_coldpool.png")), height = 6, width = 6, units = "in", res = fig_res)
print(cold_pool_grid)
graphics.off()
```
```{r fig3_nbs_ebs_map, message=FALSE, warning=FALSE, include=FALSE}
nbs_ebs_temp_breaks <- c(-Inf, seq(-1,8,1), Inf)
nbs_ebs_viridis_option <- "H" # viridis turbo palette
nbs_ebs_layers <- akgfmaps::get_base_layers(select.region = "ebs",
set.crs = coldpool:::ebs_proj_crs)
year_vec_nbs <- as.numeric(gsub("[^0-9.-]", "", names(terra::rast(coldpool:::nbs_ebs_bottom_temperature))))
year_vec_sbs <- as.numeric(gsub("[^0-9.-]", "", names(terra::rast(coldpool:::ebs_bottom_temperature))))
year_vec_grid <- tail(sort(unique(c(year_vec_nbs, year_vec_sbs))), 4)
end_nbs_year <- which.min(abs(year_vec_nbs - max_year))
max_nbs_year <- year_vec_nbs[end_nbs_year]
if(max_year %in% year_vec_nbs) {
bt_year <- terra::rast(coldpool:::nbs_ebs_bottom_temperature)[[length(year_vec_nbs)]]
} else {
bt_year <- terra::rast(coldpool:::ebs_bottom_temperature)[[length(year_vec_sbs)]]
}
bt_year_df <- as.data.frame(bt_year,
na.rm = FALSE,
xy = TRUE) |>
tidyr::pivot_longer(cols = 3) |>
sf::st_as_sf(coords = c("x", "y"),
crs = coldpool:::ebs_proj_crs) |>
dplyr::rename(year = name,
temperature = value) |>
stars::st_rasterize()
bt_year_df$temperature <- cut(bt_year_df$temperature,
breaks = nbs_ebs_temp_breaks)
bt_year_df <- bt_year_df |>
sf::st_as_sf() |>
dplyr::group_by(temperature) |>
dplyr::summarise(n = n()) |>
dplyr::select(-n) |>
dplyr::ungroup() |>
sf::st_intersection(nbs_ebs_layers$survey.area)
# Union to combine strata 31, 32 into 30, etc.
nbs_ebs_agg_strata <- nbs_ebs_layers$survey.strata |>
dplyr::mutate(agg_stratum = Stratum) |>
dplyr::mutate(agg_stratum = replace(agg_stratum, agg_stratum %in% c(31,32), 30),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(41,42,43), 40),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(61,62), 60)) |>
dplyr::group_by(agg_stratum) |>
dplyr::summarise()
# Format and layout
panel_extent <- data.frame(y = c(53, 67),
x = c(-174, -156)) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs)
n_temp_breaks <- length(nbs_ebs_temp_breaks)-1
temp_map_cbar <- coldpool::legend_discrete_cbar(breaks = nbs_ebs_temp_breaks,
colors = viridis::viridis_pal(option = nbs_ebs_viridis_option)(n_temp_breaks),
legend_direction = "horizontal",
font_size = 3,
width = 0.1,
expand_size.x = 0.3,
expand_size.y = 0.3,
expand.x = 0.3,
expand.y = 0.9,
spacing_scaling = 1,
text.hjust = 0.5,
font.family = "sans",
neat.labels = FALSE) +
annotate("text",
x = 1.15,
y = 3.5,
label = expression(bold("Bottom Temperature"~(degree*C))),
size = rel(3.2)) +
theme(plot.margin = unit(c(0,0, 0, 5), units = "mm"))
# Make map
ebs_nbs_temperature_map <- ggplot2::ggplot() +
ggplot2::geom_sf(data = nbs_ebs_layers$akland,
fill = "grey70",
color = "black") +
ggplot2::geom_sf(data = nbs_ebs_layers$survey.area,
fill = "grey85") +
ggplot2::geom_sf(data = bt_year_df,
mapping = aes(fill = temperature),
color = NA) +
ggplot2::geom_sf(data = nbs_ebs_agg_strata,
fill = NA,
color = "black") +
ggplot2::geom_text(data = data.frame(x = -158.5,
y = 62.4,
lab = "Alaska") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(8)) +
ggplot2::coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = nbs_ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = nbs_ebs_layers$lat.breaks) +
ggplot2::scale_fill_manual(values = viridis_pal(option = nbs_ebs_viridis_option)(n_temp_breaks),
drop = FALSE) +
theme_bw() +
ggplot2::theme(axis.title = element_blank(),
axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
legend.key.width = unit(12, "mm"),
legend.position = "none",
legend.direction = "horizontal",
plot.margin = unit(c(5.5, 5.5,-25,5.5), units = "pt"))
ebs_nbs_map <- cowplot::plot_grid(ebs_nbs_temperature_map,
temp_map_cbar,
nrow = 2,
rel_heights = c(0.8,0.2))
ragg::agg_png(filename = here::here("plots", paste0(max_year, "_nbs_ebs_temperature_map.png")), width = 6, height = 6, units = "in", res = fig_res)
print(ebs_nbs_map)
dev.off()
nbs_ebs_bt_stack <- terra::rast(coldpool:::nbs_ebs_bottom_temperature)
ebs_bt_stack <- terra::rast(coldpool:::ebs_bottom_temperature)
template_rast <- nbs_ebs_bt_stack[[1]]
template_sbs <- nbs_ebs_layers$survey.area |>
dplyr::filter(SURVEY == "EBS_SHELF")
for(i in 1:length(year_vec_grid)) {
if(all(tail(year_vec_grid, 4) %in% year_vec_nbs)) {
sel_layer_df <- nbs_ebs_bt_stack[[i]]
} else if(any(tail(year_vec_grid, 4) %in% year_vec_nbs)) {
if(year_vec_grid[i] %in% names(nbs_ebs_bt_stack)) {
sel_layer_df <- nbs_ebs_bt_stack[[which(names(nbs_ebs_bt_stack) == year_vec_grid[i])]]
} else {
sel_layer_df <- ebs_bt_stack[[which(names(ebs_bt_stack) == year_vec_grid[i])]] |>
terra::resample(template_rast) |>
terra::mask(template_sbs, touches = FALSE)
}
sel_layer_df <- sel_layer_df |>
as.data.frame(na.rm = FALSE,
xy = TRUE) |>
tidyr::pivot_longer(cols = 3) |>
sf::st_as_sf(coords = c("x", "y"),
crs = coldpool:::ebs_proj_crs) |>
dplyr::rename(year = name,
temperature = value) |>
stars::st_rasterize()
sel_layer_df$temperature <- cut(sel_layer_df$temperature,
breaks = nbs_ebs_temp_breaks)
sel_layer_df <- sel_layer_df |>
sf::st_as_sf() |>
dplyr::group_by(temperature) |>
dplyr::summarise(n = n()) |>
dplyr::select(-n) |>
dplyr::ungroup() |>
sf::st_intersection(nbs_ebs_layers$survey.area)
}
sel_layer_df$year <- year_vec_grid[i]
if(i == 1) {
bt_year_df <- sel_layer_df
} else{
bt_year_df <- dplyr::bind_rows(bt_year_df, sel_layer_df)
}
}
nbs_ebs_st_stack <- terra::rast(coldpool:::nbs_ebs_surface_temperature)
ebs_st_stack <- terra::rast(coldpool:::ebs_surface_temperature)
template_rast <- nbs_ebs_st_stack[[1]]
template_sbs <- nbs_ebs_layers$survey.area |>
dplyr::filter(SURVEY == "EBS_SHELF")
for(i in 1:length(year_vec_grid)) {
if(all(tail(year_vec_grid, 4) %in% year_vec_nbs)) {
sel_layer_df <- nbs_ebs_st_stack[[i]]
} else if(any(tail(year_vec_grid, 4) %in% year_vec_nbs)) {
if(year_vec_grid[i] %in% names(nbs_ebs_st_stack)) {
sel_layer_df <- nbs_ebs_st_stack[[which(names(nbs_ebs_st_stack) == year_vec_grid[i])]]
} else {
sel_layer_df <- ebs_st_stack[[which(names(ebs_st_stack) == year_vec_grid[i])]] |>
terra::resample(template_rast) |>
terra::mask(template_sbs, touches = FALSE)
}
sel_layer_df <- sel_layer_df |>
as.data.frame(na.rm = FALSE,
xy = TRUE) |>
tidyr::pivot_longer(cols = 3) |>
sf::st_as_sf(coords = c("x", "y"),
crs = coldpool:::ebs_proj_crs) |>
dplyr::rename(year = name,
temperature = value) |>
stars::st_rasterize()
sel_layer_df$temperature <- cut(sel_layer_df$temperature,
breaks = nbs_ebs_temp_breaks)
sel_layer_df <- sel_layer_df |>
sf::st_as_sf() |>
dplyr::group_by(temperature) |>
dplyr::summarise(n = n()) |>
dplyr::select(-n) |>
dplyr::ungroup() |>
sf::st_intersection(nbs_ebs_layers$survey.area)
}
sel_layer_df$year <- year_vec_grid[i]
if(i == 1) {
sst_year_df <- sel_layer_df
} else{
sst_year_df <- dplyr::bind_rows(sst_year_df, sel_layer_df)
}
}
# Four panel bottom and surface temperature maps
# Union to combine strata 31, 32 into 30, etc.
nbs_ebs_agg_strata <- nbs_ebs_layers$survey.strata |>
dplyr::mutate(agg_stratum = Stratum) |>
dplyr::mutate(agg_stratum = replace(agg_stratum, agg_stratum %in% c(31, 32), 30),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(41, 42, 43), 40),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(61, 62), 60)) |>
dplyr::group_by(agg_stratum) |>
dplyr::summarise()
ebs_nbs_bt_temperature_map <- ggplot2::ggplot() +
ggplot2::geom_sf(data = nbs_ebs_layers$akland,
fill = "grey70",
color = "black") +
ggplot2::geom_sf(data = nbs_ebs_layers$survey.area,
fill = "grey85",
color = "black") +
ggplot2::geom_sf(data = bt_year_df,
mapping = aes(fill = temperature),
color = NA) +
ggplot2::geom_sf(data = nbs_ebs_layers$survey.area,
fill = NA,
color = "black") +
ggplot2::facet_wrap(~year, ncol = 2, nrow = 2) +
ggplot2::geom_sf(data = nbs_ebs_agg_strata,
fill = NA,
color = "black") +
ggplot2::geom_sf(data = nbs_ebs_layers$graticule,
alpha = 0.3) +
ggplot2::coord_sf(xlim = nbs_ebs_layers$plot.boundary$x,
ylim = nbs_ebs_layers$plot.boundary$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = nbs_ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = nbs_ebs_layers$lat.breaks) +
ggplot2::scale_fill_manual(values = viridis_pal(option = nbs_ebs_viridis_option)(length(nbs_ebs_temp_breaks)-1),
na.value = NA) +
coldpool::theme_multi_map_blue_strip() +
theme(legend.position = "none",
plot.margin = unit(c(5,5,-5,5), units = "mm"),
axis.title = element_blank(),
axis.text = element_text(size = 9))
ebs_nbs_bt_map_grid <- cowplot::plot_grid(ebs_nbs_bt_temperature_map,
temp_map_cbar,
nrow = 2,
rel_heights = c(0.85,0.15))
ragg::agg_png(filename = here::here("plots", paste0(max_year, "_nbs_ebs_temperature_map_grid.png")), width = 6, height = 6, units = "in", res = fig_res)
print(ebs_nbs_bt_map_grid)
dev.off()
ebs_nbs_sst_temperature_map <- ggplot2::ggplot() +
ggplot2::geom_sf(data = nbs_ebs_layers$akland,
fill = "grey70",
color = "black") +
ggplot2::geom_sf(data = nbs_ebs_layers$survey.area,
fill = "grey85",
color = "black") +
ggplot2::geom_sf(data = sst_year_df,
mapping = aes(fill = temperature),
color = NA) +
ggplot2::facet_wrap(~year, ncol = 2, nrow = 2) +
ggplot2::geom_sf(data = nbs_ebs_agg_strata,
fill = NA,
color = "black") +
ggplot2::geom_sf(data = nbs_ebs_layers$graticule,
alpha = 0.3) +
ggplot2::coord_sf(xlim = nbs_ebs_layers$plot.boundary$x,
ylim = nbs_ebs_layers$plot.boundary$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = nbs_ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = nbs_ebs_layers$lat.breaks) +
ggplot2::scale_fill_manual(values = viridis_pal(option = nbs_ebs_viridis_option)(length(nbs_ebs_temp_breaks)-1),
na.value = NA,
drop = FALSE) +
coldpool::theme_multi_map_blue_strip() +
theme(legend.position = "none",
plot.margin = unit(c(5,5,-5,5), units = "mm"),
axis.title = element_blank(),
axis.text = element_text(size = 9))
sst_map_cbar <- coldpool::legend_discrete_cbar(breaks = nbs_ebs_temp_breaks,
colors = viridis::viridis_pal(option = nbs_ebs_viridis_option),
legend_direction = "horizontal",
font_size = 3,
width = 0.1,
expand_size.x = 0.3,
expand_size.y = 0.3,
expand.x = 0.3,
expand.y = 0.9,
spacing_scaling = 1.2,
text.hjust = 0.5,
font.family = "sans",
neat.labels = FALSE) +
annotate("text",
x = 1.15,
y = 3.5,
label = expression(bold("Surface Temperature"~(degree*C))),
size = rel(3.2)) +
theme(plot.margin = unit(c(0,0, 0, 5), units = "mm"))
ebs_nbs_sst_map_grid <- cowplot::plot_grid(ebs_nbs_sst_temperature_map,
sst_map_cbar,
nrow = 2,
rel_heights = c(0.85,0.15))
ragg::agg_png(filename = here::here("plots", paste0(max_year, "_nbs_ebs_sst_map_grid.png")), width = 6, height = 6, units = "in", res = fig_res)
print(ebs_nbs_sst_map_grid)
dev.off()
```
```{r fig4_mean_temperature, message=FALSE, warning=FALSE, include=FALSE}
sebs_temperatures <- coldpool:::cold_pool_index |>
dplyr::filter(YEAR <= max_year) |>
dplyr::select(YEAR, MEAN_GEAR_TEMPERATURE, MEAN_SURFACE_TEMPERATURE) |>
dplyr::rename(Bottom = MEAN_GEAR_TEMPERATURE,
Surface = MEAN_SURFACE_TEMPERATURE) |>
dplyr::mutate(group = YEAR < 2020,
region = "Eastern Bering Sea (summer BT survey)") |>
reshape2::melt(id.vars = c("YEAR", "group", "region"))
nbs_temperatures <- coldpool:::nbs_mean_temperature |>
dplyr::filter(YEAR <= max_year) |>
dplyr::select(YEAR, MEAN_GEAR_TEMPERATURE, MEAN_SURFACE_TEMPERATURE) |>
dplyr::rename(Bottom = MEAN_GEAR_TEMPERATURE,
Surface = MEAN_SURFACE_TEMPERATURE) |>
dplyr::mutate(group = YEAR,
region = "Northern Bering Sea (summer BT survey)") |>
reshape2::melt(id.vars = c("YEAR", "group", "region"))
all_temperatures <- dplyr::bind_rows(sebs_temperatures,
nbs_temperatures)
sebs_sst_mean <- mean(sebs_temperatures$value[sebs_temperatures$variable == "Surface"])
sebs_bt_mean <- mean(sebs_temperatures$value[sebs_temperatures$variable == "Bottom"])
nbs_sst_mean <- mean(nbs_temperatures$value[nbs_temperatures$variable == "Surface"])
nbs_bt_mean <- mean(nbs_temperatures$value[nbs_temperatures$variable == "Bottom"])
color_sst <- "darkgreen"
color_bt <- "darkblue"
ebs_mean_temp_df <- data.frame(region = c(rep("Eastern Bering Sea (summer BT survey)", 2),
rep("Northern Bering Sea (summer BT survey)", 2)),
variable = rep(c("Bottom", "Surface"), 2),
value = c(sebs_bt_mean,
sebs_sst_mean,
nbs_bt_mean,
nbs_sst_mean))
plot_average_temperature <- ggplot(data = all_temperatures,
mapping = aes(x = YEAR,
y = value,
color = variable,
shape = variable,
group = paste0(group, variable))) +
geom_point(size = rel(2)) +
geom_line() +
geom_hline(data = ebs_mean_temp_df,
aes(yintercept = value,
color = variable),
linetype = 2) +
scale_color_manual(values = c(color_bt, color_sst),
drop = FALSE) +
scale_y_continuous(name = expression(bold("Average Temperature"~(degree*C))),
limits = c(0,11.2),
breaks = seq(0,12,2),
expand = c(0,0)) +
scale_x_continuous(name = "Year",
breaks = seq(1980,2020,10)) +
facet_wrap(~region, scales = "free") +
theme_bw() +
theme(axis.title = element_text(color = "black", face = "bold"),
axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
panel.grid = element_blank(),
legend.title = element_blank(),
legend.position = "bottom",
legend.key = element_rect(color = NA),
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA))
plot_sebs_average_temperature <- ggplot(data = all_temperatures |>
dplyr::filter(region == "Eastern Bering Sea (summer BT survey)"),
mapping = aes(x = YEAR,
y = value,
color = variable,
shape = variable,
group = paste0(group, variable))) +
geom_point(size = rel(2)) +
geom_line() +
geom_hline(data = ebs_mean_temp_df |>
dplyr::filter(region == "Eastern Bering Sea (summer BT survey)"),
aes(yintercept = value,
color = variable),
linetype = 2) +
scale_color_manual(values = c(color_bt, color_sst),
drop = FALSE) +
scale_y_continuous(name = expression(bold("Average Temperature"~(degree*C))),
limits = c(0,11.2),
breaks = seq(0,12,2),
expand = c(0,0)) +
scale_x_continuous(name = "Year",
breaks = seq(1980,2020,10)) +
facet_wrap(~region, scales = "free") +
theme_bw() +
theme(axis.title = element_text(color = "black", face = "bold"),
axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
panel.grid = element_blank(),
legend.title = element_blank(),
legend.key = element_rect(color = NA),
legend.position = "bottom",
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA))
ragg::agg_png(file = here::here("plots", paste0(max_year, "_average_temperature.png")), width = 6, height = 3, units = "in", res = fig_res)
print(plot_average_temperature)
dev.off()
ragg::agg_png(file = here::here("plots", paste0(max_year, "_plot_sebs_average_temperature.png")), width = 6, height = 3, units = "in", res = fig_res)
print(plot_sebs_average_temperature)
dev.off()
```
```{r zscore_temperature, message=FALSE, warning=FALSE, include=FALSE}
cp_summary <- dplyr::bind_rows(
dplyr::mutate(cold_pool_index,
diff = MEAN_GEAR_TEMPERATURE - mean(MEAN_GEAR_TEMPERATURE)) |>
dplyr::mutate(sign = sign(diff),
z = diff/sd(MEAN_GEAR_TEMPERATURE)) |>
dplyr::inner_join(data.frame(sign = c(-1,1),
symbol = c("-","+"),
col = c(1,2))) |>
dplyr::select(YEAR, diff, symbol, z, col) |>
dplyr::mutate(var = "Bottom temperature"),
dplyr::mutate(cold_pool_index,
diff = MEAN_SURFACE_TEMPERATURE - mean(MEAN_SURFACE_TEMPERATURE)) |>
dplyr::mutate(sign = sign(diff),
z = diff/sd(MEAN_SURFACE_TEMPERATURE)) |>
dplyr::inner_join(data.frame(sign = c(-1,1),
symbol = c("-","+"),
col = c(1,2))) |>
dplyr::select(YEAR, diff, symbol, z, col) |>
dplyr::mutate(var = "Sea surface temperature"),
dplyr::mutate(cold_pool_index,
diff = AREA_LTE2_KM2 - mean(AREA_LTE2_KM2)) |>
dplyr::mutate(sign = sign(diff),
z = diff/sd(AREA_LTE2_KM2)) |>
dplyr::inner_join(data.frame(sign = c(-1,1),
symbol = c("-","+"),
col = c(2,1))) |>
dplyr::select(YEAR, diff, symbol, z, col) |>
dplyr::mutate(var = "Cold pool area")) |>
dplyr::mutate(group = YEAR < 2020,
var = factor(var,
levels = c("Bottom temperature",
"Sea surface temperature",
"Cold pool area")))
zscore_plot <- ggplot(data = cp_summary,
aes(x = YEAR,
y = z,
group = group)) +
geom_hline(yintercept = c(0), linetype = 1) +
geom_hline(yintercept = c(-1,1), linetype = 2) +
geom_hline(yintercept = c(-2,2), linetype = 3) +
geom_point() +
geom_line() +
geom_text(data = cp_summary,
aes(x = YEAR, y = 2.5, label = symbol, color = factor(col))) +
facet_wrap(~var, nrow = 3) +
scale_x_continuous(name = "Year") +
scale_y_continuous(name = "Anomaly") +
scale_color_manual(values = c("blue", "red")) +
theme_bw() +
theme(axis.text = element_text(color = "black"),
axis.ticks = element_line(color = "black"),
panel.border = element_rect(color = "black", fill = NA),
panel.background = element_rect(color = "black", fill = NA),
strip.text = element_text(size = 9,
color = "white",
face = "bold",
margin = margin(0.5, 0, 0.5, 0, "mm")),
strip.background = element_rect(fill = "#0055a4",
color = NA),
legend.position = "none")
ragg::agg_png(file = here::here("plots", paste0(max_year, "_anomaly.png")), width = 6, height = 6, units = "in", res = fig_res)
print(zscore_plot)
dev.off()
```
```{r maps_by_year, message=FALSE, warning=FALSE, include=FALSE}
year_vec <- c(1982:2019, 2021:2024)
nbs_years <- c(2010, 2017, 2019, 2021:2023)
temp_breaks <- c(-Inf, seq(-1,8,1), Inf)
color_pal <- "H"
fig_res <- 300
dir.create(here::here("plots", "annual_bt"))
sebs_layers <- akgfmaps::get_base_layers(select.region = "sebs",
set.crs = coldpool:::ebs_proj_crs)
nbs_layers <- akgfmaps::get_base_layers(select.region = "ebs",
set.crs = coldpool:::ebs_proj_crs, use.survey.bathymetry = TRUE)
bt_raster_sebs <- terra::rast(coldpool::ebs_bottom_temperature)
bt_raster_nbs <- terra::rast(coldpool::nbs_ebs_bottom_temperature)
bt_raster_2018 <- terra::mask(bt_raster_nbs[[names(bt_raster_nbs) == 2018]],
dplyr::filter(nbs_layers$survey.grid,
STATIONID %in% c("V-01", "U-01", "T-01", "S-01", "R-01",
"V-02", "U-02", "T-02", "S-02", "R-02",
"DD-03", "ZZ-03", "Y-03", "X-03", "W-03", "V-03", "U-03", "T-03", "S-03", "R-03",
"DD-04", "CC-04", "BB-04", "AA-04", "ZZ-04", "Y-04", "X-04", "W-04", "V-04", "U-04", "T-04", "S-04", "R-04",
"DD-05", "CC-05", "BB-05", "AA-05", "ZZ-05", "Y-05", "X-05", "W-05", "V-05", "U-05", "T-05", "S-05", "R-05",
"DD-06", "CC-06", "BB-06", "AA-06", "ZZ-06", "Y-06", "X-06", "W-06", "V-06", "U-06", "T-06", "S-06", "R-06",
"DD-07", "CC-07", "BB-07", "AA-07", "ZZ-07", "Y-07", "X-07", "W-07", "V-07", "U-07", "T-07", "S-07", "R-07",
"DD-08", "CC-08", "BB-08", "AA-08", "ZZ-08", "Y-08", "X-08", "W-08", "V-08", "U-08", "T-08", "S-08", "R-08",
"DD-09", "CC-09", "BB-09", "AA-09", "ZZ-09", "Y-09", "X-09", "W-09", "V-09", "U-09", "T-09", "S-09", "R-09",
"DD-10", "CC-10", "BB-10", "AA-10", "ZZ-10", "Y-10", "X-10", "W-10", "V-10", "U-10", "T-10", "S-10", "R-10")),
inverse = TRUE,
touches = TRUE)
for(ii in 1:length(year_vec)) {
if(year_vec[ii] == 2018) {
sel_raster <- bt_raster_2018
mask_layer <- nbs_layers$survey.area
} else {
if(year_vec[ii] %in% nbs_years) {
sel_raster <- bt_raster_nbs
mask_layer <- nbs_layers$survey.area
} else {
sel_raster <- bt_raster_sebs
mask_layer <- sebs_layers$survey.area
}
}
bt_df <- as.data.frame(sel_raster[[names(sel_raster) == year_vec[ii]]],
xy = TRUE,
na.rm = FALSE) |>
tidyr::pivot_longer(cols = 3) |>
sf::st_as_sf(coords = c("x", "y"),
crs = coldpool:::ebs_proj_crs) |>
dplyr::rename(year = name,
temperature = value) |>
stars::st_rasterize()
bt_df$temperature <- cut(bt_df$temperature,
breaks = temp_breaks)
bt_df <- bt_df |>
sf::st_as_sf() |>
dplyr::group_by(temperature) |>
dplyr::summarise(n = n()) |>
dplyr::select(-n) |>
dplyr::ungroup() |>
sf::st_intersection(mask_layer)
bt_df$year <- year_vec[ii]
if(ii == 1) {
bt_year_df <- bt_df
} else {
bt_year_df <- dplyr::bind_rows(bt_year_df, bt_df)
}
}
temp_map_cbar <- coldpool::legend_discrete_cbar(breaks = temp_breaks,
colors = viridis::viridis_pal(option = color_pal)(length(temp_breaks)-1),
legend_direction = "horizontal",
font_size = 3,
width = 0.1,
expand_size.x = 0.3,
expand_size.y = 0.3,
expand.x = 0.3,
expand.y = 0.9,
spacing_scaling = 1,
text.hjust = 0.5,
font.family = "sans",
neat.labels = FALSE) +
annotate("text",
x = 1.15,
y = 3.5,
label = expression(bold("Bottom Temperature"~(degree*C))),
size = rel(3.2)) +
theme(plot.margin = unit(c(0,0, 0, 5), units = "mm"))
for(ii in 1:length(year_vec)) {