Marine Heat Waves anomaly profiles
Marguerite Larriere & Jens Daniel Müller
13 June, 2024
Last updated: 2024-06-13
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bgc_argo_r_argodata/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 58f8e75 | mlarriere | 2024-06-13 | fixing plot size |
| html | 138cf75 | mlarriere | 2024-06-13 | Build site. |
| Rmd | 2d95d1c | mlarriere | 2024-06-13 | cleaning and documenting code |
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| Rmd | c95c0bd | mlarriere | 2024-06-13 | cleaning and documenting code |
| html | 2722ba9 | mlarriere | 2024-06-06 | Build site. |
| Rmd | 38021de | mlarriere | 2024-06-06 | cleaning code |
| html | cc29085 | mlarriere | 2024-06-06 | Build site. |
| Rmd | f35ae7a | mlarriere | 2024-06-06 | cleaning code |
| html | 2d63792 | mlarriere | 2024-05-24 | Build site. |
| Rmd | a4c7c05 | mlarriere | 2024-05-24 | Absolute maximum anomalies categorisation |
| Rmd | cebda03 | mlarriere | 2024-05-22 | Hovmoeller plot |
| html | 3ac87c9 | mlarriere | 2024-05-20 | Build site. |
| Rmd | 5304024 | mlarriere | 2024-05-20 | choosing extent |
| html | b0fb164 | mlarriere | 2024-05-16 | Build site. |
| Rmd | fbf0c64 | mlarriere | 2024-05-16 | latitude, longitude and day of the month graphs |
| html | 22e0206 | mlarriere | 2024-05-16 | Build site. |
| Rmd | d0f58b6 | mlarriere | 2024-05-16 | latitude, longitude and day of the month graphs |
| html | 96d4b76 | mlarriere | 2024-05-14 | Build site. |
| Rmd | 91e6028 | mlarriere | 2024-05-13 | adding subsection CESM comparison |
| html | af6594f | mlarriere | 2024-05-13 | Build site. |
| Rmd | 30f9250 | mlarriere | 2024-05-13 | Adding CESM subsection |
Task
Only core Argo - focus on temperature anomalies in 2023 in the eastern North Atlantic
Dependencies
temp_core_va.rds - temperature of core argo floats after vertical alignment for a given year.
core_metadata.rds - file with metadata concerning the floats such as platform number, cycle number, date, lat, lon and quality control results.
temp_anomaly_va.rds - file containing the temperature anomalies (temp core - climatology).
SST_anomaly2023_NorthAtlantic_clim2004-2019.rds - file containing SST anomalies for 2023 in the North Atlantic, for each lat, lon, month on a 1°x1° grid. Data from the HadISST dataset with same climatology than Argo, i.e. 2004-2019.
mld_2023_eastern_NorthAtlantic.rds - file containing MLD data for 2023 in the eastern North Atlantic, on a monthly basis on a 1°x1° grid. Data from the MIMOC-deBoyer dataset.
#Paths
path_emlr_utilities <- "/nfs/kryo/work/jenmueller/emlr_cant/utilities/files/"
path_basin_mask <- "/nfs/kryo/work/datasets/gridded/ocean/interior/reccap2/supplementary/"
path_argo <- '/nfs/kryo/work/datasets/ungridded/3d/ocean/floats/bgc_argo'
path_argo_core <- '/nfs/kryo/work/datasets/ungridded/3d/ocean/floats/core_argo_r_argodata_2024-03-13'
path_argo_core_preprocessed <- paste0(path_argo_core, "/preprocessed_core_data")
path_mhw<- '/net/kryo/work/datasets/gridded/ocean/2d/obs/mhw'#Area of interest: North Atlantic north west - lat:(60,30), lon:(-70,-30), North Atlantic east - lat:(0,40), lon:(-30,0)
chosen_extent <- list(
lat_min = 0, #30
lat_max = 40, #60
lon_min = -30, #-70
lon_max = 0 #-30
)
name_extent<- "East" #Northwest
#base map for the plots
world_coordinates <- map_data("world")
#year of interest
target_year<-2023Load data
Load biomes
#---------------- Biomes ----------------
#Load biome separations
region_masks_all <-
stars::read_ncdf(paste(
path_basin_mask, "RECCAP2_region_masks_all_v20221025.nc", sep = "")) %>%
as_tibble() %>%
mutate(seamask = as.factor(seamask))
region_masks_all <- region_masks_all %>%
mutate(lon = ifelse(lon > 180, lon - 360, lon)) %>% #shift longitude to be in range (-180°, 180°) for better vizualisation
pivot_longer(open_ocean:atlantic,
names_to = 'region',
values_to = 'value') %>%
mutate(value = as.factor(value))
#Biomes North Atlantic
region_masks_atlantic <- region_masks_all %>%
filter(region == 'atlantic',
value != 0) %>%
mutate(coast = as.character(coast))
biomes_atlantic <- region_masks_atlantic %>%
filter(value %in% c(1,2,3))
biomes_subset <- biomes_atlantic %>%
select(lat, lon, biome_value = value)
biomes_names<-c("SPSS", "STSS", "STPS")
#Plot
ggplot()+
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") + #base map
lims(x= c(-100, 50), y = c(0, 80))+ #North Atlantic
coord_quickmap(expand = 0) +
geom_tile(data = biomes_atlantic, aes(x = lon, y = lat, fill = value))+
scale_fill_manual(values = c("1" = "cadetblue", "2" = "azure", "3" = "lightskyblue3"),
labels = biomes_names) +
labs(title = 'Biomes - North Atlantic basin',
subtitle = 'RECCAP data',
x = "longitude", y = "latitude", fill = "Biomes") +
theme(plot.title = element_text(size = 16),
plot.subtitle = element_text(size = 12),
legend.text = element_text(size = 10),
legend.title = element_text(size = 12, face = "bold"),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm"))
| Version | Author | Date |
|---|---|---|
| cc29085 | mlarriere | 2024-06-06 |
Load Argo floats data
Load SST anomaly
#Read SST anomaly, computed using climatology:2009-2019 (from anomaly_SST_2023.Rmd)
sst_anomaly_northAtlantic<- read_rds(paste(path_argo_core_preprocessed, "/SST_anomaly2023_NorthAtlantic_clim2004-2019.rds", sep = ""))Argo floats
Distribution over North Atlantic basin
#Histogram -- number of floats per month and biome
unique_platforms_per_month <- core_anomaly_with_platform_2023 %>%
group_by(month) %>%
filter(lat>0, lat<70, lon>-80, lon<0) %>%
summarize(unique_platforms = n_distinct(platform_number))
ggplot(unique_platforms_per_month, aes(x = factor(month), y = unique_platforms)) +
geom_bar(stat = "identity", fill = "lightskyblue3",color = "black", size = 0.25) +
labs(title = "Amount of platform per month, in North Atlantic, 2023",
x = "Months", y = "Number of argo floats", fill = "Biomes") +
theme_minimal() +
guides(fill = FALSE)
| Version | Author | Date |
|---|---|---|
| 5601558 | mlarriere | 2024-06-13 |
# scale_fill_manual(values = c("1" = "#1034A6", "2" = "#f59c04", "3" = "darkred"), labels = c("1" = "SPSS", "2" = "STSS", "3" = "STPS")) +
#Number of cycle per platform
cycle_counts <- core_anomaly_with_platform_2023 %>%
group_by(platform_number) %>%
summarise(cycle_count = n_distinct(cycle_number))#Join the SST anomaly with the core Argo anomaly profiles
core_anomaly_with_platform_2023<-core_anomaly_with_platform_2023 %>%
filter(!is.na(depth)) %>%
select(-profile_range)
complete_anomaly_profile<- core_anomaly_with_platform_2023 %>%
inner_join(sst_anomaly_northAtlantic, by = c("lat", "lon", "month"))
#---Chosen subset
core_anomaly_2023_natlantic_subset<- complete_anomaly_profile %>%
filter(lat > chosen_extent$lat_min, lat < chosen_extent$lat_max,
lon > chosen_extent$lon_min, lon < chosen_extent$lon_max) %>%
select(-interpolated_temp) #Number of platform present in each lat/lon location per month
float_monthly_count <- core_anomaly_with_platform_2023 %>%
group_by(lon, lat) %>%
summarise(months_present = n_distinct(month)) %>%
ungroup()
#Mean SST anomaly over 2023
HadISST_anomaly_mean2023 <- sst_anomaly_northAtlantic %>%
group_by(lon, lat) %>%
summarise(yearly_SSTanomaly= mean(SST_anomaly, na.rm = TRUE)) %>%
ungroup()
#Plots
SST_2023_plot <- ggplot()+
geom_raster(data=HadISST_anomaly_mean2023, aes(lon, lat, fill = yearly_SSTanomaly)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
scale_fill_viridis_c(option = "magma", limits = c(0, 1.5)) +
labs(title = "SST anomaly, annual average 2023",
subtitle = "Resolution: 1°x1°",
x='Longitude', y='Latitude',
fill = "SST \nanomalies [°C]")+
coord_quickmap(expand = 0)+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(2, "cm")
)
float_distrib <- ggplot() +
geom_point(data = float_monthly_count, aes(x = lon, y = lat, color = months_present)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
labs(title = "Platform Locations",
subtitle = "Resolution: 1°x1°",
x='Longitude', y='Latitude',
color = "Months \nwith float") +
scale_color_scico(palette = "oslo", breaks = seq(1, 12, by = 1), limits = c(1, 12), direction=-1) +
coord_quickmap(expand = 0) +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(2, "cm")
)
#combining the SST anomalies plot and Float distrib
combined_plot <- SST_2023_plot + float_distrib + plot_layout(ncol = 2)
combined_plot
Distribution over East-North Atlantic
Using the SST map computed in “anomaly_SST_2023.Rmd” and ClimateReanalyser, we identify one area of particular interest for SST anomalies in 2023 in the North Atlantic Ocean: The East coast of the North Atlantic Ocean, where the SST anomalies are high on an annual basis, with a sharp increase from June onwards.
#Number of platform present per month in the chosen area
platform_counts <- aggregate(platform_number ~ month, data = core_anomaly_2023_natlantic_subset, FUN = function(x) length(unique(x)))
#Number of cycle present per month and per platform in the chosen area
cycle_count_per_platform_month <- core_anomaly_2023_natlantic_subset %>%
group_by(month, platform_number) %>%
summarise(cycle_count = n_distinct(cycle_number))
#---Plot the platform present in the region of interest for each month
custom_labeller <- function(variable, value) {
month_count <- platform_counts[platform_counts$month == value, "platform_number"]
return(paste("Month:", value, "\nNumber of floats:", month_count))
}
sst_anomaly_northAtlantic_subset<-sst_anomaly_northAtlantic %>%
filter(lat > chosen_extent$lat_min, lat < chosen_extent$lat_max,
lon > chosen_extent$lon_min, lon < chosen_extent$lon_max)
ggplot() +
geom_tile(data=sst_anomaly_northAtlantic_subset, aes(x = lon, y = lat, fill = SST_anomaly)) + #tile with SST
geom_point(data = core_anomaly_2023_natlantic_subset, aes(x = lon, y = lat), color = "lightblue") + # Point for float position
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") + #base map
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
coord_quickmap(expand = 0) +
scale_fill_viridis_c(option = "plasma") +
labs(title = "Platform Locations",
subtitle = "Resolution: 1°x1°, SST from SOM",
color = "Months with float") +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(2, "cm")
)+
facet_wrap(~month, ncol = 3, labeller = custom_labeller)
Anomaly profiles
Individual float
Inspection of single floats to understand the physical processes impacting the argo floats measurements - Float chosen is located in the Eddies Corridor (Canary Islands)
#Choosing 1 float
unique_platform<-core_anomaly_2023_natlantic_subset %>%
filter(platform_number==1902323) #in the eddies corridor
ggplot() +
geom_path(data=unique_platform, aes(x = anomaly, y = depth, color = factor(month), group = cycle_number)) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-6, 6), ylim = c(200, 0)) +
scale_color_manual(values = colorRampPalette(c("#2796A5", "#F3712B", "#880D1E"))(12)) +
labs(title = 'SST anomalies propagation \nof a single float',
subtitle = 'Location: Canaries Islands (Eddies corridor)',
x = 'Temperature (°C)', y = 'Depth (m)', color = 'Months') +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold")
)
Coloring by lat/lon
Inspection of the potential spatial gradient that may influence the SST anomalies penetration: longitude and latitude gradients.
#Calculating monthly mean anomaly for each lat/lon pair of the area
anomaly_lat_lon <- core_anomaly_2023_natlantic_subset %>%
group_by(lat, lon, depth, month, platform_number, cycle_number) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
# Longitude - gradient west-east
longitude<- ggplot(anomaly_lat_lon, aes(x = temp_anomaly_mean, y = depth,
group = interaction(platform_number, cycle_number),
color = as.numeric(lon))) +
geom_path() +
geom_vline(xintercept = 0) +
scale_y_reverse(limits = c(200, 0)) +
coord_cartesian(xlim = c(-6, 6)) +
facet_wrap(~ month, ncol = 3) +
labs( x = 'Temperature anomaly [°C]', y = 'Depth [m]', color = "Longitude") +
scale_color_viridis_c()+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 14),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(1, "cm"))
# Latitude - gradient north-south
latitude<- ggplot(anomaly_lat_lon, aes(x = temp_anomaly_mean, y = depth,
group = interaction(platform_number, cycle_number),
color = as.numeric(lat))) +
geom_path() +
geom_vline(xintercept = 0) +
scale_y_reverse(limits = c(200, 0)) +
coord_cartesian(xlim = c(-6, 6)) +
facet_wrap(~ month, ncol = 3) +
labs( x = 'Temperature anomaly [°C]', y = 'Depth [m]', color = "Latitude") +
scale_color_viridis_c()+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 14),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(1, "cm"))
combined_plot <- latitude + longitude + plot_layout(ncol = 1)+
plot_annotation(title = 'Latitude and longitude gradients',
subtitle = "All floats and cycles included",
theme = theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16))
)
combined_plot
Coloring by SST anomaly
Looking at the SST anomalies that may influence the vertical structure of the MHS penetration
#Calculating monthly mean anomaly as function of SST anomaly for each Argo cycle
anomaly_summary <- core_anomaly_2023_natlantic_subset %>%
group_by(platform_number, depth, month, cycle_number, SST_anomaly) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
#plot
ggplot(anomaly_summary, aes(x = temp_anomaly_mean, y = depth, group = interaction(platform_number, cycle_number), color = as.numeric(SST_anomaly))) +
geom_path() +
geom_vline(xintercept = 0) +
scale_y_reverse(limits = c(200, 0)) +
coord_cartesian(xlim = c(-6, 6)) +
facet_wrap(~ month, ncol = 3) +
labs(title = "Mean Anomaly Profile as a function of SST anomaly",
x = "Temperature (°C)", y = "Depth (m)", color = "SST Anomaly") +
scale_color_viridis_c()+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 14),
legend.text = element_text(size = 12),
strip.text = element_text(size = 14),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(1, "cm"))
Coloring by day within a month
#Calculating monthly mean anomaly as function of day within the month for each Argo cycle
anomaly_summary_day <- core_anomaly_2023_natlantic_subset %>%
group_by(platform_number, depth, month, cycle_number, day) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
#plot for time during month
ggplot(anomaly_summary_day, aes(x = temp_anomaly_mean, y = depth, group = interaction(platform_number, cycle_number), color = as.numeric(day))) +
geom_path() +
geom_vline(xintercept = 0) +
scale_y_reverse(limits = c(200, 0)) +
coord_cartesian(xlim = c(-6, 6)) +
facet_wrap(~ month, ncol = 3) +
labs(title = "Mean Anomaly Profile as function of time",
x = "Temperature (°C)", y = "Depth (m)", color = "day within \nthe month") +
scale_color_viridis_c()+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 14),
legend.text = element_text(size = 12),
strip.text = element_text(size = 14),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.3, "cm"),
legend.key.height = unit(1, "cm"))
Monthly anomaly profiles
# Dataset with the cycle number per float across months
cycles_per_platform_month<- core_anomaly_2023_natlantic_subset %>%
group_by(platform_number, month) %>%
summarize(unique_cycles = toString(unique(cycle_number)))
# Calculating monthly mean anomaly + std dev over the east area by averaging the anomaly of each float present
anomaly_mean <- core_anomaly_2023_natlantic_subset %>%
group_by(depth, month) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE),
temp_anomaly_sd = sd(anomaly, na.rm = TRUE))
#For each month: the SST anomaly and vertical anomaly profile plots next to each other
for (m in unique(core_anomaly_2023_natlantic_subset$month)) {
# Filter data
map_data <- filter(sst_anomaly_northAtlantic_subset, month == m)
anomaly_data <- filter(anomaly_mean, month == m)
# Plot for temperature anomaly map from HadISST dataset
map_plot <- ggplot() +
geom_tile(data=map_data, aes(x = lon, y = lat, fill = SST_anomaly)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") + #base map
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
coord_quickmap(expand = 0) +
scale_fill_viridis_c(option = "plasma") +
labs(title = paste("SST Anomaly (°C) in North Atlantic - 2023", month.name[as.numeric(m)]),
subtitle = paste0("Extent: ", name_extent),
x = "Longitude", y = "Latitude") +
theme(legend.position = 'right', legend.key.height = unit(2, "cm"),
plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.text = element_text(size = 13),
legend.title = element_text(size = 15, face = "bold")
)
# Plot for anomaly profiles
anomaly_plot <- ggplot(anomaly_data, aes(x = temp_anomaly_mean, y = depth, color = factor(month))) +
geom_path() +
geom_ribbon(aes(xmax = temp_anomaly_mean + temp_anomaly_sd,
xmin = temp_anomaly_mean - temp_anomaly_sd,
y = depth), alpha = 0.2) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-4, 4), ylim = c(200, 0)) +
labs(title = paste('Associated anomaly profile in', month.name[as.numeric(m)]),
subtitle = paste0("from surface to 200m", "\nNumber of platform:", nrow(filter(cycles_per_platform_month, month==m))),
x = 'Temperature (°C)', y = 'Depth (m)') +
theme_minimal()+
guides(color = FALSE)+
theme(legend.position = 'right', legend.key.height = unit(2, "cm"),
plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.text = element_text(size = 13),
legend.title = element_text(size = 15, face = "bold")
)
#plots side by side
combined_plot <- grid.arrange(map_plot, anomaly_plot, ncol = 2)
print(combined_plot)
}
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2 2 (1-1,2-2) arrange gtable[layout]# Monthly vertical anomaly profile for the North Atlantic subset region
ggplot(anomaly_mean, aes(x = temp_anomaly_mean, y = depth, color = factor(month))) +
geom_path() +
geom_ribbon(aes(xmax = temp_anomaly_mean + temp_anomaly_sd,
xmin = temp_anomaly_mean - temp_anomaly_sd,
y = depth), alpha = 0.2) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-4, 4), ylim = c(200, 0)) +
labs(title = paste('Monthly temperature anomaly profile'),
subtitle = paste0("Extent: eastern North Atlantic in 2023"),
x = 'Temperature anomaly [°C]', y = 'Depth [m]') +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 14),
legend.text = element_text(size = 12),
strip.text = element_text(size = 14),
legend.title = element_text(size = 14, face = "bold"))+
guides(color = FALSE)+
facet_wrap(~month)
#-- Averaging the mean anomaly profiles on a 2 months period
# Creating 2 months period
anomaly_2months <- core_anomaly_2023_natlantic_subset %>%
mutate(period=(as.numeric(month)+1)%/%2)
# Calculating mean anomaly + std dev over the eastern North Atlantic by averaging on a 2month basis
anomaly_2months<-anomaly_2months %>%
group_by(depth, period) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE),
temp_anomaly_sd = sd(anomaly, na.rm = TRUE))
#Std dev, i.e. of the entire year 2023 in the eastern North Atlantic
anomaly_2023<-core_anomaly_2023_natlantic_subset %>%
group_by(depth) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE),
temp_anomaly_sd = sd(anomaly, na.rm = TRUE))
# Monthly vertical anomaly profile in the eastern North Atlantic in 2023
ggplot() +
geom_path(data=anomaly_2months, aes(x = temp_anomaly_mean, y = depth, color = factor(period))) +
geom_ribbon(data=anomaly_2023,
aes(xmax = temp_anomaly_mean + temp_anomaly_sd,
xmin = temp_anomaly_mean - temp_anomaly_sd,
y = depth, fill = "spread"), alpha = 0.2) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-4, 4), ylim = c(200, 0)) +
labs(title = paste('Propagation of SST anomalies in the water column'),
subtitle = paste0("Extent: ", name_extent, " North Atlantic bassin in ", target_year),
x = 'Temperature (°C)', y = 'Depth (m)') +
scale_color_manual(values = colorRampPalette(c("blue", "orange", "darkred"))(6), # 2month mean anomalies color
breaks = unique(anomaly_2months$period),
labels =c("Jan-Feb", "March-April", "May-June", "July-Aug", "Sept-Oct", "Nov-Dec")) +
scale_fill_manual(values = "grey", # Spread color
labels = "yearly") +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 12),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12)) +
guides(color = guide_legend(title="Period"), fill = guide_legend(title = "Spread")) 
Hovmoeller plot
Analysis of the temporal progression of the MHW penetration using a hovmoeller plot
#---WEEKLY
#adding to the dataset the week of the year
core_anomaly_2023_natlantic_subset <- core_anomaly_2023_natlantic_subset %>%
mutate(week = week(date))
# Calculating weekly mean anomaly over the eastern North Atlantic in 2023
anomaly_weekly<-core_anomaly_2023_natlantic_subset %>%
group_by(depth, week) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
#---2WEEKS
# Calculating 2weekly mean anomaly over the eastern North Atlantic in 2023
anomaly_2weekly <- core_anomaly_2023_natlantic_subset %>%
mutate(week2=(week+1)%/%2) %>% #period of 2weeks
group_by(depth, week2) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
#---MONTHLY
# Calculating monthly mean anomaly over the eastern North Atlantic in 2023
anomaly_monthly <- core_anomaly_2023_natlantic_subset %>%
group_by(depth, month) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
#--- VISUALISATION -- scatterplot of the difference between 2weekly and daily temp anomaly
# difference anomaly weekly-biweekly
anomaly_2weekly_withdate <- core_anomaly_2023_natlantic_subset %>%
mutate(week2 = (week(date) + 1) %/% 2) %>%
group_by(week2, depth) %>%
summarise(temp_count = n(),
temp_anomaly_mean = mean(anomaly, na.rm = TRUE),
start_date = min(date),
end_date = max(date)) %>%
mutate(mid_date = as.integer((yday(start_date) + yday(end_date)) / 2))
# Calculate min and max temperature anomaly for each dataset
daily_max <- max(core_anomaly_2023_natlantic_subset$anomaly, na.rm = TRUE)
daily_min <- min(core_anomaly_2023_natlantic_subset$anomaly, na.rm = TRUE)
biweekly_max <- max(anomaly_2weekly_withdate$temp_anomaly_mean, na.rm = TRUE)
biweekly_min <- min(anomaly_2weekly_withdate$temp_anomaly_mean, na.rm = TRUE)
# Custom labels for the legend
custom_labels <- c(
'Daily' = paste0('Daily (Max: ', round(max(core_anomaly_2023_natlantic_subset$anomaly, na.rm = TRUE), 2),
', Min: ', round(min(core_anomaly_2023_natlantic_subset$anomaly, na.rm = TRUE), 2), ')'),
'Bi-weekly' = paste0('Bi-weekly (Max: ', round(max(anomaly_2weekly_withdate$temp_anomaly_mean, na.rm = TRUE), 2),
', Min: ', round(min(anomaly_2weekly_withdate$temp_anomaly_mean, na.rm = TRUE), 2), ')')
)
# Scatter plot
ggplot() +
geom_point(data = core_anomaly_2023_natlantic_subset,
aes(x = day_of_year, y = anomaly, color = 'Daily'),
alpha = 0.5) +
geom_point(data = anomaly_2weekly_withdate,
aes(x = mid_date, y = temp_anomaly_mean, color = 'Bi-weekly'),
size = 3) +
scale_color_manual(name = "Time Period", values = c('Daily' = '#A256B3', 'Bi-weekly' = 'red'), labels = custom_labels) +
labs(title = 'Comparison of Temperature Anomalies on Daily and Bi-weekly Basis',
subtitle = paste0('Extent: ', name_extent, ', year: ', target_year),
x = 'Day of Year', y = 'Temperature Anomaly (°C)') +
theme_minimal() +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold"),
legend.position = 'bottom',
legend.direction = "horizontal",
legend.box = "horizontal")
| Version | Author | Date |
|---|---|---|
| 5601558 | mlarriere | 2024-06-13 |
#---Hovmoeller plot
ggplot(data=anomaly_2weekly, aes(x = week2, y = depth, z = temp_anomaly_mean)) +
geom_contour_filled(aes(fill = after_stat(level_mid))) +
scale_fill_gradient2(name='T°C anomaly', low = "darkblue", high = "darkred", #low = "#CED3DC", high = "#906490"
breaks=seq(-0.5, 1.5, by=0.5), labels=as.character(seq(-0.5, 1.5, by=0.5)), limits = c(-0.5, 1.5)) +
coord_cartesian(ylim = c(200, 0), expand = 0) +
labs(title = "Temporal progression of SST anomalies penetration in 2023",
subtitle = paste0("Extent: ", name_extent, ", temporal resolution: 2 weeks"),
x = "Week of Year", y = "Depth (m)") +
theme_minimal() +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(3, "cm")
)
Mixed Layer Depth (MLD)
Load MLD from MIMOC-deBoyer dataset
#Read MLD (created in anomaly_SST_2023.Rmd)
mld_eastern_northAtlantic<- read_rds(paste0(path_argo_core_preprocessed,"/", "mld_",
target_year,"_eastern_NorthAtlantic.rds"))Adding MLD to the Argo observations
#clean dataset
mld_eastern_northAtlantic <-mld_eastern_northAtlantic %>%
select(-date, -time)
#Join the MLD values with the core Argo anomaly profiles
core_anomaly_with_mld_2023<- core_anomaly_with_platform_2023 %>%
inner_join(mld_eastern_northAtlantic, by = c("lat", "lon", "month", "year"))
#Plot the Argo position on a monthly basis with MLD coloring
ggplot()+
geom_tile(data=core_anomaly_with_mld_2023, aes(lon, lat, fill = mld)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") + #base map
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) + #eastern North Atlantic
scale_fill_viridis_c(option = "magma") +
labs(title = "Mixed Layer Depth",
subtitle= "Monthly average - 2023",
fill = "Mixed Layer Depth [m]")+
coord_quickmap(expand = 0)+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm")
)+
facet_wrap(~month)
| Version | Author | Date |
|---|---|---|
| 5601558 | mlarriere | 2024-06-13 |
#Plot the vertical temperature profile on a monthly basis with MLD coloring
ggplot() +
geom_path(data=core_anomaly_with_mld_2023, aes(x = anomaly, y = depth,
group = interaction(platform_number, cycle_number), color = mld)) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
scale_color_viridis_c()+
coord_cartesian(xlim = c(-6, 6), ylim = c(200, 0)) +
labs(subtitle = paste('Propagation of SST anomalies in the water column'),
x = 'Temperature anomaly [°C]', y = 'Depth [m]',
color = "MLD \nrange [m]")+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14, face = "bold"),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm")
)+
facet_wrap(~month)
| Version | Author | Date |
|---|---|---|
| 5601558 | mlarriere | 2024-06-13 |
#Group Argo floats depending on MLD: 2 classes above and below 50m
core_anomaly_with_mld_2023_grouped <- core_anomaly_with_mld_2023 %>%
mutate(mld_range = ifelse(mld <= 50, "<=50m", ">50m"))
#Plot core Argo floats location with the 2 mld classes
mld_map<- ggplot()+
geom_tile(data=core_anomaly_with_mld_2023_grouped, aes(lon, lat, fill = mld_range)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
scale_fill_manual(values = c("<=50m" = "#A1BECE",
">50m" = "#B71518")) +
labs(subtitle = "Argo floats MLD",
x='longitude', y='latitude',
fill = "MLD \nrange [m]")+
coord_quickmap(expand = 0)+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.text = element_text(size = 18),
legend.title = element_text(size = 18, face = "bold"),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm")
)+
facet_wrap(~month)
# Calculating monthly mean anomaly over the eastern North Atlantic in 2023 as function of MLD classes
anomaly_core_with_mld_monthly_mean<-core_anomaly_with_mld_2023_grouped %>%
group_by(depth, month, mld_range) %>%
summarise(temp_anomaly_mean = mean(anomaly, na.rm = TRUE))
vertical_profiles<- ggplot() +
geom_path(data=core_anomaly_with_mld_2023_grouped, aes(x = anomaly, y = depth,
group = interaction(platform_number, cycle_number), color = mld_range)) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-4, 4), ylim = c(200, 0)) +
labs(subtitle = paste('Propagation of SST anomalies in the water column'),
x = 'Temperature anomaly [°C]', y = 'Depth [m]') +
scale_color_manual(values = c("<=50m" = "#A1BECE",
">50m" = "#B71518")) +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
legend.position = 'none')+
facet_wrap(~month)+
guides(color = guide_legend(title="MLD range [m]"))
combined_plot <- vertical_profiles + mld_map +
plot_layout(ncol = 2) +
plot_annotation(
title = 'Core Argo floats with MLD on a monthly basis',
subtitle = 'Eastern North Atlantic in 2023',
theme = theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16))
)
combined_plot
# Calculate the median MLD value for each month
monthly_median_mld <- core_anomaly_with_mld_2023 %>%
group_by(year, month) %>%
summarise(median_mld = median(mld))
# Join the median MLD values to the original dataframe
core_anomaly_with_mld_2023 <- core_anomaly_with_mld_2023 %>%
left_join(monthly_median_mld, by = c("year", "month"))
# MLD category: MLD above or below monthly threshold
core_anomaly_with_mld_2023 <- core_anomaly_with_mld_2023 %>%
mutate(mld_category = ifelse(mld > median_mld, "above median", "below median"))
# Facet labels with month + monthly median MLD
core_anomaly_with_mld_2023 <- core_anomaly_with_mld_2023 %>%
mutate(facet_label = paste(month, "\nMedian MLD:", round(median_mld, 2)))
# Plot
mld_plot <- ggplot(core_anomaly_with_mld_2023, aes(x = lon, y = lat, fill = mld_category)) +
geom_tile() +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y = c(chosen_extent$lat_min, chosen_extent$lat_max)) +
labs(title = paste("MLD Maps for", target_year),
subtitle = paste("The MLD category correpond to the median MLD for each month, \ni.e. same number of Argo floats in each category"),
x = "Longitude", y = "Latitude", fill = "MLD category") +
scale_fill_manual(values = c("below median" = "lightblue", "above median" = "darkred")) +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
strip.text = element_text(size = 14),
legend.text = element_text(size = 12)) +
facet_wrap(~ facet_label, ncol = 3) +
theme_bw()
vertical_profiles<- ggplot() +
geom_path(data=core_anomaly_with_mld_2023, aes(x = anomaly, y = depth, group = interaction(platform_number, cycle_number), color = mld_category)) +
geom_vline(xintercept = 0) +
scale_y_reverse() +
coord_cartesian(xlim = c(-6, 6), ylim = c(200, 0)) +
labs(subtitle = paste('Propagation of SST anomalies in the water column'),
x = 'Temperature anomaly [°C]', y = 'Depth [m]') +
scale_color_manual(values = c("below median" = "lightblue", "above median" = "darkred")) +
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
strip.text = element_text(size = 14),
legend.position = 'none')+
facet_wrap(~ facet_label, ncol = 3)
combined_plot <- vertical_profiles + mld_plot +
plot_layout(ncol = 2) +
plot_annotation(
title = 'Core Argo floats with MLD on a monthly basis',
subtitle = 'Eastern North Atlantic in 2023',
theme = theme(
plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16)
)
)
combined_plot
| Version | Author | Date |
|---|---|---|
| 5601558 | mlarriere | 2024-06-13 |
Absolute maximum anomalies
#Absolute max anomalies for each lat-lon (1 value for each lat-lon pair)
abs_max_SSTanomalies<-core_anomaly_2023_natlantic_subset %>%
filter(!is.na(anomaly), depth<=200) %>%
group_by(lat, lon) %>%
summarize(max_SST_anomaly = max(abs(anomaly), na.rm = TRUE))
plot1<-ggplot()+
geom_tile(data=abs_max_SSTanomalies, aes(lon, lat, fill = max_SST_anomaly)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
scale_fill_viridis_c(option = "magma") +
labs(title = "Absolute maximum SST anomaly",
subtitle= "Annual average - 2023",
fill = "Absolute max \nSST anomalies [°C]")+
coord_quickmap(expand = 0)+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
strip.text = element_text(size = 14),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm")
)
#Mean depth at which max anomaly is found (maximum depth for each lat-lon pair)
mean_depth_max_anomaly<- inner_join(abs_max_SSTanomalies, core_anomaly_2023_natlantic_subset, by=c('lat', 'lon'))
mean_depth_max_anomaly <- mean_depth_max_anomaly %>%
filter(abs(anomaly) == max_SST_anomaly)
plot2<-ggplot()+
geom_tile(data=mean_depth_max_anomaly, aes(lon, lat, fill = depth)) +
geom_map(data = world_coordinates, map = world_coordinates, aes(long, lat, map_id = region), fill = "grey") +
lims(x = c(chosen_extent$lon_min, chosen_extent$lon_max), y=c(chosen_extent$lat_min, chosen_extent$lat_max)) +
scale_fill_scico(palette = "lajolla", direction = -1) +
labs(title = "Depth of maximum anomaly [m]",
subtitle = 'depth range: 0-200m',
fill = "Depth [m]")+
coord_quickmap(expand = 0)+
theme(plot.title = element_text(size = 18),
plot.subtitle = element_text(size = 16),
axis.title.x = element_text(size = 14),
axis.title.y = element_text(size = 14),
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
strip.text = element_text(size = 14),
legend.text = element_text(size = 12),
legend.title = element_text(size = 14),
legend.key.width = unit(0.5, "cm"),
legend.key.height = unit(2, "cm"))
combined_plot<-plot1+plot2
combined_plot
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.5
Matrix products: default
BLAS: /usr/local/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.2.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] scico_1.3.1 patchwork_1.1.2 broom_1.0.5
[4] paletteer_1.6.0 cluster_2.1.6 gridExtra_2.3
[7] scatterplot3d_0.3-44 viridis_0.6.2 viridisLite_0.4.1
[10] ggOceanMaps_1.3.4 ggspatial_1.1.7 oce_1.7-10
[13] gsw_1.1-1 lubridate_1.9.0 timechange_0.1.1
[16] forcats_0.5.2 stringr_1.5.0 dplyr_1.1.3
[19] purrr_1.0.2 readr_2.1.3 tidyr_1.3.0
[22] tibble_3.2.1 ggplot2_3.4.4 tidyverse_1.3.2
[25] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] googledrive_2.0.0 colorspace_2.0-3 ellipsis_0.3.2
[4] class_7.3-20 rprojroot_2.0.3 fs_1.5.2
[7] rstudioapi_0.15.0 proxy_0.4-27 farver_2.1.1
[10] fansi_1.0.3 xml2_1.3.3 codetools_0.2-18
[13] cachem_1.0.6 knitr_1.41 jsonlite_1.8.3
[16] dbplyr_2.2.1 rgeos_0.5-9 compiler_4.2.2
[19] httr_1.4.4 backports_1.4.1 assertthat_0.2.1
[22] fastmap_1.1.0 gargle_1.2.1 cli_3.6.1
[25] later_1.3.0 htmltools_0.5.8.1 tools_4.2.2
[28] gtable_0.3.1 glue_1.6.2 maps_3.4.1
[31] Rcpp_1.0.10 cellranger_1.1.0 jquerylib_0.1.4
[34] RNetCDF_2.6-1 raster_3.6-11 vctrs_0.6.4
[37] lwgeom_0.2-10 xfun_0.35 ps_1.7.2
[40] rvest_1.0.3 lifecycle_1.0.3 ncmeta_0.3.5
[43] googlesheets4_1.0.1 terra_1.7-65 getPass_0.2-2
[46] scales_1.2.1 hms_1.1.2 promises_1.2.0.1
[49] parallel_4.2.2 rematch2_2.1.2 yaml_2.3.6
[52] sass_0.4.4 stringi_1.7.8 highr_0.9
[55] e1071_1.7-12 rlang_1.1.1 pkgconfig_2.0.3
[58] evaluate_0.18 lattice_0.20-45 sf_1.0-9
[61] labeling_0.4.2 processx_3.8.0 tidyselect_1.2.0
[64] magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[67] DBI_1.2.2 pillar_1.9.0 haven_2.5.1
[70] whisker_0.4 withr_2.5.0 units_0.8-0
[73] stars_0.6-0 abind_1.4-5 sp_1.5-1
[76] modelr_0.1.10 crayon_1.5.2 KernSmooth_2.23-20
[79] utf8_1.2.2 tzdb_0.3.0 rmarkdown_2.18
[82] isoband_0.2.6 grid_4.2.2 readxl_1.4.1
[85] callr_3.7.3 git2r_0.30.1 reprex_2.0.2
[88] digest_0.6.30 classInt_0.4-8 httpuv_1.6.6
[91] munsell_0.5.0 bslib_0.4.1