Analysis of Cant estimates
Jens Daniel Müller
18 September, 2020
Last updated: 2020-09-18
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Knit directory: Cant_eMLR/
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library(tidyverse)
library(patchwork)
library(scico)
library(scales)
library(metR)1 Data sources
Cant estimates from this study:
- Mean and SD per grid cell (lat, lon, depth)
- Zonal mean and SD (basin, lat, depth)
- Inventories (lat, lon)
Cant_average <-
read_csv(here::here("data/mapping/_summarized_files",
"Cant_average.csv"))
Cant_average_zonal <-
read_csv(here::here("data/mapping/_summarized_files",
"Cant_average_zonal.csv"))
Cant_predictor_average_zonal <-
read_csv(here::here("data/mapping/_summarized_files",
"Cant_predictor_average_zonal.csv"))
Cant_inv <-
read_csv(here::here("data/mapping/_summarized_files",
"Cant_inv.csv"))C* estimates from this study:
- Mean and SD per grid cell (lat, lon, depth)
- Zonal mean and SD (basin, lat, depth)
Cstar_average <-
read_csv(here::here("data/mapping/_summarized_files",
"Cstar_average.csv"))
Cstar_average_zonal <-
read_csv(here::here("data/mapping/_summarized_files",
"Cstar_average_zonal.csv"))Cleaned GLODAPv2_2020 file as used in this study
GLODAP <-
read_csv(
here::here(
"data/GLODAPv2_2020/_summarized_data_files",
"GLODAP_MLR_fitting_ready.csv"
)
)2 Color scale
For ease of comparison with Gruber et al (2019) we adapt their color scale, including the ranges and breaks applied in various types of visualizations.
rgb2hex <- function(r, g, b)
rgb(r, g, b, maxColorValue = 100)
cols = c(rgb2hex(95, 95, 95),
rgb2hex(0, 0, 95),
rgb2hex(100, 0, 0),
rgb2hex(100, 100, 0))
Gruber_rainbow <- colorRampPalette(cols)
rm(rgb2hex, cols)3 Cant - positive
In a first series of plots we explore the distribution of Cant, taking only positive estimates into account (positive here refers to the mean Cant estimate across 10 eMLR model predictions available for each grid cell). Negative values were set to zero before calculating mean sections and inventories.
3.1 Zonal mean sections
breaks <- c(seq(0,18,1),Inf)
breaks_n <- length(breaks) - 1
Cant_average_zonal <- Cant_average_zonal %>%
mutate(Cant_pos_mean_int = cut(Cant_pos_mean,
breaks,
right = FALSE))
zonal_section <- function(df, i_basin_AIP, i_eras, var) {
name_var <- var
var <- sym(var)
lat_max <- max(df$lat)
lat_min <- min(df$lat)
df_sub <- df %>%
filter(eras == i_eras,
basin_AIP == i_basin_AIP)
surface <- df_sub %>%
ggplot(aes(lat, depth, z = !!var)) +
geom_contour_filled(breaks = breaks) +
scale_fill_manual(values = Gruber_rainbow(breaks_n),
name = "Cant") +
coord_cartesian(expand = 0,
ylim = c(500, 0),
xlim = c(lat_min, lat_max)) +
scale_y_reverse() +
theme(
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank()
) +
labs(y = "Depth (m)",
title = paste("Basin:", i_basin_AIP, "| eras:", i_eras))
deep <- df_sub %>%
ggplot(aes(lat, depth, z = !!var)) +
geom_contour_filled(breaks = breaks) +
scale_fill_manual(values = Gruber_rainbow(breaks_n),
name = "Cant") +
scale_y_reverse() +
coord_cartesian(expand = 0,
ylim = c(3000, 500),
xlim = c(lat_min, lat_max)) +
labs(x = "latitude (°N)", y = "Depth (m)")
surface / deep +
plot_layout(guides = "collect")
}
for (i_basin_AIP in unique(Cant_average_zonal$basin_AIP)) {
for (i_eras in rev(unique(Cant_average_zonal$eras))) {
print(zonal_section(Cant_average_zonal,
i_basin_AIP = i_basin_AIP,
i_eras = i_eras,
"Cant_pos_mean"))
}
}
rm(breaks, breaks_n)3.2 Isoneutral slab distribution
Mean of positive Cant within each horizontal grid cell (lon x lat) per isoneutral slab.
Please note that:
- density slabs covering values >28.1 occur by definition only either in the Atlantic or Indo-Pacific basin
- gaps in the maps represent areas where (thin) density layers fit between discrete depth levels used for mapping
Cant_gamma_maps <- Cant_average %>%
group_by(lat, lon, gamma_slab, eras) %>%
summarise(Cant_pos = mean(Cant_pos, na.rm = TRUE)) %>%
ungroup()
breaks <- c(seq(0,16,2),Inf)
breaks_n <- length(breaks) - 1
Cant_gamma_maps <- Cant_gamma_maps %>%
mutate(Cant_pos_int = cut(Cant_pos,
breaks,
right = FALSE))
ggplot() +
geom_raster(data = landmask,
aes(lon, lat),
fill = "grey30") +
geom_raster(data = Cant_gamma_maps,
aes(lon, lat, fill = Cant_pos_int)) +
scale_fill_manual(values = Gruber_rainbow(breaks_n)) +
facet_grid(gamma_slab ~ eras) +
coord_quickmap(expand = 0) +
theme(axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text = element_blank(),
legend.position = "top")
rm(Cant_gamma_maps, breaks, breaks_n)3.3 Inventory map
Column inventory of positive Cant between the surface and 3000m water depth per horizontal grid cell (lat x lon).
breaks <- c(seq(0,16,2),Inf)
breaks_n <- length(breaks) - 1
Cant_inv <- Cant_inv %>%
mutate(cant_inv_pos_int = cut(cant_inv_pos,
breaks,
right = FALSE))
Cant_inv %>%
ggplot() +
geom_raster(data = landmask,
aes(lon, lat), fill = "grey30") +
geom_raster(aes(lon, lat, fill = cant_inv_pos_int)) +
coord_quickmap(expand = 0) +
scale_fill_manual(values = Gruber_rainbow(breaks_n)) +
facet_wrap( ~ eras, ncol = 1) +
theme(axis.title = element_blank())
rm(breaks, breaks_n)4 Cant - all
In a second series of plots we explore the distribution of Cant, taking positive and negative estimates into account.
4.1 Zonal mean sections
section_zonal_average_divergent(Cant_average_zonal,
"Cant_mean",
"gamma_mean")
4.2 Isoneutral slab distribution
Mean of Cant within each horizontal grid cell (lon x lat) per isoneutral slab.
Please note that:
- density slabs covering values >28.1 occur by definition only either in the Atlantic or Indo-Pacific basin
- gaps in the maps represent areas where (thin) density layers fit between discrete depth levels used for mapping
Cant_gamma_maps <- Cant_average %>%
group_by(lat, lon, gamma_slab, eras) %>%
summarise(Cant = mean(Cant, na.rm = TRUE)) %>%
ungroup()
breaks <- c(-Inf, seq(-16, 16, 4), Inf)
breaks_n <- length(breaks) - 1
Cant_gamma_maps <- Cant_gamma_maps %>%
mutate(Cant_int = cut(Cant,
breaks,
right = FALSE))
ggplot() +
geom_raster(data = landmask,
aes(lon, lat),
fill = "grey30") +
geom_raster(data = Cant_gamma_maps,
aes(lon, lat, fill = Cant_int)) +
scale_fill_brewer(palette = "RdBu",
direction = -1) +
facet_grid(gamma_slab ~ eras) +
coord_quickmap(expand = 0) +
theme(
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text = element_blank(),
legend.position = "top"
)
rm(Cant_gamma_maps, breaks, breaks_n)4.3 Inventory map
Column inventory of positive Cant between the surface and 3000m water depth per horizontal grid cell (lat x lon).
breaks <- c(-Inf, seq(-16,16,4),Inf)
breaks_n <- length(breaks) - 1
Cant_inv <- Cant_inv %>%
mutate(cant_inv_int = cut(cant_inv,
breaks,
right = FALSE))
Cant_inv %>%
ggplot() +
geom_raster(data = landmask,
aes(lon, lat), fill = "grey80") +
geom_raster(aes(lon, lat, fill = cant_inv_int)) +
coord_quickmap(expand = 0) +
scale_fill_brewer(palette = "RdBu",
direction = -1) +
facet_wrap(~eras, ncol = 1) +
theme(
axis.title = element_blank()
)
rm(breaks, breaks_n)5 Cant - standard deviation
5.1 Across models
Standard deviation across Cant from all MLR models was calculate for each grid cell (XYZ). The zonal mean of this standard deviation should reflect the uncertainty associated to the predictor selection within each slab and era.
section_zonal_average_continous(Cant_average_zonal,
"Cant_sd_mean",
"gamma_mean")
5.2 Across basins
Standard deviation of mean Cant values was calculate across all longitudes. This standard deviation should reflect the zonal variability of Cant within the basin and era.
section_zonal_average_continous(Cant_average_zonal,
"Cant_sd",
"gamma_mean")
6 Cant - predictor contribution
for (variable in c(
"Cant_intercept",
"Cant_aou",
"Cant_oxygen",
"Cant_phosphate",
"Cant_phosphate_star",
"Cant_silicate",
"Cant_tem",
"Cant_sal")) {
print(
section_zonal_average_continous(Cant_predictor_average_zonal,
variable,
"gamma")
)
}
rm(variable)7 Cant - globale section
7.0.1 JGOFS_GO
section_global(Cant_average %>% filter(eras == "JGOFS_GO"),
"Cant_pos")
7.0.2 GO_new
section_global(Cant_average %>% filter(eras == "GO_new"),
"Cant_pos")
8 Sections by model
Zonal sections plots are produced for every 20° longitude, each era and for all models individually and can be downloaded here.
8.1 Maps
8.1.1 Surfaces
Cant concentration for selected depth levels at which mapping was performed.
Cant_average %>%
filter(depth %in% parameters$depth_levels) %>%
ggplot(aes(lon, lat, fill = Cant)) +
geom_raster(data = landmask,
aes(lon, lat), fill = "grey80") +
geom_raster() +
scale_fill_divergent(guide = "colorstrip",
breaks = MakeBreaks(5),
name = "Cant") +
guides(fill = guide_colorsteps(barheight = unit(10, "cm"))) +
coord_quickmap(expand = 0) +
facet_grid(depth ~ eras)
8.2 Cant vs model SD
Cant_average %>%
ggplot(aes(Cant, Cant_sd)) +
geom_vline(xintercept = 0) +
geom_hline(yintercept = 10) +
geom_bin2d() +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10",
name = "log10(n)") +
facet_grid(basin_AIP ~ eras)
Cant_average %>%
ggplot(aes(Cant, Cant_sd)) +
geom_vline(xintercept = 0) +
geom_hline(yintercept = 10) +
geom_bin2d() +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10",
name = "log10(n)") +
facet_grid(gamma_slab ~ basin_AIP)
8.3 Cant vs regional SD
Cant_average_zonal %>%
ggplot(aes(Cant_mean, Cant_sd)) +
geom_vline(xintercept = 0) +
geom_hline(yintercept = 10) +
geom_bin2d() +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10",
name = "log10(n)") +
facet_grid(basin_AIP ~ eras)
Cant_average_zonal %>%
ggplot(aes(Cant_mean, Cant_sd)) +
geom_vline(xintercept = 0) +
geom_hline(yintercept = 10) +
geom_bin2d() +
scale_fill_viridis_c(option = "magma",
direction = -1,
trans = "log10",
name = "log10(n)") +
facet_grid(gamma_slab ~ basin_AIP)
9 Neutral density
9.1 Slab depth
Please note that:
- density slabs covering values >28.1 occur by definition only either in the Atlantic or Indo-Pacific basin
- predictor density slabs are only shown for the upper 3000m as used for the mapping, whereas GLODAP observations are displayed for the entire water column as used for fitting eMLRs (in both cases shallow waters are excluded at low density)
gamma_maps <- Cant_average %>%
group_by(lat, lon, gamma_slab) %>%
summarise(depth_max = max(depth, na.rm = TRUE)) %>%
ungroup()
GLODAP_obs_coverage <- GLODAP %>%
count(lat, lon, gamma_slab, era)
ggplot() +
geom_raster(data = landmask,
aes(lon, lat),
fill = "grey80") +
geom_raster(data = gamma_maps,
aes(lon, lat, fill = depth_max)) +
geom_raster(data = GLODAP_obs_coverage,
aes(lon, lat), fill = "red") +
facet_grid(gamma_slab ~ era) +
coord_quickmap(expand = 0) +
scale_fill_viridis_c(direction = -1) +
theme(axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text = element_blank(),
legend.position = "top")
rm(gamma_maps, GLODAP_obs_coverage)9.2 Surface maps
map_climatology(Cant_average, "gamma")
9.3 Zonal sections
The mean zonal distribution of neutral densities was calculated. CAVEAT: Due to practical reasons, binning here does not include the two highest isoneutral density slabs in the Atlantic, yet.
9.3.1 Mean
Cant_average_zonal %>%
filter(eras == "JGOFS_GO") %>%
ggplot(aes(lat, depth, z = gamma_mean)) +
geom_contour_filled(breaks = slab_breaks) +
geom_contour(breaks = slab_breaks,
col = "white") +
geom_text_contour(breaks = slab_breaks,
col = "white",
skip = 1) +
scale_fill_viridis_d(name = "Gamma",
direction = -1) +
scale_y_reverse() +
scale_x_continuous(breaks = seq(-100, 100, 20)) +
coord_cartesian(expand = 0) +
guides(fill = guide_colorsteps(barheight = unit(10, "cm"))) +
facet_grid(basin_AIP~.)
9.3.2 SD
Higher SD of gamma in shallow, subtropical waters results from a more pronounced longitudinal variability.
Cant_average_zonal %>%
filter(eras == "JGOFS_GO") %>%
ggplot(aes(lat, depth, z = gamma_sd)) +
geom_contour_filled() +
scale_fill_viridis_d(name = "Gamma SD",
direction = -1) +
scale_y_reverse() +
scale_x_continuous(breaks = seq(-100, 100, 20)) +
coord_cartesian(expand = 0) +
guides(fill = guide_colorsteps(barheight = unit(10, "cm"))) +
facet_grid(basin_AIP~.)
10 Cstar
Cstar_average_zonal <- Cstar_average_zonal %>%
mutate(era = factor(era, c("JGOFS_WOCE", "GO_SHIP", "new_era")))
Cstar_average_zonal %>%
ggplot(aes(lat, depth, z = Cstar_mean_mean)) +
geom_contour_filled(bins = 11) +
scale_fill_viridis_d(name = "Cstar") +
geom_contour(aes(lat, depth, z = gamma_mean_mean),
breaks = slab_breaks,
col = "white") +
geom_text_contour(
aes(lat, depth, z = gamma_mean_mean),
breaks = slab_breaks,
col = "white",
skip = 1
) +
scale_y_reverse() +
coord_cartesian(expand = 0) +
guides(fill = guide_colorsteps(barheight = unit(10, "cm"))) +
facet_grid(basin_AIP ~ era)
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] metR_0.7.0 scales_1.1.1 scico_1.2.0 patchwork_1.0.1
[5] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4
[9] readr_1.3.1 tidyr_1.1.0 tibble_3.0.3 ggplot2_3.3.2
[13] tidyverse_1.3.0 workflowr_1.6.2
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