NCP reconstruction
Jens Daniel Müller
18 February, 2021
Last updated: 2021-02-18
Checks: 7 0
Knit directory: BloomSail/
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library(tidyverse)
library(ncdf4)
library(seacarb)
library(oce)
library(patchwork)
library(lubridate)
library(metR)1 Scope of this script
In order to test how well the depth-integrated CT* estimates can be reproduced if only surface CO2 data were available, the following reconstruction approaches were tested:
- Mixed layer depth: Integration of surface observation across the MLD, assuming homogeneous vertical patterns
- CT profile reconstruction: Vertical reconstruction of incremental CT changes based on profiles of incremental changes in temperature
- Temperature penetration depth: Integration of surface observation across the temperature penetration depth, assuming similar vertical extension as for CT drawdown.
Note: The reconstruction of CT* profiles and the integration across the temperature penetration depth should produce very similar results. However, the latter avoids to create misinterpretable information about the vertical distribution of CT*.
The integration depth parameterizations were tested on two data sets, namely:
- BloomSail observations, restricted to CT* data in surface water
- SOOP Finnmaid pCO2 + vertical hydrographical data from GETM model
date_CT_min <- ymd_hms("2018-07-24 07:58:29")
date_tem_max <- ymd_hms("2018-08-04 00:00:00")2 BloomSail
1m gridded, downcast profiles were used.
Mean CO2 data from upper 6 meters were used as surface values.
# read data
tm_profiles_ID <-
read_csv(here::here("data/intermediate/_merged_data_files/CT_dynamics", "tm_profiles_ID.csv"))
tm_profiles_ID <- tm_profiles_ID %>%
select(-c(date_ID))
# calculate cumulative changes
tm_profiles_ID_long <- tm_profiles_ID %>%
select(-c(pCO2, sal)) %>%
pivot_longer(c("tem", "CT_star"), values_to = "value", names_to = "var") %>%
group_by(var, dep) %>%
arrange(date_time_ID) %>%
mutate(date_time_ID_diff = as.numeric(date_time_ID - lag(date_time_ID)),
value_diff = value - lag(value, default = first(value)),
value_diff_daily = value_diff / date_time_ID_diff,
value_cum = cumsum(value_diff)) %>%
ungroup()2.1 TPD and CPD
Temperature penetration depth (TPD) and CT* penetration depth (CPD) were investigated based on the BloomSail data.
2.1.1 Cumulative profile July 9
# subset date for cumulative assesment
tm_profiles_ID_long_day <- tm_profiles_ID_long %>%
filter(ID == 180709)
# calculate integrated value of pos/neg changes for Temp/CT*
# and relative contribution with increasing water depth
tm_profiles_ID_long_day_dep <- tm_profiles_ID_long_day %>%
select(var, dep, value_cum) %>%
mutate(
value_cum = if_else(value_cum > 0 & var == "CT_star",
NaN, value_cum),
value_cum = if_else(value_cum < 0 & var == "tem",
NaN, value_cum)
) %>%
group_by(var) %>%
arrange(dep) %>%
mutate(
value_cum_i = sum(value_cum, na.rm = TRUE),
value_cum_dep = cumsum(value_cum),
value_cum_i_rel = value_cum_dep / value_cum_i * 100
) %>%
ungroup()
# cumulative integrated values
value_cum <- tm_profiles_ID_long_day_dep %>%
group_by(var) %>%
summarise(value_cum_i = mean(value_cum_i)) %>%
ungroup()
# cumulative surface values
value_surface <- tm_profiles_ID_long_day %>%
select(var, dep, value_cum) %>%
filter(dep < parameters$surface_dep) %>%
group_by(var) %>%
summarise(value_surface = mean(value_cum)) %>%
ungroup()
# calculate penentration depth for T and C
PD <- full_join(value_cum, value_surface)
PD <- PD %>%
mutate(PD = value_cum_i / value_surface)
rm(value_cum, value_surface)p_tm_profiles_ID_long <- tm_profiles_ID_long_day %>%
arrange(dep) %>%
ggplot(aes(value_cum, dep)) +
geom_hline(aes(yintercept = parameters$i_dep_lim, col = "integration")) +
geom_hline(data = PD, aes(yintercept = PD, col = "penetration")) +
geom_vline(xintercept = 0) +
geom_point() +
geom_path() +
scale_y_reverse() +
scale_color_brewer(palette = "Dark2", guide = FALSE) +
labs(y = "Depth (m)", x = "Cumulative change") +
theme(legend.position = "left") +
facet_wrap(var ~ ., ncol = 1, scales = "free_x")
p_tm_profiles_ID_long_rel <- tm_profiles_ID_long_day_dep %>%
ggplot(aes(value_cum_i_rel, dep)) +
geom_hline(aes(yintercept = parameters$i_dep_lim, col = "integration")) +
geom_hline(data = PD, aes(yintercept = PD, col = "penetration")) +
geom_vline(xintercept = 90) +
geom_point() +
geom_line() +
scale_y_reverse(limits = c(25, 0)) +
scale_color_brewer(palette = "Dark2", name = "Depth") +
scale_x_continuous(limits = c(0, NA)) +
labs(x = "Relative contribution (%)") +
facet_wrap(var ~ ., ncol = 1, scales = "free_x") +
theme(axis.title.y = element_blank())
p_tm_profiles_ID_long + p_tm_profiles_ID_long_rel
PD# A tibble: 2 x 4
var value_cum_i value_surface PD
<chr> <dbl> <dbl> <dbl>
1 CT_star -286. -28.4 10.1
2 tem 16.3 1.65 9.89rm(tm_profiles_ID_long_day_dep,
p_tm_profiles_ID_long,
p_tm_profiles_ID_long_rel)2.1.2 Incremental profile July 9
col_value <- "red"
p_CT_star <-
tm_profiles_ID_long_day %>%
filter(var == "CT_star") %>%
arrange(dep) %>%
ggplot() +
geom_col(
data = tm_profiles_ID_long_day %>%
filter(var == "CT_star", value_diff_daily < 0),
aes(x = value_diff_daily, y = dep),
width = 1,
alpha = 0.2,
orientation = "y"
) +
geom_vline(xintercept = 0) +
scale_y_reverse(expand = c(0, 0)) +
annotate(
"text",
x = -6,
y = 11,
label = "CPD",
col = col_value,
size = geom_text_size
) +
annotate(
"text",
x = -3.5,
y = 2.5,
label = "Integrated\nchange",
size = geom_text_size
) +
geom_point(aes(value_diff_daily, dep)) +
geom_path(aes(value_diff_daily, dep)) +
geom_hline(data = PD %>% filter(var == "CT_star"),
aes(yintercept = PD),
col = col_value) +
labs(y = "Depth (m)", x = expression(paste(Delta ~ C[T], "*") ~ (µmol ~ kg ^ {
-1
}))) +
theme(
legend.title = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.y = element_blank()
)
p_tem <-
tm_profiles_ID_long_day %>%
filter(var == "tem") %>%
arrange(dep) %>%
ggplot() +
geom_col(
data = tm_profiles_ID_long_day %>%
filter(var == "tem", value_diff_daily > 0),
aes(x = value_diff_daily, y = dep),
width = 1,
alpha = 0.2,
orientation = "y"
) +
geom_vline(xintercept = 0) +
scale_y_reverse(expand = c(0, 0)) +
annotate(
"text",
x = 0.4,
y = 11,
label = "PD",
col = col_value,
size = geom_text_size
) +
annotate(
"text",
x = 0.2,
y = 2.5,
label = "Integrated\nchange",
size = geom_text_size
) +
geom_point(aes(value_diff_daily, dep)) +
geom_path(aes(value_diff_daily, dep)) +
geom_hline(data = PD %>% filter(var == "tem"),
aes(yintercept = PD),
col = col_value) +
labs(y = "Depth (m)", x = expression(Delta ~ Temperature ~ (degree * C))) +
theme(legend.title = element_blank())
p_tem + p_CT_star +
plot_layout(guides = 'collect') +
plot_annotation(tag_levels = 'a')
ggsave(
here::here("output/Plots/Figures_publication/appendix",
"Fig_C4.pdf"),
width = 120,
height = 110,
dpi = 300,
units = "mm"
)
ggsave(
here::here("output/Plots/Figures_publication/appendix",
"Fig_C4.png"),
width = 120,
height = 110,
dpi = 300,
units = "mm"
)
rm(PD, tm_profiles_ID_long_day, p_tem, p_CT_star, col_value)2.1.3 Incremental time series
A time series of TPD and CPD was calculated, based on the incremental (ie from cruise day to cruise day) changes of temperature / CT*, taking only pos. / neg. changes of both parameters into account.
# surface values
diff_surface <- tm_profiles_ID_long %>%
filter(dep < parameters$surface_dep) %>%
group_by(ID, var) %>%
summarise(value_diff_surface = mean(value_diff, na.rm = TRUE)) %>%
ungroup() %>%
mutate(
value_diff_surface = if_else(value_diff_surface > 0 & var == "CT_star",
NaN, value_diff_surface),
value_diff_surface = if_else(value_diff_surface < 0 &
var == "tem",
NaN, value_diff_surface)
)
tm_profiles_ID_long <- full_join(tm_profiles_ID_long, diff_surface)
rm(diff_surface)
# calculate penetration depths for T and C
PD <- tm_profiles_ID_long %>%
mutate(
value_diff = if_else(value_diff > 0 & var == "CT_star",
NaN, value_diff),
value_diff = if_else(value_diff < 0 & var == "tem",
NaN, value_diff)
) %>%
group_by(var, ID, date_time_ID) %>%
summarise(
value_diff_int = sum(value_diff, na.rm = TRUE),
value_diff_surface = mean(value_diff_surface, na.rm = TRUE)
) %>%
ungroup() %>%
mutate(i_dep = value_diff_int / value_diff_surface)
# calculate temporal mean
PD_mean <- PD %>%
group_by(var) %>%
summarise(i_dep_mean = mean(i_dep, na.rm = TRUE),
i_dep_sd = sd(i_dep, na.rm = TRUE)) %>%
ungroup()p_surface <- PD %>%
ggplot(aes(date_time_ID, value_diff_surface)) +
geom_hline(yintercept = 0) +
geom_line() +
geom_point() +
scale_y_reverse(name = "Change surface value") +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank()) +
facet_grid(var ~ ., scales = "free_y")
p_integrated <- PD %>%
ggplot(aes(date_time_ID, value_diff_int)) +
geom_hline(yintercept = 0) +
geom_line() +
geom_point() +
scale_y_reverse(name = "Change integrated value") +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank()) +
facet_grid(var ~ ., scales = "free_y")
p_pen_dep <- PD %>%
ggplot(aes(date_time_ID, i_dep, col = var)) +
geom_hline(yintercept = 0) +
geom_hline(data = PD_mean,
aes(
yintercept = i_dep_mean,
col = var,
linetype = "mean"
)) +
geom_line(aes(linetype = "cruise")) +
geom_point() +
scale_y_reverse(name = "Penetration depth (m)", breaks = seq(0, 20, 5)) +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank())
p_surface + p_integrated + p_pen_dep +
plot_layout(ncol = 1)
PD_mean# A tibble: 2 x 3
var i_dep_mean i_dep_sd
<chr> <dbl> <dbl>
1 CT_star 10.2 1.04
2 tem 11.5 2.46CPD <- PD %>%
filter(var == "CT_star") %>%
drop_na()
rm(p_surface, p_integrated, p_pen_dep)
rm(PD, PD_mean, tm_profiles_ID_long)3 GETM model
3.1 Read netcdf file
# read netcdf file
nc <-
nc_open(here::here("data/input/GETM", "Finnmaid.E.3d.2018.nc"))
# extract latitude vector
lat <- ncvar_get(nc, "latc")
# extract start time
time_start <- nc$dim$time$units %>%
substr(start = 15, stop = 33) %>%
ymd_hms()
# create time vecotr
t <- time_start + ncvar_get(nc, "time")
rm(time_start)
# extract depths vector
d <- ncvar_get(nc, "zax")
# read model data
for (var_3d in c("salt", "temp")) {
# store the data in a 3-dimensional array
array <-
ncvar_get(nc, var_3d)
# find NA value
fillvalue <- ncatt_get(nc, var_3d, "_FillValue")
# replace NA value with NA
array[array == fillvalue$value] <- NA
for (i in seq(1, length(t), 1)) {
# i <- 3
array_slice <- array[, , i] # slices data from one day
# convert to tibble
array_slice_df <- as.data.frame(t(array_slice))
array_slice_df <- as_tibble(array_slice_df)
# rename, format and subset data
gt_3d_part <- array_slice_df %>%
set_names(as.character(lat)) %>%
mutate(dep = -d) %>%
gather("lat", "value", 1:length(lat)) %>%
mutate(lat = as.numeric(lat)) %>%
filter(
lat > parameters$getm_low_lat,
lat < parameters$getm_high_lat,
dep <= parameters$max_dep
) %>%
mutate(var = var_3d,
date_time = t[i]) %>%
select(date_time, dep, value, var)
if (exists("gt_3d")) {
gt_3d <- bind_rows(gt_3d, gt_3d_part)
} else {
gt_3d <- gt_3d_part
}
rm(array_slice, array_slice_df, gt_3d_part)
}
rm(array, fillvalue)
}
nc_close(nc)
rm(nc)
# subset time period
# calculate daily, regional mean profile in study area
gt_3d_long <- gt_3d %>%
filter(date_time >= parameters$getm_start_date &
date_time <= parameters$getm_end_date) %>%
group_by(date_time, var, dep) %>%
summarise_all(list(value = ~ mean(., na.rm = TRUE))) %>% # regional averaging
ungroup()
gt_3d <- gt_3d_long %>%
pivot_wider(values_from = value, names_from = var) %>%
rename(sal = salt, tem = temp)
rm(i, lat, d, t, var_3d)3.2 Sal and tem profiles
gt_3d_long %>%
ggplot(aes(value, dep,
col = date_time,
group = date_time)) +
geom_path() +
scale_y_reverse(expand = c(0, 0)) +
scale_color_viridis_c(name = "Date", trans = "time") +
facet_wrap( ~ var, scales = "free_x", ncol = 2)
rm(gt_3d_long)3.3 Comparison BloomSail
Vertical, 1m-gridded BloomSail CTD profiles were used for comparison with GETM results. Note that the sampling location does not match exactly.
3.3.1 Interpolate GETM to BloomSail
GETM results were linearly interpolated to the BloomSail depth levels and the mean cruise dates.
gt_3d_int <- gt_3d %>%
mutate(dep_int = dep + 0.5) %>%
group_by(date_time) %>%
mutate(sal_int = approxfun(dep, sal)(dep_int),
tem_int = approxfun(dep, tem)(dep_int)) %>%
ungroup() %>%
select(date_time,
dep = dep_int,
sal = sal_int,
tem = tem_int) %>%
drop_na()
rm(gt_3d)# join GETM and BloomSail profiles
tm_gt_3d <- full_join(
gt_3d_int,
tm_profiles_ID %>% select(date_time = date_time_ID,
dep, sal, tem),
by = c("date_time", "dep"),
suffix = c("_gt", "_tm")
)
# calculate density profiles
tm_gt_3d <- tm_gt_3d %>%
mutate(
rho_gt = swSigma(
salinity = sal_gt,
temperature = tem_gt,
pressure = dep / 10
),
rho_tm = swSigma(
salinity = sal_tm,
temperature = tem_tm,
pressure = dep / 10
)
)
# interpolate to BloomSail time stamp
tm_gt_3d <- tm_gt_3d %>%
arrange(date_time) %>%
group_by(dep) %>%
mutate(
tem_gt = approxfun(date_time, tem_gt)(date_time),
sal_gt = approxfun(date_time, sal_gt)(date_time),
rho_gt = approxfun(date_time, rho_gt)(date_time)
) %>%
ungroup() %>%
drop_na()3.3.2 S, T, rho profiles
# convert to long format
tm_gt_3d_long <- tm_gt_3d %>%
pivot_longer(
sal_gt:rho_tm,
values_to = "value",
names_to = c("var", "source"),
names_sep = "_"
)
tm_gt_3d_long %>%
ggplot(aes(value, dep,
col = date_time,
group = date_time)) +
geom_path() +
scale_y_reverse(expand = c(0, 0), name = "Depth (m)") +
scale_color_viridis_c(name = "Date", trans = "time") +
facet_grid(source ~ var, scales = "free_x")
STD profiles modeled with GETM (upper panels, gt) and measured during BloomSail campaign (lower panels, ts)
3.3.3 S, T, rho offset profiles
tm_gt_3d <- tm_gt_3d_long %>%
pivot_wider(values_from = "value", names_from = "source") %>%
mutate(value_diff = gt - tm)
tm_gt_3d %>%
ggplot(aes(value_diff, dep,
col = date_time,
group = date_time)) +
geom_vline(xintercept = 0, col = "red") +
geom_path() +
scale_y_reverse(expand = c(0, 0), name = "Depth (m)") +
scale_color_viridis_c(name = "Date", trans = "time") +
facet_grid(. ~ var, scales = "free_x") +
labs(x = "Difference GETM (gt) - Bloomsail (ts)")
Offset STD profiles comparing modeled with GETM (upper panels, gt) and measured during BloomSail campaign (lower panels, ts)
rm(tm_gt_3d, tm_gt_3d_long)4 SOOP Finnmaid
4.1 Data preparation
fm <-
read_csv(here::here("data/intermediate/_summarized_data_files",
"fm_bloomsail.csv"))
fm <- fm %>%
filter(date_time > parameters$getm_start_date,
date_time < parameters$getm_end_date) %>%
select(ID, date_time, sensor, sal, tem, pCO2) %>%
mutate(ID = as.factor(ID))4.1.1 CT* calculation
Calculate CT* based on fixed AT and salinity mean values.
# read mean bottle data
fixed_values <-
read_csv(here::here("data/intermediate/_summarized_data_files", "tb_fix.csv"))
# calculate CT*
fm <- fm %>%
mutate(
CT_star = carb(
24,
var1 = pCO2,
var2 = fixed_values$AT * 1e-6,
S = fixed_values$sal,
T = tem,
k1k2 = "m10",
kf = "dg",
ks = "d",
gas = "insitu"
)[, 16] * 1e6
)4.1.2 Regional averaging
Calculate regional mean and sd values for each crossing of the area.
fm_ID <- fm %>%
pivot_longer(c(pCO2, sal, tem, CT_star),
values_to = "value",
names_to = "var") %>%
group_by(ID) %>%
mutate(date_time_ID = mean(date_time)) %>%
ungroup() %>%
select(-date_time) %>%
group_by(ID, date_time_ID, sensor, var) %>%
summarise_all(list( ~ mean(.), ~ sd(.)), na.rm = TRUE) %>%
ungroup() %>%
rename(value = mean)4.1.3 Read tm profile data
Read original profile data and calculate surface mean and sd values.
tm_profiles <-
read_csv(
here::here(
"data/intermediate/_merged_data_files/CT_dynamics",
"tm_profiles.csv"
)
)
# surface mean calculation
tm_profiles_ID_long_surface <- tm_profiles %>%
filter(dep < parameters$surface_dep) %>%
select(-c(dep, date_ID, station, date_time, lat, lon, pCO2_corr)) %>%
mutate(ID = as.factor(ID)) %>%
pivot_longer(sal:CT_star, values_to = "value", names_to = "var") %>%
group_by(ID, date_time_ID, var) %>%
summarise_all(list( ~ mean(.), ~ sd(.)), na.rm = TRUE) %>%
ungroup()4.1.4 Timeseries
fm_ID %>%
ggplot() +
geom_rect(data = fixed_values,
aes(
xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf
),
alpha = 0.2) +
geom_path(aes(x = date_time_ID, y = value)) +
geom_ribbon(aes(
x = date_time_ID,
y = value,
ymax = value + sd,
ymin = value - sd,
fill = "Finnmaid"
),
alpha = 0.3) +
geom_ribbon(
data = tm_profiles_ID_long_surface,
aes(
x = date_time_ID,
ymin = mean - sd,
ymax = mean + sd,
fill = "BloomSail"
),
alpha = 0.3
) +
geom_point(aes(x = date_time_ID, y = value, col = sensor)) +
geom_point(data = tm_profiles_ID_long_surface,
aes(x = date_time_ID, y = mean, col = "BloomSail")) +
geom_line(data = tm_profiles_ID_long_surface,
aes(x = date_time_ID, y = mean, col = "BloomSail")) +
facet_grid(var ~ ., scales = "free_y") +
scale_color_brewer(palette = "Set1") +
scale_fill_brewer(palette = "Set1", name = "+/- SD") +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
theme(axis.title.x = element_blank())
4.1.5 Missing observations
The observational gaps in the Finnmaid SST and CT* time series were filled with:
- two BloomSail observations
- an interpolated Finnmaid value to match the starting date
The time series was restricted to the period where BloomSail observations are available.
# create data frame with start dates
tm_start_date <- tm_profiles_ID_long_surface %>%
filter(ID %in% c("180705"),
var %in% c("tem", "CT_star")) %>%
select(date_time_ID, ID, var) %>%
mutate(sensor = "interpolated")
# add start dates to Finnmaid data
fm_tm_ID <- full_join(fm_ID, tm_start_date) %>%
arrange(date_time_ID) %>%
filter(var %in% c("tem", "CT_star"))
# interpolate Finnmaid to BloomSail start date
fm_tm_ID <- fm_tm_ID %>%
group_by(var) %>%
mutate(value = approxfun(date_time_ID, value)(date_time_ID)) %>%
ungroup()
rm(tm_start_date)# subset BloomSail data in Finnmaid gap
tm_gap <- tm_profiles_ID_long_surface %>%
filter(ID %in% c("180718", "180723"),
var %in% c("tem", "CT_star")) %>%
select(date_time_ID, ID, var, value = mean) %>%
mutate(sensor = "BloomSail")
# add data to fill Finnmaid gap
fm_tm_ID <- full_join(fm_tm_ID, tm_gap) %>%
arrange(date_time_ID) %>%
select(-sd) %>%
filter(var %in% c("tem", "CT_star")) %>%
mutate(
period = "BloomSail",
period = if_else(date_time_ID < fixed_values$start, "pre-BloomSail", period),
period = if_else(date_time_ID > fixed_values$end, "post-BloomSail", period)
)
# filter only Finnmaid data within BloomSail period
fm_tm_ID <- fm_tm_ID %>%
filter(period == "BloomSail") %>%
select(-period)
rm(fm_ID, fm, tm_gap, tm_profiles_ID_long_surface, tm_profiles, fixed_values)4.1.6 Final time series
fm_tm_ID %>%
ggplot() +
geom_path(aes(date_time_ID, value)) +
geom_point(aes(date_time_ID, value, col = sensor)) +
facet_grid(var ~ ., scales = "free_y") +
scale_color_brewer(palette = "Set1") +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
theme(axis.title.x = element_blank())
5 Merge all data sets
5.1 Merge fm and gt
# convert to wide format
fm_tm_ID_wide <- fm_tm_ID %>%
filter(var %in% c("CT_star")) %>%
select(date_time_ID, var, sensor, value) %>%
pivot_wider(values_from = value, names_from = var)
# extend surface data with depth grid
fm_gt <- expand_grid(fm_tm_ID_wide, dep = unique(gt_3d_int$dep))
# join Finnmaid and GETM data
fm_gt <- full_join(fm_gt,
gt_3d_int %>% rename(date_time_ID = date_time)) %>%
arrange(date_time_ID)
rm(fm_tm_ID_wide, fm_tm_ID, gt_3d_int)5.2 Interpolate gt time stamp to fm
GETM data are interpolated to the time of Finnmaid observations.
fm_gt <- fm_gt %>%
arrange(date_time_ID) %>%
group_by(dep) %>%
mutate(
tem = approxfun(date_time_ID, tem)(date_time_ID),
sal = approxfun(date_time_ID, sal)(date_time_ID)
) %>%
ungroup() %>%
arrange(dep) %>%
filter(!is.na(CT_star))5.3 Bind tm and fm_gt
Here, we merge the in-situ sensor data from SV Tina V with the Finnmaid+GETM data set, in order to perform following computations only once.
# subset relevant columns and assign source label
tm_profiles_ID <- tm_profiles_ID %>%
select(-c(ID, pCO2)) %>%
mutate(source = "tm",
sensor = "BloomSail")
fm_gt <- fm_gt %>%
mutate(source = "fm")
# Merge data sets
tm_fm_gt <- bind_rows(tm_profiles_ID, fm_gt)
rm(fm_gt, tm_profiles_ID)5.4 Comparison
5.4.1 Surface time series
# convert to long format
tm_fm_gt_long <- tm_fm_gt %>%
pivot_longer(sal:CT_star, values_to = "value", names_to = "var")
tm_fm_gt_long %>%
filter(dep == 3.5) %>%
ggplot(aes(date_time_ID, value, col = source)) +
geom_path() +
geom_point() +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
facet_grid(var ~ ., scales = "free_y") +
labs(title = "Time series at 3.5 m") +
theme(axis.title.x = element_blank())
5.4.2 Hovmoeller temperature
bin <- 2
tm_fm_gt %>%
ggplot(aes(date_time_ID, dep, z = tem)) +
geom_contour_fill(breaks = MakeBreaks(bin)) +
geom_vline(aes(xintercept = date_time_ID),
col = "white",
linetype = "1f") +
scale_fill_viridis_c(
name = "tem",
option = "B",
guide = "colorstrip",
breaks = MakeBreaks(bin)
) +
scale_y_reverse() +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
coord_cartesian(expand = 0) +
theme(axis.title.x = element_blank()) +
facet_grid(source ~ .)
rm(bin)6 Integration depths
6.1 MLD
6.1.1 Density calculation
tm_fm_gt <- tm_fm_gt %>%
mutate(rho = swSigma(
salinity = sal,
temperature = tem,
pressure = dep / 10
))6.1.2 Hovmoeller density
bin <- 0.5
tm_fm_gt %>%
ggplot() +
geom_contour_fill(aes(date_time_ID, dep, z = rho),
breaks = MakeBreaks(bin)) +
geom_vline(aes(xintercept = date_time_ID),
col = "white",
linetype = "1f") +
scale_fill_viridis_c(
name = "rho",
option = "B",
guide = "colorstrip",
breaks = MakeBreaks(bin),
direction = -1
) +
scale_y_reverse() +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
coord_cartesian(expand = 0) +
theme(axis.title.x = element_blank()) +
facet_grid(source ~ .)
rm(bin)6.1.3 MLD calculation
tm_fm_gt_MLD <- expand_grid(tm_fm_gt, rho_lim = parameters$rho_lim_integration_depths)
tm_fm_gt_MLD <- tm_fm_gt_MLD %>%
arrange(dep) %>%
group_by(date_time_ID, source, rho_lim) %>%
mutate(d_rho = rho - first(rho)) %>%
filter(d_rho > rho_lim) %>%
summarise(MLD = min(dep)) %>%
ungroup() %>%
mutate(rho_lim = as.factor(rho_lim))6.1.4 Hovmoeller MLD
bin <- 2
tm_fm_gt %>%
ggplot() +
geom_contour_fill(aes(date_time_ID, dep, z = tem),
breaks = MakeBreaks(bin)) +
geom_path(data = tm_fm_gt_MLD, aes(date_time_ID, MLD, col = rho_lim)) +
scale_fill_gradient(
name = "Tem (°C)",
guide = "colorstrip",
breaks = MakeBreaks(bin),
high = "grey80",
low = "grey5"
) +
scale_color_viridis_d() +
scale_y_reverse() +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d") +
coord_cartesian(expand = 0) +
labs(y = "Depth (m)") +
theme(axis.title.x = element_blank()) +
facet_grid(source ~ .)
rm(bin)6.1.5 Select rho criterion
MLD <- tm_fm_gt_MLD %>%
filter(rho_lim == parameters$rho_lim) %>%
select(-rho_lim) %>%
rename(i_dep = MLD) %>%
mutate(i_method = "MLD", i_res = "daily")
rm(tm_fm_gt_MLD)6.1.6 Mean MLD
# Filter data before temperature peak, and calculate mean
MLD_mean <- MLD %>%
filter(date_time_ID <= date_tem_max) %>%
group_by(source) %>%
summarise(MLD_mean = mean(i_dep, na.rm = TRUE),
MLD_sd = sd(i_dep, na.rm = TRUE)) %>%
ungroup()
MLD_mean# A tibble: 2 x 3
source MLD_mean MLD_sd
<chr> <dbl> <dbl>
1 fm 5.5 1.18
2 tm 6 1.87# format mean MLD data frame
MLD_mean <- MLD_mean %>%
select(-MLD_sd) %>%
rename(i_dep = MLD_mean) %>%
mutate(i_method = "MLD", i_res = "mean")
MLD_dates <- MLD %>%
select(source, date_time_ID)
MLD_mean <- full_join(MLD_dates, MLD_mean)
MLD <- full_join(MLD, MLD_mean)
rm(MLD_mean)6.2 Temperature penetration depth
6.2.1 TPD calculation
tm_fm_gt_long <- tm_fm_gt %>%
select(-c(sal)) %>%
pivot_longer(c("tem", "CT_star"),
values_to = "value",
names_to = "var") %>%
group_by(source, var, dep) %>%
arrange(date_time_ID) %>%
mutate(
date_time_ID_diff = as.numeric(date_time_ID - lag(date_time_ID)),
value_diff = value - lag(value, default = first(value)),
value_diff_daily = value_diff / date_time_ID_diff,
value_cum = cumsum(value_diff)
) %>%
ungroup()
# select only temperature data
tm_fm_gt_long <- tm_fm_gt_long %>%
filter(var == "tem") %>%
select(-var)6.2.2 Cumulative temperature profile
Please note that the cumulative temperature profile of GETM shows a deep maximum below 20m, which must be attributed to water mass exchange rather than surface warming to radiation or heat uptake, which we want to capture here. Therefore, the integration depth of the GETM data was manually restricted to 19m.
tm_fm_gt_long %>%
filter(date_time_ID == date_CT_min) %>%
arrange(dep) %>%
ggplot(aes(value_cum, dep)) +
geom_vline(xintercept = 0) +
geom_hline(yintercept = parameters$getm_i_dep) +
geom_point() +
geom_path() +
scale_y_reverse() +
labs(x = "Cumulative tem change",
title = as.Date(date_CT_min)) +
theme(legend.position = "left") +
facet_grid(. ~ source, scales = "free_x")
Profiles of cumulative temperature changes from the GETM model (label fm) and as measured in the field (label tm).
6.2.3 Calculate cumulative changes
# subset data at CT* minimum
tm_fm_gt_long_day <- tm_fm_gt_long %>%
filter(date_time_ID == date_CT_min) %>%
mutate(
value_cum = if_else(value_cum < 0,
NaN, value_cum),
value_cum = if_else(source == "fm" &
dep > parameters$getm_i_dep,
NaN, value_cum)
)
# integrate cumulative changes
tm_fm_gt_long_day_dep <- tm_fm_gt_long_day %>%
select(source, dep, value_cum) %>%
group_by(source) %>%
arrange(dep) %>%
mutate(
value_cum_i = sum(value_cum, na.rm = TRUE),
value_cum_dep = cumsum(value_cum),
value_cum_i_rel = value_cum_dep / value_cum_i * 100
) %>%
ungroup()
# extract integrated cumulative value
value_cum <- tm_fm_gt_long_day_dep %>%
group_by(source) %>%
summarise(value_cum_i = mean(value_cum_i)) %>%
ungroup()
# extract surface cumulative value
value_surface <- tm_fm_gt_long_day %>%
select(source, dep, value_cum) %>%
filter(dep < parameters$surface_dep) %>%
group_by(source) %>%
summarise(value_surface = mean(value_cum)) %>%
ungroup()
# calculate TPD
TPD <- full_join(value_cum, value_surface)
TPD <- TPD %>%
mutate(i_dep = value_cum_i / value_surface)
rm(value_cum, value_surface)6.2.4 Cumulative profiles July 24
p_tm_fm_gt_long <- tm_fm_gt_long_day %>%
arrange(dep) %>%
ggplot(aes(value_cum, dep)) +
geom_hline(aes(yintercept = parameters$i_dep_lim, col = "fixed\nintegration\ndepth")) +
geom_hline(data = TPD, aes(yintercept = i_dep, col = "TPD\nestimate")) +
geom_vline(xintercept = 0) +
geom_point() +
geom_path() +
scale_y_reverse() +
scale_color_brewer(palette = "Dark2", guide = FALSE) +
labs(x = "Cumulative change") +
theme(legend.position = "left") +
facet_wrap(. ~ source, ncol = 1, scales = "free_x")
p_tm_fm_gt_long_rel <- tm_fm_gt_long_day_dep %>%
ggplot(aes(value_cum_i_rel, dep)) +
geom_hline(aes(yintercept = parameters$i_dep_lim, col = "fixed\nintegration\ndepth")) +
geom_hline(data = TPD, aes(yintercept = i_dep, col = "TPD\nestimate")) +
geom_vline(xintercept = 90) +
geom_point() +
geom_line() +
scale_y_reverse(limits = c(25, 0)) +
scale_color_brewer(palette = "Dark2", name = "") +
scale_x_continuous(limits = c(0, NA)) +
labs(x = "Relative contribution (%)") +
facet_wrap(. ~ source, ncol = 1, scales = "free_x") +
theme(axis.title.y = element_blank())
p_tm_fm_gt_long + p_tm_fm_gt_long_rel
rm(
tm_fm_gt_long_day,
tm_fm_gt_long_day_dep,
p_tm_fm_gt_long,
p_tm_fm_gt_long_rel
)
TPD_cum <- TPD
rm(TPD)6.2.5 Calculate incremental TPD
# incremental changes of surface values
diff_surface <- tm_fm_gt_long %>%
filter(dep < parameters$surface_dep) %>%
group_by(date_time_ID, source) %>%
summarise(value_diff_surface = mean(value_diff, na.rm = TRUE)) %>%
ungroup() %>%
mutate(value_diff_surface = if_else(value_diff_surface < 0,
NaN, value_diff_surface))
tm_fm_gt_long <- full_join(tm_fm_gt_long, diff_surface)
rm(diff_surface)
# calculate penetration depths
TPD <- tm_fm_gt_long %>%
mutate(
value_diff = if_else(value_diff < 0,
NaN, value_diff),
value_diff = if_else(source == "fm" & dep > 19,
NaN, value_diff)
) %>%
group_by(date_time_ID, source) %>%
summarise(
value_diff_int = sum(value_diff, na.rm = TRUE),
value_diff_surface = mean(value_diff_surface, na.rm = TRUE)
) %>%
ungroup() %>%
mutate(i_dep = value_diff_int / value_diff_surface)
# calculate mean TPD across bloom period
TPD_mean <- TPD %>%
filter(date_time_ID <= date_CT_min) %>%
group_by(source) %>%
summarise(i_dep_sd = sd(i_dep, na.rm = TRUE),
i_dep = mean(i_dep, na.rm = TRUE)) %>%
ungroup()
p_surface <- TPD %>%
ggplot(aes(date_time_ID, value_diff_surface, col = source)) +
geom_hline(yintercept = 0) +
geom_line() +
geom_point() +
scale_y_reverse(name = "Change surface value") +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank())
p_integrated <- TPD %>%
ggplot(aes(date_time_ID, value_diff_int, col = source)) +
geom_hline(yintercept = 0) +
geom_line() +
geom_point() +
scale_y_reverse(name = "Change integrated value") +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank())
p_TPD <- TPD %>%
ggplot(aes(date_time_ID, i_dep, col = source)) +
geom_hline(yintercept = 0) +
geom_hline(data = TPD_mean,
aes(
yintercept = i_dep,
col = source,
linetype = "mean"
)) +
geom_line(aes(linetype = "cruise")) +
geom_point() +
scale_y_reverse(name = "Penetration depth (m)", breaks = seq(0, 20, 5)) +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
scale_color_brewer(palette = "Set1", direction = -1) +
theme(axis.title.x = element_blank(),
legend.title = element_blank())
p_surface + p_integrated + p_TPD +
plot_layout(ncol = 1)
TPD_mean# A tibble: 2 x 3
source i_dep_sd i_dep
<chr> <dbl> <dbl>
1 fm 2.31 11.4
2 tm 2.46 12.3rm(p_surface, p_integrated, p_TPD)TPD <- TPD %>%
select(date_time_ID, source, i_dep) %>%
mutate(i_method = "TPD", i_res = "daily") %>%
filter(date_time_ID < date_tem_max) %>%
mutate(i_dep = if_else(is.na(i_dep), 0, i_dep))
TPD_cum <- TPD_cum %>%
select(source, i_dep) %>%
mutate(i_method = "TPD", i_res = "cumulative")
TPD_cum <- full_join(MLD_dates, TPD_cum)
TPD_mean <- TPD_mean %>%
select(source, i_dep) %>%
mutate(i_method = "TPD", i_res = "mean")
TPD_mean <- full_join(MLD_dates, TPD_mean)
TPD <- full_join(TPD, TPD_cum)
TPD <- full_join(TPD, TPD_mean)
rm(TPD_cum, TPD_mean)i_dep <- full_join(MLD, TPD)
rm(MLD, TPD)bin <- 2
CPD <- CPD %>%
mutate(source = "tm")
CPD <- CPD %>%
mutate(source = factor(source, c("tm", "fm"))) %>%
mutate(source = fct_recode(
source,
`SOOP Finnmaid + GETM model` = "fm",
`SV Tina V (surface only)` = "tm"
))
i_dep <- i_dep %>%
mutate(source = factor(source, c("tm", "fm"))) %>%
mutate(source = fct_recode(
source,
`SOOP Finnmaid + GETM model` = "fm",
`SV Tina V (surface only)` = "tm"
))
tm_fm_gt <- tm_fm_gt %>%
mutate(source = factor(source, c("tm", "fm"))) %>%
mutate(source = fct_recode(
source,
`SOOP Finnmaid + GETM model` = "fm",
`SV Tina V (surface only)` = "tm"
))
p_hov_dep <-
tm_fm_gt %>%
ggplot() +
geom_contour_fill(aes(date_time_ID, dep, z = tem),
breaks = MakeBreaks(bin),
col = "black",
size = 0.1) +
geom_path(data = i_dep %>% filter(i_res == "daily" & i_dep != 0),
aes(date_time_ID, i_dep, col = i_method)) +
scale_fill_gradient(
name = "Temperature\n(\u00B0C)",
guide = "colorstrip",
breaks = MakeBreaks(bin),
high = "grey90",
low = "grey20"
) +
guides(fill = guide_colorsteps(barheight = unit(35, "mm"),
barwidth = unit(4, "mm"),
frame.colour = "black",
ticks = TRUE,
ticks.colour = "black")) +
scale_color_discrete(name = "Reconstruction", guide = FALSE) +
scale_y_reverse() +
scale_x_datetime(date_breaks = "week",
date_labels = "%b %d",
sec.axis = dup_axis()) +
coord_cartesian(expand = 0) +
labs(y = expression(atop(Depth, (m)))) +
theme(
axis.title.x = element_blank(),
axis.text.x = element_blank(),
strip.background = element_blank(),
strip.text.x = element_blank(),
axis.text.x.top = element_blank(),
plot.margin = margin(0, 0, 0, 0, "cm")
) +
facet_wrap( ~ source)
p_hov_dep
rm(bin)7 Surface obs + integration depths
tm_fm_gt_surface <- tm_fm_gt %>%
filter(dep < parameters$surface_dep) %>%
select(source, date_time_ID, sensor, CT_star) %>%
group_by(source, date_time_ID, sensor) %>%
summarise(CT_star = mean(CT_star, na.rm = TRUE)) %>%
ungroup()
tm_fm_gt_surface <- tm_fm_gt_surface %>%
group_by(source) %>%
arrange(date_time_ID) %>%
mutate(
date_time_ID_diff = as.numeric(date_time_ID - lag(date_time_ID)),
CT_star_diff = CT_star - lag(CT_star, default = first(CT_star)),
CT_star_cum = cumsum(CT_star_diff)
) %>%
ungroup()iCT <- full_join(tm_fm_gt_surface, i_dep)
rm(tm_fm_gt_surface)8 iCT
iCT <- iCT %>%
mutate(CT_i_diff = CT_star_diff * i_dep)
iCT <- iCT %>%
group_by(source, i_method, i_res) %>%
arrange(date_time_ID) %>%
mutate(CT_star_i_cum = cumsum(CT_i_diff/1000)) %>%
ungroup()tm_NCP_cum <- read_csv(here::here("data/intermediate/_merged_data_files/CT_dynamics",
"tm_NCP_cum.csv"))tm_NCP_cum_flux <- tm_NCP_cum %>%
select(date_time, flux_cum)
tm_NCP_cum_flux <-
expand_grid(
tm_NCP_cum_flux,
source = unique(iCT$source),
i_method = unique(iCT$i_method),
i_res = unique(iCT$i_res)
)
NCP_flux <- full_join(iCT %>% rename(date_time = date_time_ID),
tm_NCP_cum_flux) %>%
arrange(date_time)
# linear interpolation of cumulative changes to frequency of the flux estimates estimates
NCP_flux_int <- NCP_flux %>%
filter(!(i_method == "MLD" & i_res == "cumulative")) %>%
group_by(source, i_method, i_res) %>%
mutate(
CT_star_i_cum = approxfun(date_time, CT_star_i_cum)(date_time),
flux_cum = approxfun(date_time, flux_cum)(date_time)
) %>%
fill(flux_cum) %>%
mutate(CT_star_i_flux_cum = CT_star_i_cum + flux_cum) %>%
ungroup()iCT <- iCT %>%
mutate(sensor = if_else(sensor == "BloomSail", sensor, "VOS"))
p_CT_star <- iCT %>%
ggplot() +
geom_path(aes(date_time_ID, CT_star)) +
geom_point(aes(date_time_ID, CT_star, fill = sensor), shape = 21) +
scale_fill_manual(values = c("white", "black"),
guide = FALSE) +
scale_x_datetime(breaks = "week",
date_labels = "%d %b",
expand = c(0, 0)) +
facet_wrap(~ source) +
labs(y = expression(atop(paste(C[T], "*"), (mu * mol ~ kg ^ {
-1
})))) +
theme(
axis.title.x = element_blank(),
axis.text.x = element_blank(),
plot.margin = margin(0, 0, 0, 0, "cm")
)
p_iCT <- iCT %>%
ggplot() +
geom_hline(yintercept = 0) +
geom_path(data = tm_NCP_cum, aes(date_time, CT_star_i_cum), col = "black") +
geom_path(aes(date_time_ID, CT_star_i_cum, col = i_method, linetype = i_res)) +
scale_color_discrete(name = "Reconstruction") +
scale_x_datetime(
breaks = "week",
date_labels = "%d %b",
sec.axis = dup_axis(),
expand = c(0, 0)
) +
scale_linetype(name = "Resolution") +
facet_wrap( ~ source) +
labs(y = expression(atop(Integrated ~ nC[T], (mol ~ m ^ {
-2
})))) +
guides(color = guide_legend(order = 1)) +
theme(
axis.title.x = element_blank(),
strip.background = element_blank(),
strip.text.x = element_blank(),
axis.text.x.top = element_blank()
)
p_CT_star / p_hov_dep / p_iCT
NCP_flux <- NCP_flux %>%
mutate(i_res = factor(i_res, c("mean", "cumulative", "daily")))
p_NCP <- NCP_flux_int %>%
filter(i_res %in% c("daily")) %>%
ggplot() +
geom_hline(yintercept = 0) +
geom_path(data = tm_NCP_cum,
aes(date_time, CT_star_i_flux_mix_cum, linetype = "best \U2013 guess"),
col = "black") +
geom_path(aes(
date_time,
CT_star_i_flux_cum,
col = i_method,
linetype = "reconstruction"
)) +
scale_color_discrete(name = "Integration depth") +
scale_x_datetime(
breaks = "week",
date_labels = "%d %b",
sec.axis = dup_axis(),
expand = c(0, 0)
) +
scale_linetype_manual(name = "NCP estimate",
values = c(2,1)) +
facet_wrap( ~ source) +
labs(y = expression(atop(NCP, (mol ~ m ^ {
-2
})))) +
guides(color = guide_legend(order = 1)) +
theme(
axis.title.x = element_blank(),
strip.background = element_blank(),
strip.text.x = element_blank(),
axis.text.x.top = element_blank(),
plot.margin = margin(0, 0, 0, 0, "cm")
)
p_CT_star / p_hov_dep / p_NCP +
plot_annotation(tag_levels = 'a')
ggsave(
here::here(
"output/Plots/Figures_publication/article",
"Fig_6.pdf"
),
width = 160,
height = 155,
dpi = 300,
units = "mm"
)
ggsave(
here::here(
"output/Plots/Figures_publication/article",
"Fig_6.png"
),
width = 160,
height = 155,
dpi = 300,
units = "mm"
)
sessionInfo()R version 4.0.3 (2020-10-10)
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_0.9.0 lubridate_1.7.9.2 patchwork_1.1.1 seacarb_3.2.14
[5] oce_1.2-0 gsw_1.0-5 testthat_3.0.1 ncdf4_1.17
[9] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4
[13] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.3
[17] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 viridisLite_0.3.0 here_1.0.1
[5] modelr_0.1.8 assertthat_0.2.1 highr_0.8 cellranger_1.1.0
[9] yaml_2.2.1 pillar_1.4.7 backports_1.2.1 glue_1.4.2
[13] digest_0.6.27 RColorBrewer_1.1-2 promises_1.1.1 checkmate_2.0.0
[17] rvest_0.3.6 colorspace_2.0-0 plyr_1.8.6 htmltools_0.5.0
[21] httpuv_1.5.4 pkgconfig_2.0.3 broom_0.7.3 haven_2.3.1
[25] scales_1.1.1 whisker_0.4 later_1.1.0.1 git2r_0.27.1
[29] generics_0.1.0 farver_2.0.3 ellipsis_0.3.1 withr_2.3.0
[33] cli_2.2.0 magrittr_2.0.1 crayon_1.3.4 readxl_1.3.1
[37] evaluate_0.14 ps_1.5.0 fs_1.5.0 fansi_0.4.1
[41] xml2_1.3.2 tools_4.0.3 data.table_1.13.6 hms_0.5.3
[45] lifecycle_0.2.0 munsell_0.5.0 reprex_0.3.0 isoband_0.2.3
[49] compiler_4.0.3 rlang_0.4.10 grid_4.0.3 rstudioapi_0.13
[53] labeling_0.4.2 rmarkdown_2.6 gtable_0.3.0 DBI_1.1.0
[57] R6_2.5.0 knitr_1.30 utf8_1.1.4 rprojroot_2.0.2
[61] stringi_1.5.3 Rcpp_1.0.5 vctrs_0.3.6 dbplyr_2.0.0
[65] tidyselect_1.1.0 xfun_0.19