MLD
Jens Daniel Müller
27 April, 2020
Last updated: 2020-04-27
Checks: 7 0
Knit directory: BloomSail/
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| File | Version | Author | Date | Message |
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| Rmd | f73f073 | jens-daniel-mueller | 2020-04-27 | removed Date-ID column causing error |
| html | 472c2b4 | jens-daniel-mueller | 2020-04-21 | Build site. |
| Rmd | a82b4fe | jens-daniel-mueller | 2020-04-21 | try rebuild all html |
| html | f8fcf50 | jens-daniel-mueller | 2020-04-19 | created pub figures for time series |
| html | dc275fe | jens-daniel-mueller | 2020-04-14 | Build site. |
| Rmd | 2e7d3a5 | jens-daniel-mueller | 2020-04-14 | temperature penetration depth eval TRUE |
| html | 87658c3 | jens-daniel-mueller | 2020-04-14 | Build site. |
| Rmd | 5c96a65 | jens-daniel-mueller | 2020-04-14 | temperature penetration depth |
| html | f4a27b8 | jens-daniel-mueller | 2020-04-01 | Build site. |
| Rmd | b1613b7 | jens-daniel-mueller | 2020-04-01 | re-calculated MLD, renamed objects and structured site |
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| Rmd | 2ebefdf | jens-daniel-mueller | 2020-03-31 | Finalized Baltic surface reconstruction |
| html | 6302994 | jens-daniel-mueller | 2020-03-31 | Build site. |
| Rmd | 50ab313 | jens-daniel-mueller | 2020-03-31 | implemented temperature reconstruction |
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| Rmd | d8120b3 | jens-daniel-mueller | 2020-03-30 | reconstruction BloomSail surface started, merging MLD and DT approach |
| Rmd | a135643 | jens-daniel-mueller | 2020-03-20 | renamed |
| html | a025f62 | jens-daniel-mueller | 2020-03-20 | Build site. |
| Rmd | 39c69a3 | jens-daniel-mueller | 2020-03-20 | knit BloomSail surface |
library(tidyverse)
library(seacarb)
library(oce)
library(marelac)
library(patchwork)
library(metR)1 Approach
In order to test how (and how well) the depth-integrated CT estimates can be reproduced if only surface CO2 data were available, the BloomSail observations were restricted to those made in surface water and two reconstruction approaches were tested:
- MLD: Integration of surface observation across the MLD, assuming homogenious vertical patterns
- Temperature: Vertical reconstruction of incremental CT changes based on profiles of incremental changes in temperature
2 Sensor data
1m gridded, downcast profiles, from which CO2 data other than 3.5 m water depth were removed, were used.
ts_profiles_ID <-
read_csv(here::here("Data/_merged_data_files", "ts_profiles_ID_long_cum_MLD.csv"))
ts_profiles_ID <- ts_profiles_ID %>%
select(ID, date_time_ID, dep, CT = value, CT_diff = value_diff, CT_cum = value_cum, sign, rho_lim, MLD)
ts_profiles_ID <- ts_profiles_ID %>%
mutate(CT = if_else(dep == 3.5, CT, NaN),
rho_lim = as.factor(rho_lim))3 MLD approach
MLD calculation was previously described in the CT dynamics chapter.
3.1 Timeseries
For comparison to MLD, the effective penetration depth of NCP, zeff, was calculated as the ratio of the inremental, depth-integrated change of CT, divided by the change in surface CT, for all cases where the change in surface CT was negative.
ts_profiles_ID_surface <- ts_profiles_ID %>%
filter(sign=="neg",
rho_lim == "0.5",
dep == 3.5) %>%
group_by(ID, date_time_ID) %>%
summarise(CT_diff_surf = mean(CT_diff, na.rm = TRUE)) %>%
ungroup()
ts_profiles_ID_i <- ts_profiles_ID %>%
filter(sign=="neg",
rho_lim == "0.5") %>%
group_by(ID, date_time_ID) %>%
summarise(CT_diff_i = sum(CT_diff, na.rm = TRUE))
zeff <- inner_join(ts_profiles_ID_surface, ts_profiles_ID_i)
rm(ts_profiles_ID_surface, ts_profiles_ID_i)
zeff <- zeff %>%
mutate(zeff = CT_diff_i / CT_diff_surf)ts_profiles_ID %>%
ggplot()+
geom_hline(yintercept = 0)+
geom_line(data = zeff, aes(date_time_ID, zeff, linetype="zeff"))+
geom_line(aes(date_time_ID, MLD, col=rho_lim, linetype="MLD"))+
scale_y_reverse()+
scale_color_viridis_d(name="Rho limit")+
scale_linetype(name="Estimate")+
labs(y="Depth (m)")+
theme(axis.title.x = element_blank())
rm(zeff)3.2 iCT calculation
Integrated CT depletion was calculated as the product of observed incremental CT changes in surface waters and the respective mixed layer depth.
ts_profiles_ID_surface <- ts_profiles_ID %>%
filter(dep==3.5) %>%
group_by(rho_lim) %>%
arrange(date_time_ID) %>%
mutate(iCT_diff = CT_diff * MLD / 1000,
iCT_cum = cumsum(replace_na(iCT_diff, 0))) %>%
ungroup()3.3 Incremental and cumulative timeseries
Total incremental and cumulative CT changes inbetween cruise dates were calculated.
p_iCT <- ts_profiles_ID_surface %>%
ggplot(aes(date_time_ID, iCT_diff, fill= rho_lim))+
geom_hline(yintercept = 0)+
geom_col(col="black", position = "dodge")+
scale_y_continuous(breaks = seq(-100, 100, 0.2))+
scale_fill_viridis_d()+
labs(y="integrated CT changes [mol/m2]")+
theme(axis.title.x = element_blank())
p_iCT_cum <- ts_profiles_ID_surface %>%
ggplot(aes(date_time_ID, iCT_cum,
col=rho_lim))+
geom_line()+
geom_hline(yintercept = 0)+
scale_color_viridis_d()+
scale_y_continuous(breaks = seq(-100, 100, 0.2))+
theme(strip.background = element_blank(),
strip.text = element_blank())+
labs(y="integrated, cumulative CT changes [mol/m2]", x="date")
(p_iCT / p_iCT_cum)+
plot_layout(guides = 'collect')
rm(p_iCT, p_iCT_cum)
rm(ts_profiles_ID, ts_profiles_ID_surface)4 Temperature approach
ts_profiles_ID <-
read_csv(here::here("Data/_merged_data_files", "ts_profiles_ID.csv"))
ts_profiles_ID <- ts_profiles_ID %>%
mutate(CT = if_else(dep == 3.5, CT, NaN),
ID = as.factor(ID)) %>%
select(-date_ID)4.1 CT vs temperature
As primary production (negative changes in CT) and increase in seawater temperature have a common driver (light), the relation between both changes was investigated.
ts_profiles_ID_diff <- ts_profiles_ID %>%
drop_na() %>%
arrange(date_time_ID) %>%
mutate(CT_diff = CT - lag(CT, default = first(CT)),
tem_diff = tem - lag(tem, default = first(tem)),
factor = CT_diff / tem_diff,
factor = if_else(is.na(factor), 0, factor))
ts_profiles_ID_diff %>%
ggplot(aes(tem_diff, CT_diff))+
geom_hline(yintercept = 0)+
geom_vline(xintercept = 0)+
geom_path()+
geom_point()
4.2 Reconstruction of CT dynamics
The ratio of the incremental change of CT with temperature at the seasurface was applied to calculate the CT in other water depth based on the known change in temperature.
ts_profiles_ID_diff <- ts_profiles_ID_diff %>%
select(ID, factor)
ts_profiles_ID <- full_join(ts_profiles_ID, ts_profiles_ID_diff)
rm(ts_profiles_ID_diff)
ts_profiles_ID <- ts_profiles_ID %>%
arrange(date_time_ID) %>%
group_by(dep) %>%
mutate(tem_diff = tem - lag(tem, default = first(tem))) %>%
ungroup()
ts_profiles_ID <- ts_profiles_ID %>%
mutate(CT_diff = tem_diff * factor) %>%
select(-factor)The reconstructed incremental changes are added up to derive cummulative CT changes throughout the water column.
ts_profiles_ID_long <- ts_profiles_ID %>%
select(ID, date_time_ID, dep, tem = tem_diff, CT = CT_diff) %>%
pivot_longer(4:5, names_to = "var", values_to = "value_diff") %>%
group_by(dep, var) %>%
arrange(date_time_ID) %>%
mutate(date_time_ID_diff = as.numeric(date_time_ID - lag(date_time_ID)),
date_time_ID_ref = date_time_ID - (date_time_ID - lag(date_time_ID))/2,
value_diff_daily = value_diff / date_time_ID_diff,
value_cum = cumsum(value_diff)) %>%
ungroup()4.3 Profiles of incremental changes
Changes of seawater parameters at each depth were reconstructed from one cruise day to the next and divided by the number of days inbetween.
ts_profiles_ID_long %>%
arrange(dep) %>%
ggplot(aes(value_diff, dep, col=ID))+
geom_vline(xintercept = 0)+
geom_point()+
geom_path()+
scale_y_reverse()+
scale_color_viridis_d()+
facet_wrap(~var, scales = "free_x")+
labs(x="Change of value inbetween cruises per day")
4.4 Profiles of cumulative changes
Cumulative changes of seawater parameters were calculated at each depth relative to the first cruise day on July 5.
ts_profiles_ID_long %>%
arrange(dep) %>%
ggplot(aes(value_cum, dep, col=ID))+
geom_vline(xintercept = 0)+
geom_point()+
geom_path()+
scale_y_reverse()+
scale_color_viridis_d()+
labs(x="Cumulative change of value")+
facet_wrap(~var, scales = "free_x")
4.5 Hovmoeller plots
Hoevmoeller plots were generated for the reconstructed daily and cumulative changes in CT. Absolute values are not reproducible with this approach. Furthermore, it meets our expectations
4.5.1 Daily changes
bin_CT <- 2.5
ts_profiles_ID_long %>%
filter(var == "CT") %>%
ggplot()+
geom_contour_fill(aes(x=date_time_ID_ref, y=dep, z=value_diff_daily),
breaks = MakeBreaks(bin_CT),
col="black")+
geom_point(aes(x=date_time_ID, y=c(24.5)), size=3, shape=24, fill="white")+
scale_fill_divergent(breaks = MakeBreaks(bin_CT),
guide = "colorstrip",
name="CT (µmol/kg)")+
scale_y_reverse()+
theme_bw()+
labs(y="Depth (m)")+
coord_cartesian(expand = 0)+
theme(axis.title.x = element_blank(),
axis.text.x = element_blank())
rm(bin_CT)4.5.2 Cumulative changes
bin_CT <- 20
ts_profiles_ID_long %>%
filter(var == "CT") %>%
ggplot()+
geom_contour_fill(aes(x=date_time_ID, y=dep, z=value_cum),
breaks = MakeBreaks(bin_CT),
col="black")+
geom_point(aes(x=date_time_ID, y=c(24.5)), size=3, shape=24, fill="white")+
scale_fill_divergent(breaks = MakeBreaks(bin_CT),
guide = "colorstrip",
name="CT (µmol/kg)")+
scale_y_reverse()+
theme_bw()+
labs(y="Depth (m)")+
coord_cartesian(expand = 0)+
theme(axis.title.x = element_blank(),
axis.text.x = element_blank())
rm(bin_CT)4.6 Heat penetration depth
As an alternative approach to the integration over the MLD or the reconstruction of CT profiles, we can estimate the mean penetration depth of the warming signal, which was defined the surface change in temperature devided by the integrated change in seawater temperature across depth.
tem_diff_surface <- ts_profiles_ID %>%
filter(dep == 3.5) %>%
select(ID, tem_diff_surface=tem_diff)
ts_profiles_ID <- full_join(ts_profiles_ID, tem_diff_surface)
rm(tem_diff_surface)
tem_depth <- ts_profiles_ID %>%
filter(dep < 18) %>%
group_by(ID, date_time_ID) %>%
summarise(tem_diff_int = sum(tem_diff),
tem_diff_surface = mean(tem_diff_surface),
tem_depth = tem_diff_int/tem_diff_surface) %>%
ungroup()
tem_depth %>%
ggplot(aes(date_time_ID, tem_depth))+
geom_hline(yintercept = 0)+
geom_line()+
geom_point()+
scale_y_reverse()
4.7 iCT time series
Total incremental and cumulative CT changes inbetween cruise dates were calculated for the upper 10 m of the water body.
iCT_10 <- ts_profiles_ID_long %>%
filter(dep < 10,
var == "CT") %>%
select(ID, date_time_ID, date_time_ID_ref, CT_diff=value_diff, CT_cum=value_cum) %>%
group_by(ID, date_time_ID, date_time_ID_ref) %>%
summarise(CT_i_diff = sum(CT_diff)/1000,
CT_i_cum = sum(CT_cum)/1000) %>%
ungroup()
iCT_10 %>%
ggplot()+
#geom_point(data = cruise_dates, aes(date_time_ID, 0), shape=21)+
geom_col(aes(date_time_ID_ref, CT_i_diff),
position = "dodge", alpha=0.3)+
geom_line(aes(date_time_ID, CT_i_cum))+
scale_color_viridis_d(name="Depth limit (m)")+
scale_fill_viridis_d(name="Depth limit (m)")+
labs(y="iCT [mol/m2]", x="")+
theme_bw()
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: i386-w64-mingw32/i386 (32-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_0.6.0 patchwork_1.0.0 marelac_2.1.10 shape_1.4.4
[5] seacarb_3.2.13 oce_1.2-0 gsw_1.0-5 testthat_2.3.2
[9] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.3
[13] readr_1.3.1 tidyr_1.0.2 tibble_3.0.0 ggplot2_3.3.0
[17] tidyverse_1.3.0 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 whisker_0.4 knitr_1.28 xml2_1.3.0
[5] magrittr_1.5 hms_0.5.3 rvest_0.3.5 tidyselect_1.0.0
[9] viridisLite_0.3.0 here_0.1 colorspace_1.4-1 lattice_0.20-41
[13] R6_2.4.1 rlang_0.4.5 fansi_0.4.1 broom_0.5.5
[17] xfun_0.12 dbplyr_1.4.2 modelr_0.1.6 withr_2.1.2
[21] git2r_0.26.1 ellipsis_0.3.0 htmltools_0.4.0 assertthat_0.2.1
[25] rprojroot_1.3-2 digest_0.6.25 lifecycle_0.2.0 haven_2.2.0
[29] rmarkdown_2.1 compiler_3.6.3 cellranger_1.1.0 pillar_1.4.3
[33] scales_1.1.0 backports_1.1.5 generics_0.0.2 lubridate_1.7.4
[37] jsonlite_1.6.1 httpuv_1.5.2 pkgconfig_2.0.3 rstudioapi_0.11
[41] munsell_0.5.0 httr_1.4.1 tools_3.6.3 grid_3.6.3
[45] nlme_3.1-145 data.table_1.12.8 gtable_0.3.0 checkmate_2.0.0
[49] DBI_1.1.0 cli_2.0.2 readxl_1.3.1 yaml_2.2.1
[53] crayon_1.3.4 farver_2.0.3 later_1.0.0 promises_1.1.0
[57] fs_1.4.0 vctrs_0.2.4 glue_1.3.2 evaluate_0.14
[61] labeling_0.3 reprex_0.3.0 stringi_1.4.6