Integrated CDR Efficiency Plots
Victoria Froh & Jens Daniel Müller
07 April, 2025
Last updated: 2025-04-07
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Knit directory: oae_ccs_roms/
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| File | Version | Author | Date | Message |
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| Rmd | 5a5f21a | vgfroh | 2025-04-07 | Final code push |
| html | 91e2272 | vgfroh | 2025-02-19 | Build site. |
| Rmd | a36bcfe | vgfroh | 2025-02-19 | Mixing depth and air-sea co2 flux anlaysis |
| html | dd18a78 | vgfroh | 2025-02-03 | Build site. |
| Rmd | 639b38d | vgfroh | 2025-02-03 | Column integrated plots and hovmoeller plots completed |
| html | ce19057 | vgfroh | 2025-01-05 | Build site. |
| Rmd | 009b735 | vgfroh | 2025-01-05 | Plotted time series of integrated dTA and CDREff data |
#Introduction
Plotting the results of the full-grid integrated time series of dTA, CDR efficiency, and dDIC for each 3 phases and the mean
#loading packages
library(tidyverse)
library(data.table)
library(arrow)
# Path to intermediate computation outputs
path_outputs <- "/net/sea/work/vifroh/oae_ccs_roms_data/original_grid/"
# Path to save practice plots when working on them
path_plots <- "/net/sea/work/vifroh/test_plots/"
# loading in previous saved integrated CDR data
lanina_cdreff_sum <- read_feather(
paste0(path_outputs, "lanina_CDReff_integrated.feather"))
neutral_cdreff_sum <- read_feather(
paste0(path_outputs, "neutral_CDReff_integrated.feather"))
elnino_cdreff_sum <- read_feather(
paste0(path_outputs, "elnino_CDReff_integrated.feather"))# create combined table with "phase" column to identify each of the 3
full_cdreff <- rbindlist(
list(lanina = lanina_cdreff_sum, neutral = neutral_cdreff_sum,
elnino = elnino_cdreff_sum),
idcol = "phase")
# add column for months since oae addition begins for x-axis
full_cdreff <- full_cdreff[, month := seq_len(.N), by = phase]
# computing means
full_cdreff[, ":=" (
dTA_mean = mean(dTA_sum, na.rm = TRUE),
dDIC_mean = mean(dDIC_sum, na.rm = TRUE),
CDReff_mean = mean(CDR_eff, na.rm = TRUE)
), by = month]
# save
# write_feather(full_cdreff, paste0(path_outputs,
# "full_CDReff_integrated.feather"))Integrated Line Plots of 3 Phases
# plotting dTA
ggplot(full_cdreff, aes(x = month, y = dTA_sum/1e10, color = phase)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(0, 19), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_hline(yintercept = 16.7, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated TA' [10\u00B9\u2070 mol]" #, title = "Total Added Alkalinity"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.875, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
3.5.0.
ℹ Please use the `legend.position.inside` argument of `theme()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
# ggsave(paste0(path_plots, "total_dTA_cum.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)
# plotting CDReff
ggplot(full_cdreff, aes(x = month, y = CDR_eff, color = phase)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0, 72),
expand = c(0, 0)) +
scale_y_continuous(limits = c(0, 1), expand = c(0, 0)) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated \u03B7" #, title = "Integrated CDR Efficiency"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.87, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "CDReff_int.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)
# plotting dDIC
ggplot(full_cdreff, aes(x = month, y = dDIC_sum/1e10, color = phase)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(0, 19), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_hline(yintercept = 13.36, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated DIC' [10\u00B9\u2070 mol]" #, title = "Total Change in Dissolved Inorganic Carbon"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.875, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
| Version | Author | Date |
|---|---|---|
| 91e2272 | vgfroh | 2025-02-19 |
# ggsave(paste0(path_plots, "total_dDIC_cum.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)Integrated Line Plots of Means
# to add a shaded ribbon showing the range:
full_cdreff <- full_cdreff[, ':='(
min_TA = min(dTA_sum), max_TA = max(dTA_sum),
min_DIC = min(dDIC_sum), max_DIC = max(dDIC_sum),
min_eff = min(CDR_eff), max_eff = max(CDR_eff)
), by = month]
# plotting dTA
ggplot(full_cdreff, aes(x = month, y = dTA_mean/1e10)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(0, 19), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_hline(yintercept = 16.7, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_ribbon(aes(ymin = min_TA/1e10, ymax = max_TA/1e10), fill = "#A6CEE3", alpha = 0.45) +
geom_line(linewidth = 1) +
labs(x = "Months Since OAE Start",
y = " Mean Integrated TA' [10\u00B9\u2070 mol]" #, title = "Mean Total Added Alkalinity"
) +
theme_bw() +
theme(panel.grid = element_blank(), #legend.position = c(0.9, 0.2),
# legend.text = element_text(size = 12),
# legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 13, color = "black"),
axis.title = element_text(size = 15),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "total_dTA_cum_mean.png"), plot = last_plot(),
# width = 8, height = 4, dpi = 300)
# plotting CDReff
ggplot(full_cdreff, aes(x = month, y = CDReff_mean)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_ribbon(aes(ymin = min_eff, ymax = max_eff), fill = "#A6CEE3", alpha = 0.45) +
geom_line(linewidth = 1) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0, 72),
expand = c(0, 0)) +
scale_y_continuous(limits = c(0, 1), expand = c(0, 0)) +
labs(x = "Months Since OAE Start",
y = "Mean Integrated \u03B7" #, title = "Mean Integrated CDR Efficiency"
) +
theme_bw() +
theme(panel.grid = element_blank(), #legend.position = c(0.9, 0.2),
# legend.text = element_text(size = 12),
# legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 13, color = "black"),
axis.title = element_text(size = 15),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "CDReff_int_mean.png"), plot = last_plot(),
# width = 8, height = 4, dpi = 300)
# plotting dDIC
ggplot(full_cdreff, aes(x = month, y = dDIC_mean/1e10)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(0, 19), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_hline(yintercept = 13.36, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_ribbon(aes(ymin = min_DIC/1e10, ymax = max_DIC/1e10), fill = "#A6CEE3", alpha = 0.45) +
geom_line(linewidth = 1) +
labs(x = "Months Since OAE Start",
y = "Mean Integrated DIC' [10\u00B9\u2070 mol]" #, title = "Mean Total New Dissolved Inorganic Carbon"
) +
theme_bw() +
theme(panel.grid = element_blank(), #legend.position = c(0.9, 0.2),
# legend.text = element_text(size = 12),
# legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 13, color = "black"),
axis.title = element_text(size = 15),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "total_dDIC_cum_mean.png"), plot = last_plot(),
# width = 8, height = 4, dpi = 300)Difference from Mean Plots
# plotting dTA
ggplot(full_cdreff, aes(x = month, y = (dTA_sum - dTA_mean)/1e10, color = phase)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(-1, 1), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
#geom_hline(yintercept = 16.7, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated \u0394TA' [10\u00B9\u2070 mol]" #, title = "Total Added Alkalinity"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.875, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "total_dTA_cum_dfm.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)
# plotting CDReff
ggplot(full_cdreff, aes(x = month, y = CDR_eff - CDReff_mean, color = phase)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0, 72),
expand = c(0, 0)) +
scale_y_continuous(limits = c(-.1, .1), expand = c(0, 0)) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated \u0394\u03B7" #, title = "Integrated CDR Efficiency"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.87, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "CDReff_int_dfm.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)
# plotting dDIC
ggplot(full_cdreff, aes(x = month, y = (dDIC_sum - dDIC_mean)/1e10, color = phase)) +
scale_x_continuous(breaks = seq(6, 72, by = 6), limits = c(0,72),
expand = c(0,0)) +
scale_y_continuous(limits = c(-1, 1), expand = c(0,0)) +
geom_vline(xintercept = 12, linetype = "dashed", color = "grey75", linewidth = 0.6) +
#geom_hline(yintercept = 13.36, linetype = "dashed", color = "black", linewidth = 0.6) +
geom_line(linewidth = 1) +
scale_color_discrete(labels = c("elnino" = "El Niño", "lanina" = "La Niña", "neutral" = "Neutral")
) +
labs(x = "Months Since OAE Start",
y = "Integrated \u0394DIC' [10\u00B9\u2070 mol]" #, title = "Total Change in Dissolved Inorganic Carbon"
) +
theme_bw() +
theme(panel.grid = element_blank(), legend.position = c(0.875, 0.2),
legend.text = element_text(size = 15),
legend.box.background = element_rect(color = "grey80", size = 0.5),
axis.text = element_text(size = 15, color = "black"),
axis.title = element_text(size = 16),
plot.title = element_blank(), legend.title = element_blank(),
axis.ticks = element_line(color = "black", size = 0.5),
axis.ticks.length = unit(0.3, "cm"),
panel.border = element_rect(color = "black", size = 0.5),
plot.margin = margin(15, 15, 15, 15)) +
coord_cartesian(clip = 'off', expand = FALSE)
# ggsave(paste0(path_plots, "total_dDIC_cum_dfm.png"), plot = last_plot(),
# width = 6, height = 4, dpi = 300)
rm(list = ls())
gc() used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1688229 90.2 3260507 174.2 3260507 174.2
Vcells 2981135 22.8 8388608 64.0 6327066 48.3
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: openSUSE Leap 15.6
Matrix products: default
BLAS/LAPACK: /usr/local/OpenBLAS-0.3.28/lib/libopenblas_haswellp-r0.3.28.so; LAPACK version 3.12.0
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
time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] arrow_18.1.0.1 data.table_1.16.2 lubridate_1.9.3 forcats_1.0.0
[5] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[9] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[13] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.9 utf8_1.2.4 generics_0.1.3 stringi_1.8.4
[5] hms_1.1.3 digest_0.6.37 magrittr_2.0.3 timechange_0.3.0
[9] evaluate_1.0.1 grid_4.4.2 fastmap_1.2.0 rprojroot_2.0.4
[13] jsonlite_1.8.9 processx_3.8.4 whisker_0.4.1 ps_1.8.1
[17] promises_1.3.2 httr_1.4.7 fansi_1.0.6 scales_1.3.0
[21] jquerylib_0.1.4 cli_3.6.3 crayon_1.5.3 rlang_1.1.4
[25] bit64_4.5.2 munsell_0.5.1 withr_3.0.2 cachem_1.1.0
[29] yaml_2.3.10 tools_4.4.2 tzdb_0.4.0 colorspace_2.1-1
[33] httpuv_1.6.15 assertthat_0.2.1 vctrs_0.6.5 R6_2.5.1
[37] lifecycle_1.0.4 git2r_0.35.0 bit_4.5.0 fs_1.6.5
[41] pkgconfig_2.0.3 callr_3.7.6 pillar_1.9.0 bslib_0.8.0
[45] later_1.4.1 gtable_0.3.6 glue_1.8.0 Rcpp_1.0.13-1
[49] xfun_0.49 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.49
[53] farver_2.1.2 htmltools_0.5.8.1 labeling_0.4.3 rmarkdown_2.29
[57] compiler_4.4.2 getPass_0.2-4