Analysis of Cant estimates
Jens Daniel Müller
27 August, 2020
Last updated: 2020-08-27
Checks: 7 0
Knit directory: Cant_eMLR/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200707) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version d25e2a1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rproj.user/
Ignored: data/GLODAPv1_1/
Ignored: data/GLODAPv2_2016b_MappedClimatologies/
Ignored: data/GLODAPv2_2020/
Ignored: data/Gruber_2019/
Ignored: data/WOCE/
Ignored: data/World_Ocean_Atlas_2013_Clement/
Ignored: data/World_Ocean_Atlas_2018/
Ignored: data/eMLR/
Ignored: data/mapping/
Ignored: data/pCO2_atmosphere/
Ignored: dump/
Untracked files:
Untracked: code/test_scripts/model_nested_df.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/analysis_previous_studies.Rmd) and HTML (docs/analysis_previous_studies.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | d25e2a1 | jens-daniel-mueller | 2020-08-27 | added basin AIP |
| html | b6d0e6a | jens-daniel-mueller | 2020-08-27 | Build site. |
| Rmd | 69a9be4 | jens-daniel-mueller | 2020-08-27 | XXX |
| html | f40e48b | jens-daniel-mueller | 2020-08-26 | Build site. |
| Rmd | b577ec6 | jens-daniel-mueller | 2020-08-26 | Analysis split in this and previous studies |
library(tidyverse)
library(lubridate)
library(marelac)1 Data sources
1.1 Sabine 2004
Cant_94 <- read_csv(here::here("data/GLODAPv1_1/_summarized_files",
"Cant_94.csv"))
Cant_94_inv <-
read_csv(here::here("data/GLODAPv1_1/_summarized_files",
"Cant_94_inv.csv"))1.2 Gruber 2019
Cant_07 <- read_csv(here::here("data/Gruber_2019/_summarized_files",
"Cant_07.csv"))
Cant_07_inv <-
read_csv(here::here("data/Gruber_2019/_summarized_files",
"Cant_07_inv.csv"))2 Comparison of previous estimates
Cant inventory estimates of S04 (Sabine et al, 2004) and G19 (Gruber et al, 2019) were compared.
2.1 Merge data sets
Cant_94_inv <- Cant_94_inv %>%
select(-cant_inv_incl_neg)
Cant_inv <- full_join(Cant_07_inv %>% mutate(estimate = "G19"),
Cant_94_inv %>% mutate(estimate = "S04"))
rm(Cant_07_inv, Cant_94_inv)2.2 Inventory maps
Spanning different time periods, the Cant inventories differ in magnitude.
Cant_inv %>%
ggplot() +
geom_raster(data = landmask %>% filter(region == "land"),
aes(lon, lat),
fill = "grey80") +
geom_raster(aes(lon, lat, fill = cant_inv)) +
coord_quickmap(expand = 0) +
scale_fill_viridis_c() +
facet_wrap( ~ estimate, ncol = 1) +
theme(
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank()
)
2.3 Global inventories
Global anthropogenic CO2 inventories were estimated in Pg-C. Please note that here we onyl added positive Cant values in the upper 3000m and do not apply additional corrections for areas not covered.
Cant_inv <- Cant_inv %>%
mutate(surface_area = earth_surf(lat, lon),
cant_inv_grid = cant_inv*surface_area)
Cant_inv_global <- Cant_inv %>%
mutate(surface_area = earth_surf(lat, lon),
cant_inv_grid = cant_inv*surface_area) %>%
group_by(estimate) %>%
summarise(cant_total = sum(cant_inv_grid)*12*1e-15) %>%
ungroup()
Cant_inv_global# A tibble: 2 x 2
estimate cant_total
<chr> <dbl>
1 G19 31.3
2 S04 102. 2.4 Relative inventories
Cant_inv_wide <- Cant_inv %>%
pivot_wider(values_from = c(cant_inv, cant_inv_grid),
names_from = estimate)
Cant_inv_wide <- Cant_inv_wide %>%
drop_na() %>%
mutate(G19_rel = cant_inv_grid_G19 / sum(cant_inv_grid_G19),
S04_rel = cant_inv_grid_S04 / sum(cant_inv_grid_S04),
cant_ratio_rel = G19_rel / S04_rel)
Cant_inv_rel <- Cant_inv_wide %>%
pivot_longer(cols = c(G19_rel, S04_rel),
names_to = "estimate",
values_to = "cant_inv_rel")Cant_inv_rel %>%
ggplot() +
geom_raster(data = landmask %>% filter(region == "land"),
aes(lon, lat),
fill = "grey80") +
geom_raster(aes(lon, lat, fill = cant_inv_rel*100)) +
coord_quickmap(expand = 0) +
scale_fill_viridis_c() +
facet_wrap( ~ estimate, ncol = 1) +
theme(
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank()
)
2.5 Relative inventory ratios
Cant_inv_wide %>%
filter(cant_ratio_rel < 10,
cant_ratio_rel > 0.1) %>%
ggplot() +
geom_raster(data = landmask %>% filter(region == "land"),
aes(lon, lat),
fill = "grey80") +
geom_contour_filled(aes(lon, lat, z = log10(cant_ratio_rel))) +
coord_quickmap(expand = 0) +
scale_fill_brewer(palette = "RdBu", direction = -1) +
labs(title = "Cant inventory distribution | 1994-2007 vs preind-1994",
subtitle = "Log ratio of relative contributions to total inventory") +
theme(
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.title = element_blank()
)
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] marelac_2.1.10 shape_1.4.4 lubridate_1.7.9 forcats_0.5.0
[5] stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4 readr_1.3.1
[9] tidyr_1.1.0 tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0
[13] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 here_0.1 utf8_1.1.4 assertthat_0.2.1
[5] rprojroot_1.3-2 digest_0.6.25 R6_2.4.1 cellranger_1.1.0
[9] backports_1.1.8 reprex_0.3.0 evaluate_0.14 httr_1.4.2
[13] pillar_1.4.6 rlang_0.4.7 readxl_1.3.1 rstudioapi_0.11
[17] whisker_0.4 blob_1.2.1 rmarkdown_2.3 labeling_0.3
[21] munsell_0.5.0 broom_0.7.0 compiler_4.0.2 httpuv_1.5.4
[25] modelr_0.1.8 xfun_0.16 pkgconfig_2.0.3 htmltools_0.5.0
[29] tidyselect_1.1.0 viridisLite_0.3.0 fansi_0.4.1 crayon_1.3.4
[33] dbplyr_1.4.4 withr_2.2.0 later_1.1.0.1 gsw_1.0-5
[37] grid_4.0.2 jsonlite_1.7.0 gtable_0.3.0 lifecycle_0.2.0
[41] DBI_1.1.0 git2r_0.27.1 magrittr_1.5 seacarb_3.2.13
[45] scales_1.1.1 cli_2.0.2 stringi_1.4.6 oce_1.2-0
[49] farver_2.0.3 fs_1.4.2 promises_1.1.1 testthat_2.3.2
[53] xml2_1.3.2 ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2
[57] RColorBrewer_1.1-2 tools_4.0.2 glue_1.4.1 hms_0.5.3
[61] yaml_2.2.1 colorspace_1.4-1 isoband_0.2.2 rvest_0.3.6
[65] knitr_1.29 haven_2.3.1