Anthropogenic CO2 from 1994 to 2007
Jens Daniel Müller
20 August, 2020
Last updated: 2020-08-20
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 cc5d91b. 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/
Ignored: figure/
Unstaged changes:
Modified: analysis/_site.yml
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/read_Sabine_2004_Cant.Rmd) and HTML (docs/read_Sabine_2004_Cant.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 |
|---|---|---|---|---|
| html | 1064ef8 | jens-daniel-mueller | 2020-08-19 | Build site. |
| html | 29a537a | jens-daniel-mueller | 2020-08-18 | Build site. |
| Rmd | 7fb61d5 | jens-daniel-mueller | 2020-08-18 | rerun with all parameters in one file |
| html | 499c834 | jens-daniel-mueller | 2020-08-14 | Build site. |
| Rmd | 23556f6 | jens-daniel-mueller | 2020-08-14 | changed cant naming in sabine inventory |
| html | a3b6b68 | jens-daniel-mueller | 2020-08-13 | Build site. |
| html | 333ea4b | jens-daniel-mueller | 2020-08-13 | Build site. |
| Rmd | f3a7d4e | jens-daniel-mueller | 2020-08-13 | Gruber Sabine comparison |
| html | cfb48c7 | jens-daniel-mueller | 2020-08-13 | Build site. |
| Rmd | e9adb7b | jens-daniel-mueller | 2020-08-13 | Minor formating |
| html | 00c2120 | jens-daniel-mueller | 2020-08-13 | Build site. |
| html | bf69270 | jens-daniel-mueller | 2020-08-13 | Build site. |
| html | 1176c9a | jens-daniel-mueller | 2020-08-12 | Build site. |
| html | f094087 | jens-daniel-mueller | 2020-08-12 | Build site. |
| Rmd | fa43c80 | jens-daniel-mueller | 2020-08-12 | harmonized coordinates and plotting |
| html | 81b9c5b | jens-daniel-mueller | 2020-08-12 | Build site. |
| Rmd | 1dd027d | jens-daniel-mueller | 2020-08-12 | harmonized coordinates, calculated inventories |
| html | f143b2d | jens-daniel-mueller | 2020-08-12 | Build site. |
| html | 2d179e7 | jens-daniel-mueller | 2020-08-12 | Build site. |
| html | 5d33341 | jens-daniel-mueller | 2020-08-11 | Build site. |
| html | 8a010ca | jens-daniel-mueller | 2020-08-11 | Build site. |
| html | a01041a | jens-daniel-mueller | 2020-08-11 | Build site. |
| html | e18e59a | jens-daniel-mueller | 2020-08-10 | Build site. |
| Rmd | d202c61 | jens-daniel-mueller | 2020-08-10 | Read Cant Sabine added |
library(tidyverse)
library(lubridate)1 Data source
- Anthropogenic CO2 estimates (1994-2007) by Gruber et al. (2019) downloaded in August 2020 from NOAA/NCEI Ocean Carbon Data System (OCADS)
2 Read ncdfs
AnthCO2_data <- read_csv("data/GLODAPv1_1/GLODAP_gridded.data/AnthCO2.data/AnthCO2.data.txt",
col_names = FALSE,
na = "-999",
col_types = list(.default = "d"))
Depth_centers <- read_file("data/GLODAPv1_1/GLODAP_gridded.data/Depth.centers.txt")
Depth_centers <- Depth_centers %>%
str_split(",") %>%
as_vector()
Lat_centers <- read_file("data/GLODAPv1_1/GLODAP_gridded.data/Lat.centers.txt")
Lat_centers <- Lat_centers %>%
str_split(",") %>%
as_vector()
Long_centers <- read_file("data/GLODAPv1_1/GLODAP_gridded.data/Long.centers.txt")
Long_centers <- Long_centers %>%
str_split(",") %>%
as_vector()
names(AnthCO2_data) <- Lat_centers
Long_Depth <- expand_grid(depth = Depth_centers, lon = Long_centers) %>%
mutate(lon = as.numeric(lon),
depth = as.numeric(depth))
Cant <- bind_cols(AnthCO2_data, Long_Depth)
Cant <- Cant %>%
pivot_longer(1:180, names_to = "lat", values_to = "cant") %>%
mutate(lat = as.numeric(lat))
Cant <- Cant %>%
drop_na()
Cant <- Cant %>%
mutate(lon = if_else(lon < 20, lon + 360, lon))
rm(AnthCO2_data, Long_Depth, Depth_centers, Lat_centers, Long_centers)3 Apply basin mask
Cant <- inner_join(Cant, basinmask)4 Inventory calculation
source(here::here("code", "inventory_calculation.R"))
Cant <- layer_inventory(Cant, "cant")
Cant_inv <- Cant %>%
filter(depth <= parameters$inventory_depth) %>%
group_by(lon, lat, basin) %>%
summarise(cant_inv = sum(layer_inv_pos, na.rm = TRUE) / 1000,
cant_inv_incl_neg = sum(layer_inv, na.rm = TRUE) / 1000) %>%
ungroup()5 Cant plots
Below, following subsets of the climatologies are plotted for all relevant parameters:
- Horizontal planes at 0, 100, 500, 2000m
- Meridional sections at longitudes:
- Atlantic: 335.5
- Pacific: 190.5
- Indian ocean: 70.5
Section locations are indicated as white lines in maps.
5.1 Horizontal plane maps
map_climatology(Cant, "cant")
5.2 Sections
section_climatology(Cant, "cant")
5.3 Sections shallow
section_climatology_shallow(Cant, "cant")
5.4 Inventory maps
map_climatology_inv(Cant_inv, "cant_inv")
5.5 Write files
Cant %>%
write_csv(here::here("data/GLODAPv1_1/_summarized_files",
"Cant_94.csv"))
Cant_inv %>%
write_csv(here::here("data/GLODAPv1_1/_summarized_files",
"Cant_94_inv.csv"))6 Open tasks
7 Questions
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] lubridate_1.7.9 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0
[5] purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.3
[9] ggplot2_3.3.2 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.16 haven_2.3.1 colorspace_1.4-1
[5] vctrs_0.3.2 generics_0.0.2 viridisLite_0.3.0 htmltools_0.5.0
[9] yaml_2.2.1 blob_1.2.1 rlang_0.4.7 isoband_0.2.2
[13] later_1.1.0.1 pillar_1.4.6 withr_2.2.0 glue_1.4.1
[17] DBI_1.1.0 dbplyr_1.4.4 modelr_0.1.8 readxl_1.3.1
[21] lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0
[25] rvest_0.3.6 evaluate_0.14 labeling_0.3 knitr_1.29
[29] httpuv_1.5.4 fansi_0.4.1 broom_0.7.0 Rcpp_1.0.5
[33] promises_1.1.1 backports_1.1.8 scales_1.1.1 jsonlite_1.7.0
[37] farver_2.0.3 fs_1.4.2 hms_0.5.3 digest_0.6.25
[41] stringi_1.4.6 rprojroot_1.3-2 grid_4.0.2 here_0.1
[45] cli_2.0.2 tools_4.0.2 magrittr_1.5 crayon_1.3.4
[49] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2
[53] reprex_0.3.0 assertthat_0.2.1 rmarkdown_2.3 httr_1.4.2
[57] rstudioapi_0.11 R6_2.4.1 git2r_0.27.1 compiler_4.0.2