Last updated: 2020-09-07

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.

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(20200707)

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.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: fe673db

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 fe673db. 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/

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_Gruber_2019_Cant.Rmd) and HTML (docs/read_Gruber_2019_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 da445a6 jens-daniel-mueller 2020-09-04 Build site.
html fa11a74 jens-daniel-mueller 2020-09-02 Build site.
html 429aab3 jens-daniel-mueller 2020-09-01 Build site.
html f4216dd jens-daniel-mueller 2020-09-01 Build site.
html 13a76d5 jens-daniel-mueller 2020-08-28 Build site.
html 27404de jens-daniel-mueller 2020-08-27 Build site.
html d240341 jens-daniel-mueller 2020-08-27 Build site.
Rmd a06009a jens-daniel-mueller 2020-08-27 added section plots add regular longitudes
html f6980f7 jens-daniel-mueller 2020-08-27 Build site.
Rmd d3cbe4f jens-daniel-mueller 2020-08-27 updated plots
html 06c2578 jens-daniel-mueller 2020-08-27 Build site.
Rmd c54a7fc jens-daniel-mueller 2020-08-27 updated plots
html b6d0e6a jens-daniel-mueller 2020-08-27 Build site.
html f40e48b jens-daniel-mueller 2020-08-26 Build site.
html ec20f40 jens-daniel-mueller 2020-08-24 Build site.
html 5ffe187 jens-daniel-mueller 2020-08-20 Build site.
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 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 6a06ce9 jens-daniel-mueller 2020-08-13 Build site.
Rmd 5d72981 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 a792c78 jens-daniel-mueller 2020-08-12 Build site.
Rmd 831c910 jens-daniel-mueller 2020-08-12 fig asp adjusted
html 8b32ee1 jens-daniel-mueller 2020-08-12 Build site.
Rmd 092a504 jens-daniel-mueller 2020-08-12 harmonized coordinates, labels, plots and basin mask
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.
html dbb4da6 jens-daniel-mueller 2020-08-07 Build site.
Rmd dfa906f jens-daniel-mueller 2020-08-07 formating
html ae310c7 jens-daniel-mueller 2020-08-07 Build site.
Rmd 8b6b8d8 jens-daniel-mueller 2020-08-07 formating
html 7d7900a jens-daniel-mueller 2020-08-07 Build site.
Rmd ceb438a jens-daniel-mueller 2020-08-07 rebuild with Gruber Cant 
library(tidyverse)
library(lubridate)
library(tidync)
library(stars)

1 Data source

2 Read ncdfs

dcant <- tidync(here::here("data/Gruber_2019",
                               "dcant_emlr_cstar_gruber_94-07_vs1.nc"))

dcant <- dcant %>%  activate(DCANT_01)
dcant <- dcant %>% hyper_tibble()

# harmonize column names and coordinates
dcant <- dcant %>% 
  rename(lon = LONGITUDE,
         lat = LATITUDE,
         depth = DEPTH,
         cant = DCANT_01) %>% 
  mutate(lon = if_else(lon < 20, lon + 360, lon))
dcant_inv <- tidync(here::here("data/Gruber_2019",
                               "inv_dcant_emlr_cstar_gruber_94-07_vs1.nc"))

dcant_inv <- dcant_inv %>%  activate(DCANT_INV01)
dcant_inv <- dcant_inv %>% hyper_tibble()

# harmonize column names and coordinates
dcant_inv <- dcant_inv %>% 
  rename(lon = LONGITUDE,
         lat = LATITUDE,
         cant_inv = DCANT_INV01) %>% 
  mutate(lon = if_else(lon < 20, lon + 360, lon))

3 Apply basin mask

dcant <- inner_join(dcant, basinmask)
dcant_inv <- inner_join(dcant_inv, basinmask)

4 Cant plots

Below, following subsets of the climatologies are plotted for all relevant parameters:

  • Horizontal planes at 150, 500, 1000, 2000m
  • Meridional sections at longitudes: 335.5, 190.5, 70.5

Section locations are indicated as white lines in maps.

4.1 Horizontal plane maps

map_climatology(dcant %>% filter(cant < 25), "cant")

4.2 Surface Inventory map

map_climatology_inv(dcant_inv, "cant_inv")

4.3 Sections basin

section_climatology(dcant, "cant")

4.4 Sections at regular longitudes

section_climatology_regular(dcant %>% filter(cant < 30), "cant")

4.5 Sections shallow

section_climatology_shallow(dcant, "cant")

5 Write files

dcant %>% 
  write_csv(here::here("data/Gruber_2019/_summarized_files",
                       "Cant_07.csv"))

dcant_inv %>% 
  write_csv(here::here("data/Gruber_2019/_summarized_files",
                       "Cant_07_inv.csv"))

6 Open tasks

7 Questions

  • Why are there no negative Cant estimates?

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] stars_0.4-3     sf_0.9-5        abind_1.4-5     tidync_0.2.4   
 [5] lubridate_1.7.9 forcats_0.5.0   stringr_1.4.0   dplyr_1.0.0    
 [9] purrr_0.3.4     readr_1.3.1     tidyr_1.1.0     tibble_3.0.3   
[13] ggplot2_3.3.2   tidyverse_1.3.0 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2         jsonlite_1.7.0     viridisLite_0.3.0  here_0.1          
 [5] modelr_0.1.8       assertthat_0.2.1   blob_1.2.1         cellranger_1.1.0  
 [9] yaml_2.2.1         pillar_1.4.6       backports_1.1.8    glue_1.4.1        
[13] digest_0.6.25      promises_1.1.1     rvest_0.3.6        colorspace_1.4-1  
[17] htmltools_0.5.0    httpuv_1.5.4       pkgconfig_2.0.3    broom_0.7.0       
[21] haven_2.3.1        scales_1.1.1       whisker_0.4        later_1.1.0.1     
[25] git2r_0.27.1       generics_0.0.2     farver_2.0.3       ellipsis_0.3.1    
[29] withr_2.2.0        cli_2.0.2          magrittr_1.5       crayon_1.3.4      
[33] readxl_1.3.1       evaluate_0.14      fs_1.4.2           ncdf4_1.17        
[37] fansi_0.4.1        xml2_1.3.2         lwgeom_0.2-5       class_7.3-17      
[41] tools_4.0.2        hms_0.5.3          lifecycle_0.2.0    munsell_0.5.0     
[45] reprex_0.3.0       isoband_0.2.2      compiler_4.0.2     e1071_1.7-3       
[49] RNetCDF_2.3-1      rlang_0.4.7        classInt_0.4-3     units_0.6-7       
[53] grid_4.0.2         rstudioapi_0.11    labeling_0.3       rmarkdown_2.3     
[57] gtable_0.3.0       DBI_1.1.0          R6_2.4.1           ncmeta_0.2.5      
[61] knitr_1.29         rprojroot_1.3-2    KernSmooth_2.23-17 stringi_1.4.6     
[65] parallel_4.0.2     Rcpp_1.0.5         vctrs_0.3.2        dbplyr_1.4.4      
[69] tidyselect_1.1.0   xfun_0.16