Last updated: 2020-09-01

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 b7a8f92. 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/config_nomenclature.Rmd) and HTML (docs/config_nomenclature.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 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 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.
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 a3b6b68 jens-daniel-mueller 2020-08-13 Build site.
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 1a078e7 jens-daniel-mueller 2020-08-12 Build site.
Rmd 6344282 jens-daniel-mueller 2020-08-12 updated lon conversion, variable names and masks
html f143b2d jens-daniel-mueller 2020-08-12 Build site.
html 2d179e7 jens-daniel-mueller 2020-08-12 Build site.
html cee0e89 jens-daniel-mueller 2020-08-11 Build site.
Rmd c9e2d65 jens-daniel-mueller 2020-08-11 plot maps from function
html 5d33341 jens-daniel-mueller 2020-08-11 Build site.
Rmd 3ff89bb jens-daniel-mueller 2020-08-11 created config navbar element
html 8a010ca jens-daniel-mueller 2020-08-11 Build site.
Rmd 638cddb jens-daniel-mueller 2020-08-11 created config navbar element
html a01041a jens-daniel-mueller 2020-08-11 Build site.
Rmd 39d06f0 jens-daniel-mueller 2020-08-11 created config navbar element

1 Variables

Variables from source data files are converted and harmonized to satisfy following naming convention throughout the project:

  • coordinates on 1x1 degree grid

    • lon: longitude (20.5 to 379.5 °E)
    • lat: latitude (-89.5 to 89.5 °N)
  • depth: water depth (m)

  • bottomdepth: bottomdepth (m)

  • sal: salinity (Check scales!)

  • tem: insitu temperature in deg C (Check scales!)

  • theta: potential temperature in deg C (Check scales!)

  • gamma: neutral density

  • cant: anthropogenic CO2 (mol kg^{-1})

2 Data sets / objects

3 Chunk label naming within .Rmd files

  • read_xxx: open new data set
  • clean_xxx: subset rows of a data set
  • calculate_xxx: perform calculations on a data set (add or modify rows)
  • write_xxx: write summarized data file to disk

4 Folder structure

  • data: contains all data, not synced to Github
    • subfolder for each data product
      • _summarized_data_files: data sets created along analysis

5 Open tasks

  • check temperature and salinity scales

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] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5      rstudioapi_0.11 whisker_0.4     knitr_1.29     
 [5] magrittr_1.5    R6_2.4.1        rlang_0.4.7     stringr_1.4.0  
 [9] tools_4.0.2     xfun_0.16       git2r_0.27.1    htmltools_0.5.0
[13] ellipsis_0.3.1  rprojroot_1.3-2 yaml_2.2.1      digest_0.6.25  
[17] tibble_3.0.3    lifecycle_0.2.0 crayon_1.3.4    later_1.1.0.1  
[21] vctrs_0.3.2     promises_1.1.1  fs_1.4.2        glue_1.4.1     
[25] evaluate_0.14   rmarkdown_2.3   stringi_1.4.6   compiler_4.0.2 
[29] pillar_1.4.6    backports_1.1.8 httpuv_1.5.4    pkgconfig_2.0.3