Last updated: 2020-11-26

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Knit directory: Cant_eMLR/

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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

  • phosphate

  • nitrate

  • silicate

  • oxygen

  • aou

  • tco2

  • talk

  • cant: anthropogenic CO2 (mol kg-1)

  • cstar: C* (mol kg-1)

2 Variable and data set post fix

  • _mean: mean value
  • _sd: standard deviation
  • _inv: column inventory
  • _pos: positive values only (ie negative values set to zero)

3 Data sets / objects

4 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
  • chunks producing plots are named according to the plot content, because the generated plot file will be named after the chunk

5 Functions

Functions are stored in separate .R files. This include function for:

  • mapping with a prefix “m_”
  • plotting with a prefix “p_”
  • biogeochemical calculations with a prefix “b_”

6 Folder structure

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

7 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_1.30     
 [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