Last updated: 2020-11-27

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Knit directory: emlr_obs_preprocessing/

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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 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.1

Matrix products: default
BLAS:   /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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_2.5.0         rlang_0.4.8      stringr_1.4.0   
 [9] tools_4.0.3      xfun_0.18        git2r_0.27.1     htmltools_0.5.0 
[13] ellipsis_0.3.1   rprojroot_1.3-2  yaml_2.2.1       digest_0.6.27   
[17] tibble_3.0.4     lifecycle_0.2.0  crayon_1.3.4     later_1.1.0.1   
[21] vctrs_0.3.4      promises_1.1.1   fs_1.5.0         glue_1.4.2      
[25] evaluate_0.14    rmarkdown_2.5    stringi_1.5.3    compiler_4.0.3  
[29] pillar_1.4.6     backports_1.1.10 httpuv_1.5.4     pkgconfig_2.0.3