Last updated: 2020-04-28

Checks: 7 0

Knit directory: BloomSail/

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Repository version: 5ebd364

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/Finnmaid_2018/
    Ignored:    data/GETM/
    Ignored:    data/Maps/
    Ignored:    data/Ostergarnsholm/
    Ignored:    data/TinaV/
    Ignored:    data/_merged_data_files/
    Ignored:    data/_summarized_data_files/
    Ignored:    output/Plots/Figures_publication/.tmp.drivedownload/
    Ignored:    output/Plots/Figures_publication/Appendix/

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    Untracked:  output/Plots/read_in/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/nomenclature.Rmd) and HTML (docs/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
Rmd 5ebd364 jens-daniel-mueller 2020-04-28 revised
html b5722a7 jens-daniel-mueller 2020-04-28 Build site.
Rmd 058c709 jens-daniel-mueller 2020-04-28 Moved nomenlacture to seperate Rmd

Throughout this analysis, the following naming conventions for objects (data sets) and variables are used.

1 Nomenclature of objectes / data sets

The following names should be identical for stored files and objectes in R environment

  • source
    • ts: TinaV Sea-Bird SBE 16 sensor
    • th: TinaV HydroC CO2
    • tm: ts + th merged
    • tb: TinaV discrete bottle
    • tt: TinaV track data (coordinates + timestamp)
    • fm: finnmaid
    • og: ostergarnsholm tower
    • gt: GETM (high-res huydographical model)
    • mp: bathymetric map
  • subsetting and modification levels
    • profiles vs surface: operation mode tina 5
    • ID: mean values for cruise (reduced temporal resolution)
    • daily: daily mean values
    • long: data stored in long format (all observations in only 2 columns “var” and “value”)
    • fix: constant, unique values such as long-term means, starting dates, etc
    • iCT: includes cumulative numbers as iCT estimates
    • NCP: includes cumulative numbers as NCP estimates
    • CT_tem: data subset to analyse changes of CT with tem
    • 3d vs 2d: surface vs depth resolved GETM data

2 Nomenclature of variables

  • Descriptive variables
    • date
    • date_time
    • date_time_ID: mean date of cruise
    • date_time_ID_diff: time differences in between cruises
    • date_time_ID_ref: mean date in between cruises corresponding to observed incremental changes
    • station
    • ID: character identifying starting date of cruise as YYMMDD
    • dep: 1m depth intervals
    • lat
    • lon
  • Observed variables: column names, or identifier in column “var” for long-format tables
    • pCO2_analog: analog HydroC signal recorded on SeaBird CTD
    • pCO2_raw: HydroC signal recorded internally
    • pCO2_corr: HydroC signal recorded internally postprocessed by manufacturer
    • pCO2: Response time corrected pCO2_corr
    • sal
    • tem
    • nCT: CT calculated from pCO2, temperature, and fixed AT, S
    • CT: Measured dissolved inorganic carbon
    • AT: Measured total alkalinity
    • U10: wind speed at 10m
    • mld: mixed or mixing layer depth
  • Variable name extension
    • mean
    • sd
    • min
    • max
    • int: interpolated value
    • grid: value gridded to a coarser resolution
    • diff: difference to previous value
    • diff_daily: difference to previous value divided by number of days
    • i: intergrated over depth
    • cum: cumulative value over time
    • sign: identifier for pos. or neg. differences
  • p_XXX: ggplot object

3 Chunk labeling

  • criteria_: Definition of criteria for subsetting etc (should be at the beginning of each Rmd file)
  • read_: read data
  • calc_: perform calculations, mutate variables, etc
  • chunks for plotting are labeled according to plot content, because name controls plot file name

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: i386-w64-mingw32/i386 (32-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_1.6.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4      rprojroot_1.3-2 digest_0.6.25   later_1.0.0    
 [5] R6_2.4.1        backports_1.1.5 git2r_0.26.1    magrittr_1.5   
 [9] evaluate_0.14   stringi_1.4.6   rlang_0.4.5     fs_1.4.0       
[13] promises_1.1.0  whisker_0.4     rmarkdown_2.1   tools_3.6.3    
[17] stringr_1.4.0   glue_1.3.2      httpuv_1.5.2    xfun_0.12      
[21] yaml_2.2.1      compiler_3.6.3  htmltools_0.4.0 knitr_1.28