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

1 Nomenclature of objects and data sets

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

  • source

    • tx: data recorded on SV Tina V, where x stands for:

      • s: Sea-Bird SBE 16 sensor
      • h: Contros HydroC CO2 sensor
      • t: track data (coordinates + timestamp)
      • m: ts + th + tt merged (variables within tm are interpolated to a common time stamp)
      • b: discrete bottle samples

    • fm: data recorded on SOOP Finnmaid

    • og: data recorded on Ostergarnsholm ICOS flux tower

    • gt: GETM (high-res huydographical model)

    • mp: bathymetric map

  • subsetting and modification levels

    • profiles vs surface: operation mode SV Tina V
    • 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
    • deployment
    • Zero: Zeroing period of HydroC Sensor
    • Flush: Period following zero, reading recovers to ambient value
    • mixing: Two phases of the Flush period

  • Observed variables: column names, or identifier in column “var” for long-format tables

    • pCO2: partial pressure of carbon dioxide, with following postfix indicating manipulation level

      • _analog: analog HydroC signal recorded on SeaBird CTD
      • _raw: HydroC signal recorded internally
      • _corr: pCO2_raw postprocessed by manufacturer
      • _equi: pCO2_corr at the end of an in-water equilibration period at constant depth
      • _RT: Response time corrected pCO2_corr
      • _RT_mean: running mean of pCO2_RT
      • none: pCO2_RT_mean gridded to regular depth levels

    • sal

    • tem

    • nCT: CT normalized to AT, or calculated from pCO2, temperature, and fixed AT, S (please note that this variable is referred to as CT* in the accompanying manuscript)

    • CT: Measured dissolved inorganic carbon

    • AT: Measured total alkalinity

    • U10: wind speed at 10m

    • mld: mixed or mixing layer depth

  • Variable name extension

    • mean: mean value
    • sd: standard deviation
    • min: min value
    • max: max value
    • 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
    • delta: offset from an alternative estimate of the same parameter
    • i: intergrated over depth
    • cum: cumulative value over time
    • sign: identifier for pos. or neg. differences
    • rel: relative to some absolute value

  • p_XXX: ggplot object

3 Code chunk labelling

  • read_: read data
  • calc_: perform calculations, mutate variables, etc
  • chunks for plotting are labeled according to plot content, because name controls plot file name

4 ToD0

Github repo Explain subsetting of deployments Explain metadata creation

CT dynamics Map data preparation in read-in file

Reconstruction fm + gt in read_in und merging section implement exact subsetting coordinated for getm data


sessionInfo()
R version 4.0.3 (2020-10-10)
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_0.13 whisker_0.4     knitr_1.30     
 [5] magrittr_2.0.1  R6_2.5.0        rlang_0.4.10    stringr_1.4.0  
 [9] tools_4.0.3     xfun_0.19       git2r_0.27.1    htmltools_0.5.0
[13] ellipsis_0.3.1  rprojroot_2.0.2 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_0.3.6     promises_1.1.1  fs_1.5.0        glue_1.4.2     
[25] evaluate_0.14   rmarkdown_2.6   stringi_1.5.3   compiler_4.0.3 
[29] pillar_1.4.7    httpuv_1.5.4    pkgconfig_2.0.3