Last updated: 2020-10-01

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Knit directory: BloomSail/

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    Ignored:    .Rhistory
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Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   code/Workflowr_project_managment.R
    Modified:   output/Plots/Figures_publication/Appendix/Phytoplankton_mean_total_biomass.pdf
    Modified:   output/Plots/Figures_publication/Appendix/TPD_CPD_cumulative.pdf
    Modified:   output/Plots/Figures_publication/Appendix/TPD_CPD_cumulative.png
    Modified:   output/Plots/Figures_publication/Appendix/pCO2_RT_corrected_profile_example.pdf
    Modified:   output/Plots/Figures_publication/Appendix/pCO2_RT_corrected_profile_mean_abs_offset.pdf
    Modified:   output/Plots/Figures_publication/Appendix/tau_fit_example.pdf
    Modified:   output/Plots/Figures_publication/Appendix/tb_profiles.pdf
    Modified:   output/Plots/Figures_publication/Appendix/tb_profiles.png
    Modified:   output/Plots/Figures_publication/Article/Hov_abs_profiles_cum.pdf
    Modified:   output/Plots/Figures_publication/Article/Hov_abs_profiles_cum.png
    Modified:   output/Plots/Figures_publication/Article/atm_water_timeseries.pdf
    Modified:   output/Plots/Figures_publication/Article/atm_water_timeseries.png
    Modified:   output/Plots/Figures_publication/Article/data_coverage.pdf
    Modified:   output/Plots/Figures_publication/Article/profiles_all.pdf
    Modified:   output/Plots/Figures_publication/Article/profiles_all.png
    Modified:   output/Plots/Figures_publication/Article/reconstruction_NCP_timeseries.pdf
    Modified:   output/Plots/Figures_publication/Article/reconstruction_NCP_timeseries.png
    Modified:   output/Plots/Figures_publication/Article/reconstruction_iCT_timeseries.pdf
    Modified:   output/Plots/Figures_publication/Article/reconstruction_iCT_timeseries.png
    Modified:   output/Plots/Figures_publication/Article/station_map.pdf
    Modified:   output/Plots/merging_interpolation/Zero_time_synchronization.pdf
    Modified:   output/Plots/read_in/th_deployments.pdf
    Modified:   output/Plots/response_time/all_plots.pdf
    Modified:   output/Plots/response_time/profiles_pCO2.pdf
    Modified:   output/Plots/response_time/profiles_pCO2_delta_grid.pdf
    Modified:   output/Plots/response_time/profiles_pCO2_delta_rel_grid.pdf
    Modified:   output/Plots/response_time/profiles_pCO2_grid.pdf
    Deleted:    output/Plots/response_time/profiles_pCO2_mean.pdf
    Deleted:    output/Plots/response_time/profiles_pCO2_mean_grid.pdf
    Modified:   output/Plots/response_time/tau_determination_pCO2_corr_flushperiods_nls.pdf
    Modified:   output/Plots/response_time/time_series_depth_pCO2_corr_by_profile.pdf

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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
    • tx: data recorded on SV Tina V, where x stands for:
      • s: Sea-Bird SBE 16 sensor
      • h: Contros HydroC CO2
      • t: track data (coordinates + timestamp)
      • m: ts + th + tt merged (variables within tm are interpolated to a common time stamp)
      • b: TinaV discrete bottle
    • 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
    • deployment
    • Zero: Zeroing period of HydroC Sensor
    • Flush: Period following zero, reading recovers to ambient value (600sec)
    • mixing: Two phases of the Flush period (initial 20 sec for internal mixing)
  • 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
    • 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
    • delta: offset from same parameter but estimated differently
    • i: intergrated over depth
    • cum: cumulative value over time
    • sign: identifier for pos. or neg. differences
    • rel: relative to some absolute value

Preset subsetting values are identified by postfix _lim and coded seperately

  • 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 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