Last updated: 2020-04-28

Checks: 7 0

Knit directory: BloomSail/

This reproducible R Markdown analysis was created with workflowr (version 1.6.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20191021) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 058c709. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


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/

Unstaged changes:
    Modified:   output/Plots/Figures_publication/Article/Hov_abs_profiles_cum.pdf
    Modified:   output/Plots/Figures_publication/Article/data_coverage.pdf
    Modified:   output/Plots/Figures_publication/Article/profiles_all.pdf
    Modified:   output/Plots/Figures_publication/Article/station_map.pdf

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


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 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: tina 5 sensor
    • tb: tina 5 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
  • 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