Last updated: 2021-02-20

Checks: 7 0

Knit directory: BloomSail/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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 031f46a. 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/
    Ignored:    output/Plots/Figures_publication/.tmp.drivedownload/

Unstaged changes:
    Modified:   code/Workflowr_project_managment.R
    Modified:   output/Plots/Figures_publication/Appendix/Fig_A1.pdf
    Modified:   output/Plots/Figures_publication/Appendix/Fig_A1.png
    Modified:   output/Plots/Figures_publication/Appendix/Fig_A2.pdf
    Modified:   output/Plots/Figures_publication/Appendix/Fig_A2.png
    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
    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

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/index.Rmd) and HTML (docs/index.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
html 6b47f30 jens-daniel-mueller 2021-02-20 Build site.
Rmd 5009016 jens-daniel-mueller 2021-02-20 cleaning
html 516b294 jens-daniel-mueller 2021-02-18 Build site.
html 70a8950 jens-daniel-mueller 2021-02-11 Build site.
html 8051798 jens-daniel-mueller 2021-02-10 Build site.
html cc7009b jens-daniel-mueller 2021-02-08 Build site.
Rmd 3cd1aab jens-daniel-mueller 2021-02-08 code and output cleaning
html c5fc34c jens-daniel-mueller 2021-01-22 Build site.
html 4277235 jens-daniel-mueller 2021-01-05 Build site.
html 9a3f42a jens-daniel-mueller 2020-10-24 Build site.
html 05248bf jens-daniel-mueller 2020-10-20 Build site.
html 1c4fe8e jens-daniel-mueller 2020-10-20 table with time series in depth intervals added
html 6896725 jens-daniel-mueller 2020-10-01 Build site.
html 9f66019 jens-daniel-mueller 2020-10-01 Build site.
html 27c5431 jens-daniel-mueller 2020-09-29 Build site.
html 1d01685 jens-daniel-mueller 2020-09-28 Build site.
html 1278900 jens-daniel-mueller 2020-09-25 Build site.
html 904f0f7 jens-daniel-mueller 2020-09-23 Build site.
html 603af23 jens-daniel-mueller 2020-05-25 Build site.
html 3414c23 jens-daniel-mueller 2020-05-25 Build site.
html b5722a7 jens-daniel-mueller 2020-04-28 Build site.
Rmd 058c709 jens-daniel-mueller 2020-04-28 Moved nomenlacture to seperate Rmd
html 472c2b4 jens-daniel-mueller 2020-04-21 Build site.
html f8fcf50 jens-daniel-mueller 2020-04-19 created pub figures for time series
html a6c4c22 jens-daniel-mueller 2020-03-30 Build site.
html 80c78b3 jens-daniel-mueller 2020-03-30 Build site.
html 5f8ca30 jens-daniel-mueller 2020-03-20 Build site.
html 2a20453 jens-daniel-mueller 2020-03-20 Build site.
html 473ab25 jens-daniel-mueller 2020-03-19 Build site.
html 81f022e jens-daniel-mueller 2020-03-18 Build site.
html 1e39d85 jens-daniel-mueller 2020-03-18 Build site.
html 2105236 jens-daniel-mueller 2020-03-18 Build site.
html 05b9bdc jens-daniel-mueller 2020-03-17 Build site.
html 0202742 jens-daniel-mueller 2020-03-16 Build site.
html 8e83afd jens-daniel-mueller 2020-03-12 Build site.
html a3ddea4 jens-daniel-mueller 2020-03-12 Build site.
html 52621ea jens-daniel-mueller 2020-03-12 Build site.
html e43a6f2 jens-daniel-mueller 2019-12-19 Build site.
html d921065 jens-daniel-mueller 2019-11-14 Build site.
html d61a468 jens-daniel-mueller 2019-11-14 Build site.
html f3277a5 jens-daniel-mueller 2019-11-08 Build site.
html 4256bcf jens-daniel-mueller 2019-11-08 Build site.
html 72687ee jens-daniel-mueller 2019-11-08 Build site.
html 74212a6 jens-daniel-mueller 2019-11-08 Build site.
html 33e3659 jens-daniel-mueller 2019-10-22 Build site.
html 1595fe9 jens-daniel-mueller 2019-10-21 Build site.
html a059c41 jens-daniel-mueller 2019-10-21 Build site.
html 32ec4f7 jens-daniel-mueller 2019-10-21 Build site.
html bafa88f jens-daniel-mueller 2019-10-21 Build site.
html 076a36b jens-daniel-mueller 2019-10-21 Build site.
html b2d0164 jens-daniel-mueller 2019-10-21 Build site.
html f2becd1 jens-daniel-mueller 2019-10-21 Build site.
Rmd f448895 jens-daniel-mueller 2019-10-21 updated index Rmd
html f91f17d jens-daniel-mueller 2019-10-21 Build site.
Rmd 6e00940 jens-daniel-mueller 2019-10-21 updated index Rmd
html fd500ed jens-daniel-mueller 2019-10-21 Build site.
html 9c7a03e jens-daniel-mueller 2019-10-21 Build site.
Rmd 31a2608 jens-daniel-mueller 2019-10-21 Start workflowr project.

On this website, you find code and explanations to quantify the net community production (NCP) during a cyanobacteria bloom in the Baltic Sea through vertically resolved pCO2 measurements.

The outcome of this study was submitted to the Copernicus Journal Biogeosciences where it is handled as: bg-2021-40

Please navigate trough the navbar on top to take a look at the various chapters of this project.

The links in the upper right corner bring you to the source code of this project and back to Jens’ main homepage.

To re-run the analysis presented here, a copy of all code together with all relevant data sets is available through Zenodo.org:

Dr. Jens Daniel Müller, 2021


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