Last updated: 2023-12-04

Checks: 7 0

Knit directory: WP1/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(20210216)

The command set.seed(20210216) 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.

Session information: recorded

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

Cache: none

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

File paths: relative

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

Repository version: f36a8ac

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 f36a8ac. 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/MUR/
    Ignored:    data/analyses/CCI_all.RData
    Ignored:    data/analyses/OISST_all.RData
    Ignored:    data/analyses/clean_all.RData
    Ignored:    data/analyses/clean_all_clean.RData
    Ignored:    data/analyses/ice_4km_proc.RData
    Ignored:    data/full_data/
    Ignored:    data/model/
    Ignored:    data/pg_data/
    Ignored:    data/restricted/
    Ignored:    data/sst_CCI_sval.RData
    Ignored:    data/sst_CCI_trom.RData
    Ignored:    data/sst_gland.RData
    Ignored:    data/sst_sval.RData
    Ignored:    data/sst_trom.RData
    Ignored:    metadata/globalfishingwatch_API_key.RData
    Ignored:    metadata/is_gfw_database.RData
    Ignored:    metadata/is_mst_database.RData
    Ignored:    metadata/pangaea_parameters.tab
    Ignored:    metadata/pg_EU_ref_meta.csv
    Ignored:    poster/SSC_2021_landscape_files/paged-0.15/
    Ignored:    presentations/2023_Ilico.html
    Ignored:    presentations/2023_fjord_intercomp.html
    Ignored:    presentations/2023_seminar.html
    Ignored:    presentations/2023_summary.html
    Ignored:    presentations/ASSW_2023.html
    Ignored:    presentations/ASSW_side_2023.html
    Ignored:    shiny/dataAccess/coastline_hi_sub.csv
    Ignored:    shiny/dataAccess/full_data
    Ignored:    shiny/kongCTD/credentials.RData
    Ignored:    shiny/kongCTD/data/
    Ignored:    shiny/test_data/

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/2021_analysis.Rmd) and HTML (docs/2021_analysis.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 610ff35 Robert 2023-08-30 Build site.
html 6ad5b79 Robert William Schlegel 2023-08-24 Build site.
html bd4819b Robert 2023-08-23 Build site.
html 4ddbb12 robwschlegel 2023-07-24 Build site.
html e8997de Robert 2023-05-30 Build site.
html 2ea419c Robert 2023-05-30 Build site.
html f59b5f2 robwschlegel 2022-11-28 Re-published site
html cc87bdd Robert 2022-09-23 Build site.
html 8a8fd0b Robert 2022-05-27 Build site.
html b32f47e robwschlegel 2022-04-21 Build site.
html 1da6285 Robert 2021-12-14 Build site.
html 860f5d3 Robert 2021-12-10 Build site.
html 2725466 Robert 2021-12-10 Merge
html 64a5252 Robert 2021-12-10 Build site.
html 807675e robwschlegel 2021-12-06 Build site.
html 104acbc Robert 2021-12-03 Build site.
html 26ce5f6 robwschlegel 2021-12-01 Build site.
html 1e379a2 robwschlegel 2021-11-25 Build site.
html 79b2932 Robert 2021-11-10 Build site.
html 7caf87b Robert 2021-11-09 Build site.
html 49b83b1 robwschlegel 2021-11-01 Build site.
html 7261aeb Robert 2021-10-07 Build site.
html e9a3b71 Robert 2021-10-07 Build site.
html 566cac3 robwschlegel 2021-10-04 Build site.
Rmd b66e5b7 robwschlegel 2021-10-04 Re-built site.
html ca5002a robwschlegel 2021-10-04 Build site.
Rmd c61c1b0 robwschlegel 2021-10-04 Added some references to analysis talk
html c61c1b0 robwschlegel 2021-10-04 Added some references to analysis talk
Rmd 964cba0 robwschlegel 2021-10-04 Final draft of analysis talk
html 964cba0 robwschlegel 2021-10-04 Final draft of analysis talk
Rmd 0f6dfdb robwschlegel 2021-10-03 Final draft of analysis talk
html 0f6dfdb robwschlegel 2021-10-03 Final draft of analysis talk
Rmd 33add1c robwschlegel 2021-10-03 Restructuring analysis talk
html 33add1c robwschlegel 2021-10-03 Restructuring analysis talk
html 3e117d4 Robert 2021-09-30 Build site.
Rmd b3cfda8 Robert 2021-09-30 Re-built site.
html ad77318 Robert 2021-09-30 Build site.
Rmd 72feb91 Robert 2021-09-30 Rough plots for analysis talk
html 72feb91 Robert 2021-09-30 Rough plots for analysis talk
Rmd 657b15d Robert 2021-09-29 More work towards the analysis talk
Rmd c03fcc9 Robert 2021-09-28 More work on analysis talk and sourced the Svalbard population data
html c03fcc9 Robert 2021-09-28 More work on analysis talk and sourced the Svalbard population data
Rmd a010b46 Robert 2021-09-28 Workflowr issues
html a010b46 Robert 2021-09-28 Workflowr issues
Rmd 31b16a4 Robert 2021-09-28 Rearrange talks to now be part of the WP1 website. Full version of summary talk complete.
html 31b16a4 Robert 2021-09-28 Rearrange talks to now be part of the WP1 website. Full version of summary talk complete.


Anthropogenic impacts on Isfjorden

  • What can we currently say about local anthropogenic effects on Isfjorden?
    • With a specific focus on social science data
  • Keep in mind this analysis is just an example to stimulate thought about real analyses
    • These then are to be used for the review paper

Isfjorden data

Figure 1: High level overview of the data available for Isfjorden. The acronyms for the variable groups seen throughout the figure are: bio = biology, chem = chemistry, cryo = cryosphere, phys = physical, soc = social (currently there are no social data for Isfjorden). A) Metadata showing the range of values available within the data. B) Spatial summary of data available per ~1 km grouping. Note that there are some important moorings outside of this bounding box that are included in the data counts. C) Temporal summary of available data. D) Summmary of data available by depth. Note that all of the data summaries are log10 transformed. For C) and D) the log10 transformation is applied before the data are stacked by category, which gives the impression that there are much more data are than there are.”
Figure 1: High level overview of the data available for Isfjorden. The acronyms for the variable groups seen throughout the figure are: bio = biology, chem = chemistry, cryo = cryosphere, phys = physical, soc = social (currently there are no social data for Isfjorden). A) Metadata showing the range of values available within the data. B) Spatial summary of data available per ~1 km grouping. Note that there are some important moorings outside of this bounding box that are included in the data counts. C) Temporal summary of available data. D) Summmary of data available by depth. Note that all of the data summaries are log10 transformed. For C) and D) the log10 transformation is applied before the data are stacked by category, which gives the impression that there are much more data are than there are.”


Human presence on Svalbard

Pop

Statistics Norway (2021)
Statistics Norway (2021)

Tourists

Statistics Norway (2021)
Statistics Norway (2021)

Nights

Statistics Norway (2021)
Statistics Norway (2021)

Nutrient data

Nutrients

ChlA

Vader et al. (2020)
Vader et al. (2020)

ChlA vs. Pop

Summary

  • The aggregated data products showcased in this talk are intended to be used by other FACE-IT members
    • For their research as well as the review paper of change in the FACE-IT study sites
  • The review paper is designed to be a collaborative process for many members of FACE-IT
    • Co-authorship requires contribution of data, text, figures, ideas etc.
    • Site coordinators will be contacted first
  • Timeline:
    • Data collection (underway)
    • Analyses (October 2021 - April 2022)
    • Writing up (May - September 2022)
    • Manuscript submitted for review (October 2022)

References

  • Statistics Norway. www.ssb.no. Accessed 2021-09-30
  • University Centre in Svalbard (2020). ISA_Svalbard_Chlorophyll_A_2011_2019 [Data set]. Norstore. https://doi.org/10.11582/2020.00063

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.1         knitr_1.45       
 [5] rlang_1.1.2       xfun_0.41         stringi_1.8.2     processx_3.8.2   
 [9] promises_1.2.1    jsonlite_1.8.7    glue_1.6.2        rprojroot_2.0.4  
[13] git2r_0.33.0      htmltools_0.5.7   httpuv_1.6.12     ps_1.7.5         
[17] sass_0.4.7        fansi_1.0.5       rmarkdown_2.25    jquerylib_0.1.4  
[21] tibble_3.2.1      evaluate_0.23     fastmap_1.1.1     yaml_2.3.7       
[25] lifecycle_1.0.4   whisker_0.4.1     stringr_1.5.1     compiler_4.3.2   
[29] fs_1.6.3          pkgconfig_2.0.3   Rcpp_1.0.11       rstudioapi_0.15.0
[33] later_1.3.1       digest_0.6.33     R6_2.5.1          utf8_1.2.4       
[37] pillar_1.9.0      callr_3.7.3       magrittr_2.0.3    bslib_0.6.1      
[41] tools_4.3.2       cachem_1.0.8      getPass_0.2-2