Last updated: 2024-10-01

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.


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(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.

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 d1a5761. 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:    metadata/coastline_full_df.RData

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_summary.Rmd) and HTML (docs/2021_summary.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 34593d0 Robert William Schlegel 2024-03-20 Build site.
html 2bba2c0 Robert William Schlegel 2024-01-25 Build site.
html 9228f25 Robert William Schlegel 2023-12-20 Build site.
html 0926ac4 Robert William Schlegel 2023-12-12 Build site.
html 7ad8a78 Robert William Schlegel 2023-12-12 Build site.
html 77b2a61 Robert 2023-12-04 Build site.
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.
Rmd 8d91bc0 Robert William Schlegel 2023-08-17 First draft of talk for 2023 FACE-IT annual meeting
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 ca5002a robwschlegel 2021-10-04 Build site.
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
Rmd 657b15d Robert 2021-09-29 More work towards the analysis talk
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.
html 0f93d06 Robert 2021-09-28 Build site.
html 6f949b1 Robert 2021-09-28 Build site.
Rmd 97cfbfa Robert 2021-09-28 Re-built site.
html 5786d9e Robert 2021-09-28 Build site.
html 72675ee Robert 2021-09-28 Build site.
Rmd d74f765 Robert 2021-09-28 Re-built site.


Structure


  • Lead: Jean-Pierre Gattuso

  • Data Scientist: Robert Schlegel
  • Identify and analyse major drivers of change for fjord and adjacent socioecological systems
  • Collect, manage, and disseminate data and analyses both within and outside the consortium
  • Key drivers identified in WP1 form the operative base for all WPs


Deliverables


Key drivers (D1.1: 6 months)

Table 1: The key drivers of changes on Arctic fjord and adjacent coastal systems as identified by the experts in FACE-IT for the relevant fields. The drivers have been separated into the following categories for convenience: Cryosphere, Physical, Chemistry, Biology, Social. Full list available via ‘Key drivers’ tab above.
Category Drivers
Cryosphere Coastal ice, fast ice, glacier, permafrost, sea ice, snow cover
Physical Bathymetry, current, evaporation, heatflux, Kd, MLD, precipitation, river discharge, salinity, SLP, air/sea temperature, sedimentation rate, suspended matter, wind
Physical Calcium carbonate (CaCO3), DIC, DOC, DON, O2, nutrients, pCO2, pH, total alkalinity
Biology Calcification, nitrogen fixation, photosynthesis, primary production, respiration, species presence/abundance
Social Fish/game landings, local and national resource management, national statistics, tourist arrivals/vessels


Meta-database (D1.2: 12 months)


Other deliverables


Cross-package interactions


  • Ny-Ålesund, Kongsfjorden, Svalbard (July - August, 2021)
    • Participated in fieldwork for WP3
    • Worked adjacent to WP2


Data issues


Complex data

  • What to do with complex data types?
    • e.g. Seabird (animal) database and geospatial data like glacier fronts
  • Who are the contacts in each WP with an opinion on this issue?

Effective data collection and dissemination

  • Who has other people working with data collection/production?
  • WP1 is tasked with archiving the FACE-IT data on PANGAEA
  • WP1 is of service to all of FACE-IT but we need to be informed
  • Ensure that Milestones are being reached

Inglefieldbukta

  • Expand the small study area of Inglefieldbukta to the much larger semi-open fjord of Storfjorden
  • WP1 has no issues with this, are there any objections?


What’s next?


  • Review article: Drivers of change in FACE-IT study sites (D1.3: 24 months)
  • Follow up meeting with site and social science coordinators


Summary


  • Who has use for the data collected and processed by WP1?
    • How would they like to access them?
    • What format(s) is most useful? (e.g. .csv, .Rdata, .nc)
    • Who has their own data collection efforts?

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.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] DT_0.33          kableExtra_1.4.0 lubridate_1.9.3  forcats_1.0.0   
 [5] stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2      readr_2.1.5     
 [9] tidyr_1.3.1      tibble_3.2.1     ggplot2_3.5.1    tidyverse_2.0.0 
[13] workflowr_1.7.1 

loaded via a namespace (and not attached):
 [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    xml2_1.3.6       
 [5] stringi_1.8.4     hms_1.1.3         digest_0.6.37     magrittr_2.0.3   
 [9] timechange_0.3.0  evaluate_0.24.0   grid_4.4.1        fastmap_1.2.0    
[13] rprojroot_2.0.4   jsonlite_1.8.8    processx_3.8.4    whisker_0.4.1    
[17] ps_1.8.0          promises_1.3.0    httr_1.4.7        fansi_1.0.6      
[21] crosstalk_1.2.1   viridisLite_0.4.2 scales_1.3.0      jquerylib_0.1.4  
[25] cli_3.6.3         rlang_1.1.4       munsell_0.5.1     withr_3.0.1      
[29] cachem_1.1.0      yaml_2.3.10       tools_4.4.1       tzdb_0.4.0       
[33] colorspace_2.1-1  httpuv_1.6.15     vctrs_0.6.5       R6_2.5.1         
[37] lifecycle_1.0.4   git2r_0.33.0      htmlwidgets_1.6.4 fs_1.6.4         
[41] pkgconfig_2.0.3   callr_3.7.6       pillar_1.9.0      bslib_0.8.0      
[45] later_1.3.2       gtable_0.3.5      glue_1.7.0        Rcpp_1.0.13      
[49] systemfonts_1.1.0 highr_0.11        xfun_0.47         tidyselect_1.2.1 
[53] rstudioapi_0.16.0 knitr_1.48        htmltools_0.5.8.1 svglite_2.1.3    
[57] rmarkdown_2.28    compiler_4.4.1    getPass_0.2-4