Last updated: 2019-11-06

workflowr checks: (Click a bullet for more information)
  • 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.

  • Repository version: 17f85e9

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    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/global/
        Ignored:    data/global_results.Rda
        Ignored:    data/global_test_trend.Rda
        Ignored:    data/global_var_trend.Rda
        Ignored:    data/global_var_trend_old.Rda
        Ignored:    data/random_bp_results_100.Rda
        Ignored:    data/random_bp_results_1000.Rda
        Ignored:    data/random_results_100.Rda
        Ignored:    data/random_results_1000.Rda
        Ignored:    data/sst_ALL_bp_results.Rda
    Untracked files:
        Untracked:  analysis/WA_pixels.Rda
        Untracked:  analysis/WA_pixels_res.Rda
    Unstaged changes:
        Modified:   .DS_Store
        Modified:   .Rprofile
        Modified:   .gitignore
        Modified:   LICENSE
        Modified:   LaTeX/FMars.csl
        Modified:   LaTeX/Frontiers_Template.docx
        Modified:   LaTeX/MHWdetection.docx
        Modified:   LaTeX/MHWdetection.tex
        Modified:   LaTeX/PDF examples/frontiers.pdf
        Modified:   LaTeX/PDF examples/frontiers_SupplementaryMaterial.pdf
        Modified:   LaTeX/README
        Modified:   LaTeX/Supplementary_Material.docx
        Modified:   LaTeX/YM-logo.eps
        Modified:   LaTeX/fig_1.jpg
        Modified:   LaTeX/fig_1.pdf
        Modified:   LaTeX/fig_1_flat.jpg
        Modified:   LaTeX/fig_1_flat.pdf
        Modified:   LaTeX/fig_2.jpg
        Modified:   LaTeX/fig_2.pdf
        Modified:   LaTeX/fig_3.jpg
        Modified:   LaTeX/fig_3.pdf
        Modified:   LaTeX/fig_4.jpg
        Modified:   LaTeX/fig_4.pdf
        Modified:   LaTeX/fig_5.jpg
        Modified:   LaTeX/fig_5.pdf
        Modified:   LaTeX/fig_6.jpg
        Modified:   LaTeX/fig_6.pdf
        Modified:   LaTeX/fig_S1.jpg
        Modified:   LaTeX/fig_S1.pdf
        Modified:   LaTeX/fig_S2.jpg
        Modified:   LaTeX/fig_S2.pdf
        Modified:   LaTeX/fig_S3.jpg
        Modified:   LaTeX/fig_S3.pdf
        Modified:   LaTeX/fig_S4.jpg
        Modified:   LaTeX/fig_S4.pdf
        Modified:   LaTeX/fig_S5.jpg
        Modified:   LaTeX/fig_S5.pdf
        Modified:   LaTeX/
        Modified:   LaTeX/frontiers.tex
        Modified:   LaTeX/frontiersFPHY.cls
        Modified:   LaTeX/frontiersHLTH.cls
        Modified:   LaTeX/frontiersSCNS.cls
        Modified:   LaTeX/frontiersSCNS.log
        Modified:   LaTeX/frontiers_SupplementaryMaterial.tex
        Modified:   LaTeX/frontiers_suppmat.cls
        Modified:   LaTeX/frontiersinHLTH&FPHY.bst
        Modified:   LaTeX/frontiersinSCNS_ENG_HUMS.bst
        Modified:   LaTeX/logo1.eps
        Modified:   LaTeX/logo1.jpg
        Modified:   LaTeX/logo2.eps
        Modified:   LaTeX/logos.eps
        Modified:   LaTeX/logos.jpg
        Modified:   LaTeX/stfloats.sty
        Modified:   LaTeX/table_1.xlsx
        Modified:   LaTeX/table_2.xlsx
        Modified:   LaTeX/test.bib
        Modified:   MHWdetection.Rproj
        Modified:   TODO
        Modified:   _references/1-s2.0-S0921818106002736-main.pdf
        Modified:   _references/1-s2.0-S092181810600275X-main.pdf
        Modified:   _references/1-s2.0-S0921818106002761-main.pdf
        Modified:   _references/1-s2.0-S0921818106002852-main.pdf
        Modified:   _references/1405.3904.pdf
        Modified:   _references/
        Modified:   _references/2013_Extremes_Workshop_Report.pdf
        Modified:   _references/24868781.pdf
        Modified:   _references/24870362.pdf
        Modified:   _references/26192647.pdf
        Modified:   _references/994.full.pdf
        Modified:   _references/A_1019841717369.pdf
        Modified:   _references/Banzon et al 2014.pdf
        Modified:   _references/Brown_et_al-2008-Journal_of_Geophysical_Research%3A_Atmospheres_%281984-2012%29.pdf
        Modified:   _references/Different_ways_to_compute_temperature_re.pdf
        Modified:   _references/Gilleland et al 2013.pdf
        Modified:   _references/Gilleland_2006.pdf
        Modified:   _references/Kuglitsch_et_al-2010-Geophysical_Research_Letters.pdf
        Modified:   _references/Modeling Waves of Extreme Temperature The Changing Tails of Four Cities.pdf
        Modified:   _references/Normals-Guide-to-Climate-190116_en.pdf
        Modified:   _references/Reynolds et al 2007.pdf
        Modified:   _references/Risk_of_Extreme_Events_Under_Nonstationa.pdf
        Modified:   _references/Russo_et_al-2014-Journal_of_Geophysical_Research%3A_Atmospheres.pdf
        Modified:   _references/WCDMP_72_TD_1500_en__1.pdf
        Modified:   _references/WMO 49 v1 2015.pdf
        Modified:   _references/WMO No 1203.pdf
        Modified:   _references/WMO-TD No 1377.pdf
        Modified:   _references/WMO_100_en.pdf
        Modified:   _references/bams-d-12-00066.1.pdf
        Modified:   _references/c058p193.pdf
        Modified:   _references/cc100.pdf
        Modified:   _references/clivar14.pdf
        Modified:   _references/coles1994.pdf
        Modified:   _references/ecology.pdf
        Modified:   _references/joc.1141.pdf
        Modified:   _references/joc.1432.pdf
        Modified:   _references/returnPeriod.pdf
        Modified:   _references/s00382-014-2287-1.pdf
        Modified:   _references/s00382-014-2345-8.pdf
        Modified:   _references/s00382-015-2638-6.pdf
        Modified:   _references/s10584-006-9116-4.pdf
        Modified:   _references/s10584-007-9392-7.pdf
        Modified:   _references/s10584-010-9944-0.pdf
        Modified:   _references/s10584-012-0659-2.pdf
        Modified:   _references/s10584-014-1254-5.pdf
        Modified:   _references/s13253-013-0161-y.pdf
        Modified:   _references/wcrpextr.pdf
        Modified:   _workflowr.yml
        Deleted:    analysis/about.Rmd
        Modified:   analysis/bibliography.bib
        Modified:   code/
        Modified:   data/.gitignore
        Modified:   data/best_table_average.Rda
        Modified:   data/best_table_focus.Rda
        Modified:   data/python/clim_py.csv
        Modified:   data/python/clim_py_joinAG_1.csv
        Modified:   data/python/clim_py_joinAG_5.csv
        Modified:   data/python/clim_py_joinAG_no.csv
        Modified:   data/python/clim_py_minD_3.csv
        Modified:   data/python/clim_py_minD_7.csv
        Modified:   data/python/clim_py_pctile_80.csv
        Modified:   data/python/clim_py_pctile_95.csv
        Modified:   data/python/clim_py_pctile_99.csv
        Modified:   data/python/clim_py_random.csv
        Modified:   data/python/clim_py_spw_11.csv
        Modified:   data/python/clim_py_spw_51.csv
        Modified:   data/python/clim_py_spw_no.csv
        Modified:   data/python/clim_py_whw_3.csv
        Modified:   data/python/clim_py_whw_7.csv
        Modified:   data/python/mhwBlock.csv
        Modified:   data/python/mhws_py.csv
        Modified:   data/python/mhws_py_joinAG_1.csv
        Modified:   data/python/mhws_py_joinAG_5.csv
        Modified:   data/python/mhws_py_joinAG_no.csv
        Modified:   data/python/mhws_py_minD_3.csv
        Modified:   data/python/mhws_py_minD_7.csv
        Modified:   data/python/mhws_py_pctile_80.csv
        Modified:   data/python/mhws_py_pctile_95.csv
        Modified:   data/python/mhws_py_pctile_99.csv
        Modified:   data/python/mhws_py_random.csv
        Modified:   data/python/mhws_py_spw_11.csv
        Modified:   data/python/mhws_py_spw_51.csv
        Modified:   data/python/mhws_py_spw_no.csv
        Modified:   data/python/mhws_py_whw_3.csv
        Modified:   data/python/mhws_py_whw_7.csv
        Modified:   data/python/sst_WA.csv
        Modified:   data/python/sst_WA_miss_ice.csv
        Modified:   data/python/sst_WA_miss_random.csv
        Modified:   data/sst_ALL_results.Rda
        Modified:   data/table_1.csv
        Modified:   data/table_2.csv
        Modified:   docs/portrait.pdf
        Modified:   output/
        Modified:   output/effect_event.pdf
        Modified:   output/fig_2_missing_only.pdf
        Modified:   output/stitch_plot_WA.pdf
        Modified:   output/stitch_sub_plot_WA.pdf
        Modified:   poster/Figures/CSIRO_logo.jpeg
        Modified:   poster/Figures/Dal_logo.jpg
        Modified:   poster/Figures/all_logo_long.jpg
        Modified:   poster/Figures/all_logos.jpg
        Modified:   poster/Figures/logo_stitching.odp
        Modified:   poster/Figures/ofi_logo.jpg
        Modified:   poster/Figures/uwc-logo.jpg
        Modified:   poster/MHWdetection.bib
        Modified:   poster/MyBib.bib
        Modified:   poster/landscape.Rmd
        Modified:   poster/landscape.pdf
        Modified:   poster/portrait.Rmd
        Modified:   poster/portrait.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.
Expand here to see past versions:
    File Version Author Date Message
    Rmd 61bf228 robwschlegel 2019-11-06 Prepped trend vignette for site re-build
    Rmd 819f11e Robert William Schlegel 2019-11-04 Updating the foundation of workflowr GitHub site
    Rmd 158aa0b robwschlegel 2019-05-06 Updated project interface
    html fb80070 Robert Schlegel 2019-05-06 Update
    Rmd 5b638ef Robert Schlegel 2019-05-06 Uploaded poster to GitHub page
    html 74aff6b Robert Schlegel 2019-05-03 Build site.
    Rmd acee19f Robert Schlegel 2019-05-03 Some updates
    Rmd 502aacf Robert Schlegel 2019-05-03 Created JPG versions of figures for draft submission
    Rmd f5fba8f Robert Schlegel 2019-05-03 Polished poster
    Rmd d5ed0d0 Robert William Schlegel 2019-05-02 Working on poster
    Rmd 9285aaa robwschlegel 2019-04-30 Snag list
    Rmd f79c3e9 robwschlegel 2019-04-30 Polished Conclusions
    Rmd c1fa0d7 robwschlegel 2019-04-30 Polished Discussion
    Rmd ad94e1d robwschlegel 2019-04-30 Polished results
    Rmd 4920c7a robwschlegel 2019-04-30 Polished Methods
    Rmd 897141e robwschlegel 2019-04-29 Created Figure 1
    Rmd 8e53a5c robwschlegel 2019-04-29 Further polishing of text
    Rmd 4dc55c8 robwschlegel 2019-04-28 Final round of comments addressed in part
    Rmd 151f5d1 robwschlegel 2019-04-26 Creating remaining figures
    Rmd bb135c3 robwschlegel 2019-04-25 Working on length fix
    Rmd 50aa5e4 robwschlegel 2019-04-24 Troubleshot the global analysis output
    Rmd 104d600 Robert Schlegel 2019-04-18 Unpacking and calculating slopes for global results
    Rmd b80fa5c robwschlegel 2019-04-17 Expanded tests to 0.5C/dec trend and 99% missing data
    Rmd d1891c0 robwschlegel 2019-04-16 Edited manuscript through to the discussion section
    Rmd 4447589 robwschlegel 2019-04-15 Global analysis error trapping
    Rmd 33966d0 robwschlegel 2019-04-15 Finished writing global analysis code and began running it
    Rmd 87caad7 robwschlegel 2019-04-14 Implemented and ran code for fixes to sub-optimal data
    Rmd 7ba5f65 robwschlegel 2019-04-11 Working towards answering Question 2
    Rmd 584d848 robwschlegel 2019-03-25 Basic figures for the re-sample workflow complete
    html 8ef792c robwschlegel 2019-03-20 Build site.
    Rmd 9f45ef7 robwschlegel 2019-03-20 Update
    html 81a2ed5 robwschlegel 2019-03-19 Build site.
    Rmd 62fe75f robwschlegel 2019-03-19 Publish the news file
    html 36100c0 robwschlegel 2019-03-19 Build site.
    Rmd 0aac666 robwschlegel 2019-03-19 Publish the menu files


  • The GitHub research website for this manuscript was updated to match the changes from the first round of revisions


  • Quite a lot has happened in the intersticing time
  • The curious reader will need to refer to the git push logs for a more detailed account unfortunately
  • The manuscript was re-submitted on November 1st # 2019-05-06

  • Uploaded poster to GitHub page
  • Updated project interface


  • Polished poster
  • Fixed a couple of figures
  • Created JPG versions of figures for draft submission
  • Submitted to FMarS MHW special issue
  • Updatted project website


  • Created a poster for the OceanPredict19 conference in Halifax


  • Added some info required in the submission process


  • Re-created all figures as necessary
  • Polished Methods
  • Polished Results
  • Polished Discussion
  • Polished Conclusions
  • Snag list


  • Further polishing of text
  • Created Figure 1
  • Prepping for LaTeX typesetting


  • Final round of comments addressed in part


  • Creating remaining figures


  • Working on length fix


  • Troubleshot the global analysis output


  • Unpacking and calculating slopes for global results
  • Re-writing Intro
  • Fleshing out Discussion


  • Expanded tests to 0.5C/dec trend and 99% missing data


  • Edited manuscript through to the discussion section
  • First pass at global analysis nearly finished


  • Global analysis error trapping


  • Implemented and ran code for fixes to sub-optimal data
  • Wrote global analysis code
  • Began running global analysis code


  • Finished first pass on answer to Question 2


  • Working towards Question 2


  • Basic figures for the re-sample workflow complete


  • Working on the consolidated workflow script


  • Switching from pkgdown to workflowr for project management/visualisation


  • Incorporated first round of edits from AJH
  • Began writing new decadal detection chunk


  • Incorporated first round of edits from AJS


  • Worked out basic event count results for all vignettes
  • Final skeleton of paper


  • More missing data work
  • Worked through basic decadal trend results


  • Working through the missing data analyses


  • Working through the duration analyses


  • More work on the skeleton
  • Beginning to flesh out the sections


  • Working over the skeleton


  • Back to business


  • Looking over skeleton of main text
  • Python issue was addressed
    • The difference was caused by the default nature of how each language did/did not interpolate missing data
    • The calculations otherwise still remained the same


  • Performed a deep dive on the issues around missing data and the quantile thresholds
    • Must look at step-by-step process in Python code to determine the issue


  • Checked that R and Python base results still match up after heatwaveR v0.3.6 release
    • The threshold calculations appear to be affected differently by large amounts of missing data


  • More editing on the time series length vignette


  • Big changes coming through
  • Added two new vignettes:
    • Assessing the effects of long-term trends
    • Assessing the effects of variance


  • Finished editing the “simply shorter” section of the time series length vignette


  • Beginning aggressive editing of text
  • Allowing calculation of events for all year ranges from 3 – 34
    • Not just 10 20, and 30 years
  • Removing all var results


  • Incorporated ECJO’s most recent round of comments into the main two vignettes.


  • Added comparison to r_vs_python.Rmd for how the two languages handle missing data to create climatologies and calculate events.
  • Completed the Ice coverage section in missing_data.Rmd


  • Finished up new proposed work on time_series_duration.Rmd
  • Output word document version of time_series_duration.Rmd and missing_data.Rmd
  • Recompiled vignettes


  • Finished up initially proposed work on missing_data.Rmd
  • Rebuilt site to reflect upversion to v0.0.3


  • Minor additions


  • Further editing to time_series_duration.Rmd


  • Finished preliminary random missing data results
  • Fixed CI issues with short time series vignette


  • Further editing to time_series_duration.Rmd
  • Began writing missing_data.Rmd
  • Rebuilt site to host changes


  • Added AJS and ECJO feedback into MHWdetection.Rmd
  • Added AJS and ECJO feedback into time_series_duration.Rmd


  • More in-depths category comparisons made


  • Some pre-emptive thoughts about more category comparisons


  • Finished up basic comparisons of categories for different clim periods


  • Added significance tests for clims of different lengths for both single and re-sampled clims


  • More work on duration section


  • More work on duration section


  • Smoothed out issues preventing site from being built
  • Tweaks to benchmarking of the languages


  • Second section of duration vignette nearly finished


  • Completed the first section of the duration vignette


  • Some musings added to the short duration vignette


  • Skeleton vignettes for the proposed research created


  • Regenerated vignettes to reflect corrections made in heatwaveR code
  • Regenerated site to reflect fixes in site structure
  • Added LaTeX folder


  • Added a file to track changes to the package.
  • Ported over the relevant vignettes that were cluttering up the heatwaveR site

This reproducible R Markdown analysis was created with workflowr 1.1.1