The scripts and data used to determine common air-sea states during MHWs along the coast of South Africa.

• The raw text of the paper may be found in "LaTeX/Schlegel_et_al.tex"
• The code used to calculate the MHWs and fit the SOM may be found in "2.Model_fitting.R"
• The code used to create the figures seen in the paper may be found in "3.Figures.R"
• The code used to create the tables seen in the paper may be found in "4.Tables.R"
• The code used to generate the specific values given in the text may be found in "5.Text.R"
• The "data" folder contains the processed data used in the analyses as well as the output of "2.Model_fitting.R"
• The "func" folder contains custom made functions used in the analyses
• The "graph" folder contains the files necessary to create maps as well as the output of "3.Figures.R"
• The "setupParams" folder contains the SACTN site list and analysis period data
• The "LaTeX" folder contains the files used to compile "/LaTeX/...", the body of the text
• The "old" folder contains scripts and data from previous versions of the analysis/ methodology

• All for loops removed from extreme event calculation work flow
• A for loop is still used to "grow" the SAWS data, allowing for it to be compared against each SACTN time series
• All possible extreme events combinations etc. have been calculated as per current agreement on methodology

• All for loops removed from the co-occurrence calculations
• Co-occurrence calculated for all combinations of SACTN and SAWS sites including tmean, tmin and tmax

• Corrected error in calculation of co-occurrence proportions
• Produced a medley of initial figures to visualise first round of results

• Removed for loop used to "grow" the SAWS data
• All extreme events re-calculated with same results

• Calculated extreme events for SAWS time series based on a static analysis period (1981 - 2010)
• Changed file naming convention for extreme event results to differentiate the results calculated with the static period
• Created function that calculates distance AND bearing between any two sites
• Calculated distance and bearing between all possible sites within and among datasets

• Improved co-occurrence workflow to allow for calculation of extreme events between AND within datasets
• Expanded results of co-occurrence analysis to also include the statistics of the co-occurring events
• No longer constraining co-occurrence rates by set periods of days
• Now the difference in days between the latest occurring events is recorded

• Calculated latest occurring events between AND within all sites AND datasets
• Added distance, bearing and coastal section metrics for compared sites
• Created a .Rmd file to explain the co-occurrence step of the work-flow

• Created figures for the largest (int_cum) heat wave and cold spell for each time series
• Explored relationships between SAWS and SACTN heat waves occurring within 7 and 2 days of one another

• A small bug was detected in the original SACTN data set
• Improved screening methods were implemented at the source to smooth this issue
• These improved methods were applied to the load step in this project as well
• All scripts were re-run with the newly screened data and all calculations/ figures compiled anew
• The final co-occurrence rates are ever so slightly higher than previously

• Fix issues in which missing SACTN values were saved as NaN instead of NA
• This had no effect on the calculations

• Wind data for Port Nolloth added to project
• Function created that can calculate mean daily wind vectors
• First draft of a figure that shows wind vectors with temperatures

• Worked out a couple of preliminary techniques for how best to visualise air, sea and wind data together during co-occurrence

• The preliminary round of air, sea, wind figures

• Updated exploratory analyses
• More work done with wind data
• Two new reports written up and knitted

• Script created to download BRAN data
• These data are saved in an external folder as they are to multitudinous for GitHub
• First steps taken for the creation of the LaTeX version of the manuscript

• Function created to load BRAN data into R in long format
• Additional text added to manuscript

• Function created to load ERA Interim data into R in long format
• First proof of concept figure for synoptic air-sea view during events created

• Reanalysis data processing pipeline improved
• Wind vectors visualised

• Summary data boxes added to synoptic air-sea figure
• Rough draft of introduction complete

• Outline of synoptic air-sea figure complete

• Calculation of daily climatologies for air-sea state
• The data frames are not stored here as they are too large

• Temperature anomalies added to synoptic figure

• Current and wind anomalies added

• Daily climatologies for girded reanalysis temperatures have now all been smoothed
• This allows for smoother temperature anomaly values to be calculated

• Cosmetic adjustments to synoptic figure

• Synoptic figure output now also saves the temp and uv values in a separate list for SOMs

• All synoptic figures created

• Proof of concept for SOMs

• SOM code automated
• Initial results visualised

• Seasonality added to output
• Individual SOMs run for each coastal section

• All functions created for SOM work flow moved to a separate script
• Alternative rescaling function for SOM results added

• Ran hierarchical cluster analysis for air-sea states during MHWs
• Began investigation into clustering of air-sea states for daily climatologies

• Hierarchical cluster analysis for air-sea state during daily climatologies

• First step towards running the three agreed upon cluster analyses on all data

• More work towards the cluster analyses

• More work towards the cluster analyses

• All variables that could affect the results of a clustering technique have been analysed

• Updates to cluster results code

• Now using principal component initialisation (PCI) rather than random initialisation (RI) for SOMs
• All SOM modelling in "LaTeX/cluster_results.Rmd" updated accordingly

• "LaTeX/cluster_results.Rmd" completed

• Additions to methods section

• Edits to intro and methods sections
• Additions to methods and results sections
• Began cleaning workflow for publication

• "1.Data_assembly.R" complete
• Removed data from GitHub not cleared for public access
• Began moving unused scripts and data to the "old" folder

• Began "2.Model_assembly.R"
• More files moved to "old" folder

• Re-created data packets for use with SOMs and synoptic figures

• Smoothing out Git push issues
• Complete documentation provided for all files

• More modeling, figures, and one table
• Additional intro, methods, and results edits

• References for clustering added to methods section
• More results written up

• Writing for results, discussion and conclusion added

• Table 2 modified
• Two new figures included
• Additional writing in manuscript

• Minor edits
• First draft complete

• First round of co-author edits

• More literature added in support of the introduction

• Additional co-author comments incorporated into text

• Code for Figure 1 added

• All comments for the Introduction section incorporated

• Progress made on methods section

• Comments for methods section wrapped up

• Phasing out BRAN in favour of AVISO and OISST
• Recalculated ERA daily clims based on new longer period
• Calculated OISST daily clims

• More phasing out of BRAN
• Calculated AVISO daily clims

• Analysis with new OISST+AVISO data complete
• New data packets created
• New synoptic atlas figures created
• New SOM figures created

• New colour palette used for SOM nodes
• SOM nodes described in the results

• Editing of results and discussion sections

• Calculated MDS and HCA with new data
• Created biplot and dendrogram
• Edits to figure 1
• Some edits to text

• More edits to text

• Notes on atmosphere

• Edits throughout texts

• Second draft ready for co-author revisions

• Figure tweaks
• Some few revisions from co-authors

• More text edits

• A few edits

• AJ's direct .tex edits
• Tweaks to most figures

• All coments on figures incorporated
• All coments not requiring re-writes incorporated

• All minor repetitive text changes made
• LaTeX file converted to Frontiers standard

• All final co-authors comments incorporated
• Several minor tweaks
• Manuscript ready for submission
• Created word document for abstract
• Created word document for cover letter
• Created the required 300dpi .tiff files for figures

• Most of round one reviewer comments addressed

• Several edits from AJ
• More reviewer comments addressed

• All reviewer comments addressed
• Manuscript re-submitted

• Minor tweaks for author proofs