seus-mbon-cruise-ctd-processing

CTD processing & reporting for the SEUS MBON research cruise data

Usage

1. clone this repository
2. put data into data/01_raw/raw_ctd_data
   • raw "mostafa/combined_data_updated" with original names
   • "mostafa/raw_ctd_data_renamed" - stations renamed to align between cruises
   • "mostafa/cleaned_Cruises" - after oce cleaning
     • see Cruise_naming_conventions.Rmd
3. build the site: quarto render --no-cache
   • NOTE: you can run with cache, but this may not generate the data/cleaned/*.csv files
4. view the site: quarto preview
5. publish to github pages: quarto publish

generated report structure

Running quarto render will complete several pre-render steps to create the following directory structure:

└── cruise_report/
    ├── cruise_report_template.qmd
    ├── ctd_report_template.qmd
    └── cruise_reports/
        ├── {cruise_id}/
        │   ├── {cruise_id}.qmd  <- generate_cruise_reports --  cruise_report_template
        │   └── ctd_reports/  
        │       ├── {ctd_id}.qmd <- generate_ctd_reports -- ctd_report_template
        │       └── ...
        └── ... 

The pre-render steps used to generate the above directory structure are summarized by the mermaid chart below.

graph TD

get_cruise_list{{get_cruise_list.R}}
  --> cruise_list[[cruise_list.csv]]

cruise_list -.->
prerender_cruise_reports[/prerender_cruise_reports.R\]
  === foreach_cruise 

%% rendering is implied for every .qmd
%% cruise_report -.->
%%   render{{render}}
%%   --> cruise_report_html[["cruise_(cruise_id)_report.html"]]

subgraph foreach_cruise
  cruise_report{{"cruise_(cruise_id)_report.qmd"}}
  prerender_cast_reports[/prerender_cast_reports.R\]
    === foreach_cast
end

subgraph foreach_cast
  cast_report{{"ctd_(cruise_id)_(cast_id)_report.qmd"}}
end

%% subgraph legend
%% script{{script.R}} 
%%   -- creates --> file[[file.txt]]

%% file -. depends .->
%%   report{{report.qmd}}

%% map[/map\]

%% reduce[\reduce/]

%%db[(database.sqlite)]

%% end