Measles outbreak report

[PBBlomquist]

As part of the end 2024 project with MSF, Applied Epi is creating shortened versions of sitrep templates.

The overall action is to:

• Convert the output to suit the MSF intersectional linelist format and shorten it
• Split each sitrep into two Rmds for the recoding (from generic to intersectional linelist) and the report generating part of the report

I have gone through the measles template and made the following changes:

• Removed all the instructions and created a guidance document to accompany the outbreak generating (there will be one vignette per Rmd)
• Removed the chunks that convert other linelist formats (although note originally these files are suited for DHIS2)
• Require that users specify what adm1, adm2, adm3 mean in the top 'definitions' chunk
• Removal of chunks that cannot be calculated with columns/linelist shared by Greg, e.g. related to inpatients or time to death or case definitions or facility type. Upcate: removal of many chunks as not needed for short sitrep.
• Combined/rearranged some chunks
  • Those related to loading data into one chunk called load_data.
  • Epicurves into one epicurve chunk
  • Removal of factor_vars, and code moved into standardise_values and create_vars
• Adjusted the reporting week to be a reporting date
• Added nutritional status table, and made content a bit more similar to report shared by Greg
• Move content around so there is a summary and it's not structured person, place, time (as really they all overlap!)
• So far this has reduced report producing code from 2600 to 1000 lines!

The design means it should be adaptable to the other diseases without too much trouble.

Some bits that still need work are

• Fixing of epitabulate functions: add_cfr() in overall_cfr, cfr_by_sex, cfr_by_age_group, and add_ar attack_rate_by_age_group. Note that for add_ar I just used the attack_rate() function instead.
• Create the data recoding Rmd and the guidance doc
  • note - eval = T?
  • Add data dictionary
  • What chunks should get printed?
• Finish the outbreak report and guidance
  • Fix CFRs to be clear on denominator
  • Can probably still shorten the code to remove unused objects/cols
  • Create fake data?
  • Clean up the report generating guidance doc
  • Add detailed maps - Not needed anymore
  • finalise linelist_cleaned vs linelist_processing? (recode should be linelist_recoded?)
• Generally review terminlogy - e.g. 'column' or 'variable'?
• Have them reviewed/agreed
• Add them into the package

Other (now sorted):

• Reporting weeks are strange in these reports. E.g. the report says data is as of X week but is designed for that week to be incomplete (unless MSF just uses "week of report" instead of date of report??). Cases with symptom date after the reporting week are removed but not cases with late/illogical notification date.