Skip to content

Latest commit

 

History

History
55 lines (42 loc) · 2.81 KB

CHANGELOG.md

File metadata and controls

55 lines (42 loc) · 2.81 KB

20210701

  • Enable interactive tabs for all three models: SEIRD, SEIaImIsRD, SEIRDAges
  • Currently copy-and-paste all sub-models into global.R, which will be replaced by a simple import after merging branches in comomodels

20210708

  • Use dashboard for better layout and design.
  • SEIRDAge: interactive selecting specific age_range group for visualization of simulation.

20210720

  • SEIRDAge: interactive loading contact matrices from selecting paths; interactive selecting country from list; automatically show list of age groups from loaded contact matrices

20210812

  • Built conda environment yml for the package
  • Default sliderInputs for transmission params are toggled. Display each param sliderInput bar only clicking on corresponding activeButtons in the "Model" diagram panel

20210813

  • Display each param sliderInput bar only when clicking on corresponding nodes ub the "Model" diagram panel (Ben's suggestion)

20210820

  • Add description for each population group or parameter (node) on the model diagram when clicking on.
  • Add a separate plot for Incidence and Daily deaths.
  • Aesthetics restructured (two cols in main panel)

20211012-20211013

  • Add SEIRDV
  • Add SEIRD_RU
  • Aesthetics restructured (color_breweri; not using textsize=20)

202111

  • Deployed at shinyapps.io

20220115

  • Updated all current models (SEIRD, SEIaImIsRD, SEIRDAge, SEIRDV, SEIRD_RU) with latest comomodels main branch
  • Replace actual packages codes by comomodels github packages installation
  • Set default transmission params according to those in comomodels function covid_transmission_parameters() in SEIRD, SEIRD_RU, part of SEIRDAge & SEIRDV

To do

  • Check which default covid params can be applied to which model(s)
  • New submodels to include: SEIRDVAge, SEIRDNPIAge, SEIRD_BD, SEIRD_CT
  • Interactive modification: simulation time (start, end, interval)
  • Interactive modification: contact matrices (age & time dependent)
  • [SEIRDAge] [SEIRD_RU] diagram
  • Add a brief description on how to read the SEIRD diagram.
  • [SEIRDAge] data missing for some countries in population.rda
  • [SEIRDAge] automatically identify how many contact matrices are loaded, get object names and process accordingly
  • [SEIRDV] Add to slidebar: parameters of interventions
  • [SEIRD_RU] Add plots with population summed across the R and Y communities

Problems & thoughts

  • [SEIRD_Age, SEIRD_RU] data/{population,percentrural_by_country,agedemographics_by_country,country.codetoname}.rda; consistent with the contact matrices?
  • [SEIRD_RU] For some countries, the contact_all_urban[[country]] contains NAs -> error reading contact matrices
  • [SEIRD_RU] Diagram showing showing 1-2-1 connections within/between communities, with strength (line width?) of connection depending on Connectedness param?