CHANGELOG.md

In Como-DTC-Collaboration/comomodels-explore: A shiny app accompanied with the package comomodels

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?

Como-DTC-Collaboration/comomodels-explore documentation built on Jan. 20, 2022, 4:49 p.m.