auxiliary/docsfordevelopers/notes-and-to-do.md

In ahgroup/DSAIRM: Dynamical Systems Approach to Immune Response Modeling

To-do list for DSAIRM package

Specific Code Improvements

• Adjust color palette for plotly to be same as ggplot (and make color blind friendly). Seems to work in generate_ggplot() but not yet in generate_plotly()
• Make sure floating taskbar works ok with inputs and is always above all other content (currently some of the inputs and the top bar are above float)

• Provide a 'download scenario' button, which downloads code that reproduces a given scenario. To that end, finish implementing download_code in develop branch, once it works move over to main. Download_code related:

• rewrite run_model.R such that it calls construct_simulation_code instead of repeating code.

• run_model.R should also be calling a separate function ( generate_output() ) that processes results returned from the app calls so it can be used with generate_() functions.
• move all code that is related to writing the R script from app.R into a generate_downloadcode function.
• improve formatting of output code by adding line breaks, e.g. every modelsetting entry in its own line.
• Don't use colons in variable names (no my.result). Instead just call it 'result' or such.
• The code that is produced by generate_downloadcode() should ONLY include the call to simulate_ and the generate_plot/text DSAIRM functions. No other DSAIRM function (including these new ones) should be used inside the code script given to users.

General Code Improvements

• Continue implementing unit tests using the testthat package
• Add checks to parameter settings, don't allow unreasonable (e.g. negative) ones
• Continue streamlining code base to make it more general/modular/flexible
• Fix/finish plot function edits (see code in generate_ggplot)

Content Improvement

• Re-create all diagrams with flowdiagramr
• Write tasks for extended bacteria and bacteria model fitting apps
• Check learning objectives to each overview tab
• Implement further apps, see below
• Once flowdiagramr is ready, use it to re-do model diagrams

Apps to be implemented

• More complicated HCV PK/PD (SISMID-U4-3/4)
• U/S analysis using regression instead of correlation (U6-us3)
• models with memory/dummy compartments (U9-memory)
• discrete-time model with noise (U9-noise)
• fitting of multiple datasets and types of data, e.g. Pawelek 2016 model
• fitting of multiple-condition datasets, e.g. with and without drug present (find old R code for this)
• fitting using different likelihood approaches (instead of just SSR)
• co-infection model

Documentation / Outreach / Advertisement

• Make list of related courses, email instructors
• Create more docs
• Find classes/instructors who could use package.
• Make videos for levels 1/2/3 for packages

General thoughts and comments

• Maybe change name of package
• look into R consortium package certification
• Get best practices badge: https://bestpractices.coreinfrastructure.org/en
• Maybe submit for Ropensci review: https://github.com/ropensci/onboarding
• Hashtags on twitter when promoting DSAIRM app: #rstats, #dynamicalsystems #immunology #infectiousdisease

ahgroup/DSAIRM documentation built on Oct. 4, 2023, 6:50 a.m.