Maintenance Road Map

[steffilazerte]

Hi @annecori (CC @CyGei, @noamross)

👋🏼 I'm @steffilazerte (with rOpenSci, we chatted a couple of weeks ago), and I've been tasked with helping to organize the maintenance needs of RECON packages. The first thing we want to do is figure out what this packages need, maintenance-wise.

Based on the conversations we've had and the issues currently open in the repository, below I've listed what I think are the maintenance needs for EpiEstim. I've also created a couple of draft issues in the RECON Maintenance Roadmap. If you agree with this outline, I'll create these issues in EpiEstim, and then the next step will be to decide what the priorities are and what kind of support you need to get started (i.e. funds to hire a developer, or help from a developer from rOpenSci, etc.).

Let me know if you have any questions, of if I've missed something important. Thank you! 🙏🏼

---

📝 - Indicates a draft issue in the Project only for now (I'll turn them into real issues once you've had a chance to review/approve)

• 📝 Update Documentation

  • Struggling to interpret discr_si  #142
  • Document use of incidence2 as inputs #154
  • vignettes are not automatically visible #149
  • estimate of serial interval  #107
  • vdiffr tests broken #106
  • Uncertain-SI resampling process does not conform to description #103
  • Add info to README.md as in RECON packages #43
  • add reference to Thompson et al. #37
  • Clearer deliniation illustrative and live vignette code #165

• 📝 General Code Review

  • 📝 Release on CRAN
    • estimate_advantage is not available if the package is installed using install.packages() #151
  • more helpful error message if incidence format and structure issues #136
  • Catch non-integer inputs #134
  • Check for zero incidence in estimate_joint  #130
  • estimate_join fails with uninformative error #120
  • change distribution names to be more meaningful #39
  • 📝Clean up stale branches

• 📝Fix, add, and update tests

  • 📝 Update tests (Part of Change default value of backimputation_window #167)

• 📝 Improve compatibility with RECON packages

  • make EpiEstim compatible with incidence2 #166
  • Use incidence2 inputs #153
  • 📝 Make compatible with indidence::incidence()(Part of Change default value of backimputation_window #167)

• Improved functionality

  • Combine backimputation_window & aggregated incidence #168
  • 📝 Decide on functionality (Part of Change default value of backimputation_window #167)
  • Change default value of backimputation_window #167
  • Matching vector lengths to original timeseries #162
  • Turn estimate_R into a generic with S3 methods #152
  • Return posterior draws for R in estimate_R #150
  • When reordering incidence, also change the priors in estimate_advantage #137
  • improvement for mutivariants #124
  • Improve implementation of reordering within estimate_joint #118
  • Handle imported cases in multi-variant estimation #117
  • estimate_joint should return similar output to estimate_R #115
  • Create S3 classes for outputs #46

• Bug fixes

  • estimate_joint fails when location is 1 (duplicate issues)
    • trying with single location #121
    • Estimate_joint fails when number of locations = 1 #119
    • estimate_joint fails when number of locations is 1 #114
  • method argument not used in make_config() #157
  • estimate_R() error when dates are not consecutive #141

• Done/Stale?

  • Create a pkgdown website for EpiEstim #155 & Add website #45
  • TODO for weekly work #147
  • For more than 3 variants, rate update is incorrect #123
  • Initial value for epsilon is really high in estimate_joint #122
  • Changing the title of estimate_R plot #104
  • Apply EpiEstim to real daily covid data #102
  • Comparison of EpiEstim::wallinga_teunis and R0::est.R0.TD #94
  • Allow negative-valued SI (COVID-19 modelling) #90
  • Clean the doc #53 (part of general Code Review, but now would recommend markdown)
  • compatibility with old CRAN version #40
  • change outputs of functions to be snake_case #32
  • change example dataset names to be snake_case #31
  • change argument names to be snake_case #30

[annecori]

• estimate of serial interval estimate of serial interval  #107 - I don't think this is a documentation issue but a potential bug
• clean up stale branches - @steffilazerte can you lead that?
• clean the doc Clean the doc #53 - @steffilazerte same question?
• change argument names to be snake_case #30, change example dataset names to be snake_case #31 and change outputs of functions to be snake_case #32 same, with some caveats noted int he comments of the issues
• update tests - for the specific issue on back calculation I tagged @sangeetabhatia03. I think @sangeetabhatia03 is best placed to review all tests and add some but @steffilazerte if you can support perhaps by identifying areas of poor test coverage etc that would be great.

[steffilazerte]

Hi @anne, yes I can do this! I'll start by reviewing what's going on then let you know my plan of attack/get started, depending on the task.

[steffilazerte]

Hi @annecori!

I'm going to get started on these tasks and will tackle them as follows:

0. I'll also report on test coverage as I go as this doesn't require too much active coding to get figured out.
1. Clean up the docs, I'll do this quickly in a new PR and we can hopefully get it merged in before too much other work gets going
2. Check the name cases (I'll probably keep an eye out as I work on cleaning the docs)
3. Finally I'll clean up and confer with others bout the stale branches.