serofoi 1.0.2 release

[ntorresd]

This PR corresponds to the release of serofoi 1.0.2. The most important changes had been reviewed by the development team in the development branch. See for instance:

• Simulation functions and vignette plus other things #199
• Add unit test for fit_seromodel() #213
• Fix simulate_serosurvey unit testing and examples #217
• 215 add unit test for visualisation functionalities #223
• Add missing documentation entries #243
• Addresses R-CMD check notes about dependencies #245
• Clean dplyr syntax and references accross the package #249

serofoi 1.0.2

New features

• Serological surveys simulation functionalities

  • Introduce enhanced data simulation functionalities to support a broader range of use cases for serosurvey analysis.
  • Add a dedicated vignette for data simulation to guide users on simulating data for serosurveys.

• Enables the implementation of a wide variety of new models

  • Add forward random walk age-varying models with uniform and normal priors.
  • Improves previous implementation of forward random walk time-varying models.
  • Enables prior distributions specifications by means of package specific functions like sf_normal() and sf_uniform().
  • Support for seroreversion rate estimation for all models with uniform and normal priors.

Breaking changes

• Replaced old modelling and visualization functions, making Bayesian model selection and specification more flexible.
• New models and functionalities include constant, time-varying, and age-varying models, as well as options for estimating seroreversion rates.
• Updated the R-hat convergence threshold for model convergence diagnostics to R-hat<1.01,
  following Vehtari et al. (2021).

Minor changes

• Remove the simdata_* datasets from the package and replaced them with code-based simulation in vignettes.
• Add missing examples to exported functions
• Add missing documentation entries

Internal changes

• Unit testing

  • Added unit tests for key package functionalities, including:
    • fit_seromodel() function (Add unit test for fit_seromodel() #213).
    • Visualization functionalities (Add unit test for visualisation functionalities #215).
    • build_stan_data and related functions (Add test for functions in build_stan_data.R #232).
    • Validation functions (Add unit tests for validation functions #235).
  • Test coverage increased to 100%

• Refactorization of simulation examples

  • Replaced static simulated datasets in tests and vignettes with dynamic examples using data simulation functions.

• Documentation improvements

  • Enhanced documentation for new functionalities and updated vignettes to reflect recent changes.

[github-actions]

This pull request:

• Adds 2 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 1 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (a608a0d) to head (4be70e3).

Additional details and impacted files

@@             Coverage Diff              @@
##             main      #265       +/-   ##
============================================
+ Coverage   42.83%   100.00%   +57.16%     
============================================
  Files           4         6        +2     
  Lines         747      1015      +268     
============================================
+ Hits          320      1015      +695     
+ Misses        427         0      -427     

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[zmcucunuba]

Hello. Seem ready for release!

[github-actions]

This pull request:

• Adds 2 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 1 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

[zmcucunuba]

Ready for release