Export LFMCMC

[apulsipher]

This pull request introduces several significant updates, including the addition of a new Likelihood-Free Markov Chain Monte Carlo (LFMCMC) functionality, various improvements to the codebase, and updates to documentation and configuration files.

New Features:

• Likelihood-Free Markov Chain Monte Carlo (LFMCMC):
  • Added the LFMCMC class and associated methods for performing LFMCMC simulations (R/LFMCMC.R).
  • Introduced corresponding C++ functions for LFMCMC (R/cpp11.R).
  • Updated NAMESPACE to export new LFMCMC-related functions (NAMESPACE). [1] [2] [3] [4]

Codebase Improvements:

• Docker and VSCode Configuration:
  • Updated Dockerfile to install debugging tools (.devcontainer/Dockerfile).
  • Added cinttypes to VSCode settings (.vscode/settings.json).
• Makefile Enhancements:
  • Fixed a typo in the docs target and added a new dev target for building without vignettes (Makefile).

Documentation and Configuration:

• Documentation Updates:
  • Corrected the roxygenize function call in the Makefile (Makefile).
• Project Configuration:
  • Updated project settings to avoid cleaning before installing (epiworldR.Rproj).

Minor Enhancements:

• C++ Enhancements:
  • Added new methods to the DataBase class for transition matrices and recording transmissions (inst/include/epiworld/database-bones.hpp, inst/include/epiworld/database-meat.hpp). [1] [2] [3] [4] [5]
  • Updated LFMCMC class to use std::shared_ptr for the random number engine (inst/include/epiworld/math/lfmcmc/lfmcmc-bones.hpp).
  • Introduced a new distributions.hpp file for mathematical distributions (inst/include/epiworld/math/distributions.hpp).

Version Update:

• Version Bump:
  • Incremented the minor and patch version numbers (inst/include/epiworld/epiworld.hpp).

These changes collectively enhance the functionality, maintainability, and usability of the codebase.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 6 lines in your changes missing coverage. Please review.

Project coverage is 19.07%. Comparing base (b9a29fc) to head (08e677b).

Files with missing lines	Patch %	Lines
R/LFMCMC.R	0.00%	3 Missing ⚠️
src/lfmcmc.cpp	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #27      +/-   ##
==========================================
- Coverage   19.14%   19.07%   -0.07%     
==========================================
  Files          34       36       +2     
  Lines        1776     1782       +6     
==========================================
  Hits          340      340              
- Misses       1436     1442       +6     

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[apulsipher]

@gvegayon I implemented set_kernel_fun and set_proposal_fun. For the vignette, I wrote R versions of kernel_fun_uniform and proposal_fun_normal because the gaussian kernel and the norm reflective proposal functions are more complicated and I felt it would clutter the vignette. However, the result of the vignette is now much different from the example in the C++ library. Is that going to be okay? Or should I revert the vignette to have use_proposal_norm_reflective and use_kernel_fun_gaussian instead of the R-defined versions?

[gvegayon]

I haven't executed the C++ version in a while, so maybe it is not so different now! Anyhow, I think that, for the moment, the only relevant issue is the following warning reported by R CMD check:

Found the following significant warnings:
  ../inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp:55:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]

That is on the C++ side, so it would need to be addressed directly on epiworld C++. Can you fix that via a PR (another patch update). Once that's done, I think we can merge 🥳!

[gvegayon]

A couple of comments before merging. The main one is to ensure the version in DESCRIPTION matches the version of epiworld.hpp. Once that's addressed, you can merge!

[apulsipher]

@gvegayon Does everything look okay now?

[gvegayon]

Please squash and merge :)