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Export LFMCMC#27

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apulsipher merged 73 commits intomainUofUEpiBio/epiworldR:mainfrom 25-export-lfmcmcUofUEpiBio/epiworldR:25-export-lfmcmcCopy head branch name to clipboardNov 5, 2024

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Commits

Commits on Oct 15, 2024

• Create LFMCMC.R and lfmcmc.cpp

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• Fix pre-commit style failures

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• Using tidyverse 4.4.0 as base dev image

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• Merge branch 'dev-image' of github.com:UofUEpiBio/epiworldR into 25-export-lfmcmc

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• Fix roxygenize typo in Makefile

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• Run 'make docs' and add cpp11, NAMESPACE, and roxygen files

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• Add config.log and config.status to gitignore

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• Run pre-commit on existing docs files

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Commits on Oct 16, 2024

• Add epiworld_double macro to Makevars

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• Add run method to LFMCMC

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• Add set_observed_data to LFMCMC

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• Add set_proposal_fun, set_simulation_fun, set_summary_fun, and set_kernel_fun

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• Document LFMCMC functions

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• Add basic example and try resolving generic run class warning

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• Run roxygen2 on LFMCMC

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Commits on Oct 17, 2024

• Rename LFMCMC run function to run_lfmcmc

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• Add epiworld_double macro to Makevars.win

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• Create likelihood-free0mcmc.Rmd

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• Add TODO tags to mark needed work

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• Add seed, set_param_nams_, set_stats_names, print to lfmcmc

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• Update documentation on LFMCMC

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• Document params for print.epiworld_lfmcmc

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• Setup function ordering for likelihood-free-mcmc.Rmd

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• Make lfmcmc vignette simpler to start

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• Add set_simulation_fun in lfmcmc vignette

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• Try vignette without piping

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Commits on Oct 21, 2024

• Add UseMethod export for base version of LFMCMC class methods

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• Clean up vignette to separate failing block

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Commits on Oct 22, 2024

• Add create_LFMCMCMSimFun_cpp()

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• Add lambda return type

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• Fix lambda param mismatch with LFMCMCMSimFun and set correctly in se_simulation_fun_cpp

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• Add factory methods for summary, proposal, kernel functions

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Commits on Oct 23, 2024

• Add set_rand_engine function and update constructor to extract rand_engine from model

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• Document param in updated LFMCMC constructor

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• Update LFMCMC example in .R file

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• Make lfmcmc constructor more readable

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• Add factory methods for norm_reflective proposal function and gaussian kernel function

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• Delete prop and kernel function defs after using factory methods

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• Add cinttypes to .vscode/settings.json

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Commits on Oct 24, 2024

• Minor tweaks to lfmcmc vignette simfun

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• Minor changes and adding valgrind to docker

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• Add simpler use proposal/kernel functions

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• Clean up create sum and create sim fun in lfmcmc.cpp

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Commits on Oct 29, 2024

• Remove 'create' lfmcmc methods to instead create the function within the 'set' methods and add temp test code

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• New version of epiworld

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• Getting closer

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• Updating epiworld

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Commits on Oct 31, 2024

• Sync with latest version of epiworld

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• Add dev option to Makefile to build and install without vignettes

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• Now is running

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• Changing param

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• Clean up Makefile

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• Clean up comments and unneed function

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Commits on Nov 4, 2024

• Clean up LFMCMC vignette

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• Remove second parameter in R version of simulation and summary functions

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• Restore seed_lfmcmc_cpp()

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• Cleaning up files

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• Resolve merge conflicts

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• Merge branch 'main' of github.com:UofUEpiBio/epiworldR into 25-export-lfmcmc

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• Sync with C++ epiworld library

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• Remove seed_lfmcmc

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• Add seed to run_lfmcmc

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• Update LFMCMC.R to match order of lfmcmc.cpp

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• Add comment blocks to lfmcmc.cpp to improve file navigation

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• Implement set_kernel_fun

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• Implement set_proposal_fun

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• Update comments in vignette

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• Sync with c++ library

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• Fill out fields for roxygen docs of LFMCMC

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• Create test-lfmcmc.R and populate with example from vignette

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Commits on Nov 5, 2024

• Sync with C++ epiworld library

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• Sync with c++ epiworld library

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• Update version number to match C++ library

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