Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Export LFMCMC #27

Merged
merged 73 commits into from
Nov 5, 2024
Merged

Export LFMCMC #27

merged 73 commits into from
Nov 5, 2024

Commits on Oct 15, 2024

  1. Create LFMCMC.R and lfmcmc.cpp

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    ae2a80f View commit details
    Browse the repository at this point in the history

  2. Fix pre-commit style failures

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    bbdb724 View commit details
    Browse the repository at this point in the history

  3. Using tidyverse 4.4.0 as base dev image

    @gvegayon
    gvegayon committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    ab29fa1 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'dev-image' of github.com:UofUEpiBio/epiworldR into 25-e… 

    …xport-lfmcmc
    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    6b8cff8 View commit details
    Browse the repository at this point in the history

  5. Fix roxygenize typo in Makefile

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    7d2de78 View commit details
    Browse the repository at this point in the history

  6. Run 'make docs' and add cpp11, NAMESPACE, and roxygen files

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    037aef6 View commit details
    Browse the repository at this point in the history

  7. Add config.log and config.status to gitignore

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    4c18125 View commit details
    Browse the repository at this point in the history

  8. Run pre-commit on existing docs files

    @apulsipher
    apulsipher committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    08e677b View commit details
    Browse the repository at this point in the history

Commits on Oct 16, 2024

  1. Add epiworld_double macro to Makevars

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    b57e6cc View commit details
    Browse the repository at this point in the history

  2. Add run method to LFMCMC

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    c3d529f View commit details
    Browse the repository at this point in the history

  3. Add set_observed_data to LFMCMC

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    a6ba174 View commit details
    Browse the repository at this point in the history

  4. Add set_proposal_fun, set_simulation_fun, set_summary_fun, and set_ke… 

    …rnel_fun
    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    7259eab View commit details
    Browse the repository at this point in the history

  5. Document LFMCMC functions

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    15c6965 View commit details
    Browse the repository at this point in the history

  6. Add basic example and try resolving generic run class warning

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    fe5b263 View commit details
    Browse the repository at this point in the history

  7. Run roxygen2 on LFMCMC

    @apulsipher
    apulsipher committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    af3d486 View commit details
    Browse the repository at this point in the history

Commits on Oct 17, 2024

  1. Rename LFMCMC run function to run_lfmcmc

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    0ed6889 View commit details
    Browse the repository at this point in the history

  2. Add epiworld_double macro to Makevars.win

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    badf863 View commit details
    Browse the repository at this point in the history

  3. Create likelihood-free0mcmc.Rmd

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    202c489 View commit details
    Browse the repository at this point in the history

  4. Add TODO tags to mark needed work

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    4610179 View commit details
    Browse the repository at this point in the history

  5. Add seed, set_param_nams_, set_stats_names, print to lfmcmc

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    0dfb9a2 View commit details
    Browse the repository at this point in the history

  6. Update documentation on LFMCMC

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    91e031d View commit details
    Browse the repository at this point in the history

  7. Document params for print.epiworld_lfmcmc

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    ea35a86 View commit details
    Browse the repository at this point in the history

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

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    b4c2c6a View commit details
    Browse the repository at this point in the history

  9. Make lfmcmc vignette simpler to start

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    c512812 View commit details
    Browse the repository at this point in the history

  10. Add set_simulation_fun in lfmcmc vignette

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    4c26e7b View commit details
    Browse the repository at this point in the history

  11. Try vignette without piping

    @apulsipher
    apulsipher committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    20e83c6 View commit details
    Browse the repository at this point in the history

Commits on Oct 21, 2024

  1. Add UseMethod export for base version of LFMCMC class methods

    @apulsipher
    apulsipher committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    44c72c7 View commit details
    Browse the repository at this point in the history

  2. Clean up vignette to separate failing block

    @apulsipher
    apulsipher committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    6d59026 View commit details
    Browse the repository at this point in the history

Commits on Oct 22, 2024

  1. Add create_LFMCMCMSimFun_cpp()

    @apulsipher
    apulsipher committed Oct 22, 2024
    Configuration menu
    Copy the full SHA
    19fb187 View commit details
    Browse the repository at this point in the history

  2. Add lambda return type

    @apulsipher
    apulsipher committed Oct 22, 2024
    Configuration menu
    Copy the full SHA
    cb76f1e View commit details
    Browse the repository at this point in the history

  3. Fix lambda param mismatch with LFMCMCMSimFun and set correctly in se_… 

    …simulation_fun_cpp
    @apulsipher
    apulsipher committed Oct 22, 2024
    Configuration menu
    Copy the full SHA
    f02d864 View commit details
    Browse the repository at this point in the history

  4. Add factory methods for summary, proposal, kernel functions

    @apulsipher
    apulsipher committed Oct 22, 2024
    Configuration menu
    Copy the full SHA
    7cf7281 View commit details
    Browse the repository at this point in the history

Commits on Oct 23, 2024

  1. Add set_rand_engine function and update constructor to extract rand_e… 

    …ngine from model
    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    f48be56 View commit details
    Browse the repository at this point in the history

  2. Document param in updated LFMCMC constructor

    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    eb3da6c View commit details
    Browse the repository at this point in the history

  3. Update LFMCMC example in .R file

    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    3475207 View commit details
    Browse the repository at this point in the history

  4. Make lfmcmc constructor more readable

    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    bff88cd View commit details
    Browse the repository at this point in the history

  5. Add factory methods for norm_reflective proposal function and gaussia… 

    …n kernel function
    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    055a464 View commit details
    Browse the repository at this point in the history

  6. Delete prop and kernel function defs after using factory methods

    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    eacdc22 View commit details
    Browse the repository at this point in the history

  7. Add cinttypes to .vscode/settings.json

    @apulsipher
    apulsipher committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    cb89885 View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2024

  1. Minor tweaks to lfmcmc vignette simfun

    @apulsipher
    apulsipher committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    20bb6f3 View commit details
    Browse the repository at this point in the history

  2. Minor changes and adding valgrind to docker

    @gvegayon
    gvegayon committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    3d566f1 View commit details
    Browse the repository at this point in the history

  3. Add simpler use proposal/kernel functions

    @apulsipher
    apulsipher committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    108621a View commit details
    Browse the repository at this point in the history

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

    @apulsipher
    apulsipher committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    634d783 View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2024

  1. Remove 'create' lfmcmc methods to instead create the function within … 

    …the 'set' methods and add temp test code
    @apulsipher
    apulsipher committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    67e4137 View commit details
    Browse the repository at this point in the history

  2. New version of epiworld

    @gvegayon
    gvegayon committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    194ed2d View commit details
    Browse the repository at this point in the history

  3. Getting closer

    @gvegayon
    gvegayon committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    aa44003 View commit details
    Browse the repository at this point in the history

  4. Updating epiworld

    @gvegayon
    gvegayon committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    30d985c View commit details
    Browse the repository at this point in the history

Commits on Oct 31, 2024

  1. Sync with latest version of epiworld

    @apulsipher
    apulsipher committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    bfb0b49 View commit details
    Browse the repository at this point in the history

  2. Add dev option to Makefile to build and install without vignettes

    @apulsipher
    apulsipher committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    f9724db View commit details
    Browse the repository at this point in the history

  3. Now is running

    @gvegayon
    gvegayon committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    13a7b4d View commit details
    Browse the repository at this point in the history

  4. Changing param

    @gvegayon
    gvegayon committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    01e370d View commit details
    Browse the repository at this point in the history

  5. Clean up Makefile

    @apulsipher
    apulsipher committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    0ec4628 View commit details
    Browse the repository at this point in the history

  6. Clean up comments and unneed function

    @apulsipher
    apulsipher committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    5d8930f View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2024

  1. Clean up LFMCMC vignette

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    71e6fc1 View commit details
    Browse the repository at this point in the history

  2. Remove second parameter in R version of simulation and summary functions

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    2d0571c View commit details
    Browse the repository at this point in the history

  3. Restore seed_lfmcmc_cpp()

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    ad0cda0 View commit details
    Browse the repository at this point in the history

  4. Cleaning up files

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    dfb6827 View commit details
    Browse the repository at this point in the history

  5. Resolve merge conflicts

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    2d7920e View commit details
    Browse the repository at this point in the history

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

    …-lfmcmc
    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    af1d788 View commit details
    Browse the repository at this point in the history

  7. Sync with C++ epiworld library

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    cba14ea View commit details
    Browse the repository at this point in the history

  8. Remove seed_lfmcmc

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    9ae85f9 View commit details
    Browse the repository at this point in the history

  9. Add seed to run_lfmcmc

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    bdc3a0f View commit details
    Browse the repository at this point in the history

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

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    81ed52b View commit details
    Browse the repository at this point in the history

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

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    24d8b2b View commit details
    Browse the repository at this point in the history

  12. Implement set_kernel_fun

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    9eca06f View commit details
    Browse the repository at this point in the history

  13. Implement set_proposal_fun

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    822a522 View commit details
    Browse the repository at this point in the history

  14. Update comments in vignette

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    16461b2 View commit details
    Browse the repository at this point in the history

  15. Sync with c++ library

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    1f1e43f View commit details
    Browse the repository at this point in the history

  16. Fill out fields for roxygen docs of LFMCMC

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    d9a2f48 View commit details
    Browse the repository at this point in the history

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

    @apulsipher
    apulsipher committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    5870f7e View commit details
    Browse the repository at this point in the history

Commits on Nov 5, 2024

  1. Sync with C++ epiworld library

    @apulsipher
    apulsipher committed Nov 5, 2024
    Configuration menu
    Copy the full SHA
    5e298d8 View commit details
    Browse the repository at this point in the history

  2. Sync with c++ epiworld library

    @apulsipher
    apulsipher committed Nov 5, 2024
    Configuration menu
    Copy the full SHA
    5cb9fa9 View commit details
    Browse the repository at this point in the history

  3. Update version number to match C++ library

    @apulsipher
    apulsipher committed Nov 5, 2024
    Configuration menu
    Copy the full SHA
    48c220d View commit details
    Browse the repository at this point in the history