DO NOT MERGE {main-> niehs} #4
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Commits on Jun 19, 2021
Commits on Jun 21, 2021
Commits on Jun 22, 2021
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Merge branch 'SL_dataviz' of https://github.com/wheelemw/RBMDS into S…
…L_dataviz Starting Merge for SL's final commit
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Merge branch 'SL_dataviz' into ToxicR
merge current ToxicR with SL_dataviz#
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Commits on Jun 23, 2021
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Merge branch 'ToxicR' of https://github.com/wheelemw/RBMDS into ToxicR
Merging stuff for simulations
Commits on Jun 26, 2021
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Merge branch 'master' into EMVL
Conflicts: ToxicR/src/Makevars ToxicR/src/code_base/bmdStruct.h ToxicR/src/code_base/continuous_entry_code.cpp ToxicR/src/include/mcmc_analysis.h
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Commits on Aug 11, 2021
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Commits on Aug 16, 2021
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Commits on Aug 23, 2021
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Shirley is done. Shirley you can't be serious. I am serious and don't…
… call me Shirley.
Commits on Aug 24, 2021
Commits on Aug 25, 2021
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Added checking for negative deviances and dfs for GSL CDF call. Fixed…
… issues with compilation on Visual Studio.
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Commits on Aug 30, 2021
Commits on Sep 13, 2021
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Added calcs for parameter confidence intervals. Fixed wrapper so that…
… log-normal distributions only run for exponential models
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Commits on Sep 17, 2021
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Fixed (again) wrapper so that log-normal distributions only run for e…
…xponential models
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Commits on Nov 16, 2021
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* Tests for single continuous models (Laplace and MLE)
* One test for model averaging models * Added required dependencies to DESCRIPTION file
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* Dichotomous model tests * Fixed BMD list to have correct names for Laplace MA models
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* Fixed minor bug with model$bmd named lists
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* Power / log-normal priors generate an error message
* Cleveland plots work for MCMC models * Testing for all MCMC single models * Plot testing for single and MA models
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* Structure of MCMC models is now the same as Laplace/MLE
* Plots updated to reflect MCMC model structure changes * Additional tests for plots
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MLE Hill and Polynomial bounds now depend on whether response is incr…
…easing or decreasing.
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* Goodness of fit added to R object for dichotomous models
* All fit functions now take vectors as well as matrices (tests also updated) * Multithreaded compilation turned on
Commits on Nov 17, 2021
Commits on Nov 18, 2021
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Commits on Jan 3, 2022
Commits on Jan 7, 2022
Commits on Jan 11, 2022
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Added checking of BMD values for valid result. Added alpha restrictio…
…n for poly model
Commits on Jan 19, 2022
Commits on Jan 25, 2022
Commits on Jan 26, 2022
Commits on Feb 18, 2022
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Merge branch 'main' of https://github.com/NIEHS/ToxicR into EMVL
Conflicts: .gitignore LICENSE README.md
Commits on Mar 7, 2022
Commits on Mar 8, 2022
Commits on Mar 14, 2022
Commits on Apr 11, 2022
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Commits on Apr 21, 2022
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Merge branch 'main' of https://github.com/wheelemw/ToxicR into main Conflicts: .gitignore CHANGELOG.md NAMESPACE R/.Rhistory R/summary_continuous.R R/summary_dichotomous.R README.md src/.Rhistory src/code_base/.Rhistory src/include/.Rhistory tests/testthat/test-ma_dichotomous.R vignettes/.gitignore
Commits on Apr 22, 2022
Commits on Apr 26, 2022
Commits on May 18, 2022
Commits on May 24, 2022
Commits on May 25, 2022
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add gitlab continuous integration (#2)
* gitlab ci? * updates * keep going... * keep going... * add template * make executable * build * more * take 2 * updates * only save the so
Commits on May 28, 2022
Commits on Jun 10, 2022
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Merge branch 'main' of https://github.com/NIEHS/ToxicR into main
Conflicts: CHANGELOG.md DESCRIPTION NAMESPACE R/dichotomous_wrappers.R R/model_averaging_fits.R R/predict.R R/summary_continuous.R R/summary_dichotomous.R README.md configure.ac src/Makevars src/code_base/continuous_entry_code.cpp src/code_base/dichotomous_entry_code.cpp src/main_entry.cpp tests/testthat/helper.R tests/testthat/test-single_dichotomous_mle_2.R
Commits on Jun 27, 2022
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Commits on Aug 26, 2022
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reimplemented adv dir restricted exp condition. Added checks for dof=…
…0 for p-value return value
Commits on Sep 28, 2022
Commits on Nov 22, 2022
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pybmds + license + github actions (#7)
* begin work * fix install issues * add makefile tests * remove report info * add cache restore * add pycpp * update wheels * ci changes * updates? * fix tests? * debugging * rewrite tests from debugging * move things to setup.py> * Revert "move things to setup.py>" * simplify package for proper wheels? * remove pythonpath * Revert "remove pythonpath" * Revert "simplify package for proper wheels?" * Revert "Revert "move things to setup.py>"" * Revert "move things to setup.py>" * Revert "rewrite tests from debugging" * Revert "debugging" * fix wheel generation? * wheel cleanup? * cleanup and final tests * change when actions are executed * final cleanup of makefile * Update README.md
Commits on Jan 31, 2023
Commits on Feb 21, 2023
Commits on Feb 23, 2023
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* build updates * Added debug output for continous_analysis struct * more edits * remove debug * remove more cout * add strip to libDRBMD.so to reduce filesize * remove custom gsl * update * update dockerfile * update build * updates * fix path * updates * updates gitlab ci * fix path * python 3.11 and remove hard-coded environments * fix missing $ * fix final copy? * remove old types --------- Co-authored-by: Cody Simmons <[email protected]>
Commits on Mar 10, 2023
Commits on Mar 14, 2023
Commits on Apr 25, 2023
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change build system to use Cmake (#9)
* cmake build 1st draft * clean up for linux build process * Added Windows build commands * updates for python builds and versions * python version bump; start actions work * updates from CI * cleanup for pull request. changed python module name. * updated tests to remove version assert * run `make format` --------- Co-authored-by: Andy Shapiro <[email protected]>
Commits on Apr 26, 2023
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switch python linters to ruff (#10)
* cmake build 1st draft * clean up for linux build process * Added Windows build commands * updates for python builds and versions * python version bump; start actions work * updates from CI * cleanup for pull request. changed python module name. * updated tests to remove version assert * run `make format` * add build/dist commands on windows * switch to ruff * remove setuptools.cfg * remove old zip_safe --------- Co-authored-by: Cody Simmons <[email protected]>
Commits on Apr 27, 2023
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* setup workspace * sudo * again * again * fix parens * gsl? * change dir * config * ? * another * ?? * d * remove override * let cmake do its thing * nlopt * add eigen * cpp * add manual trigger
Commits on May 1, 2023
Commits on May 8, 2023
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* basic struct to pybind11 * First draft of python compatible structs * Finished single dicho analysis
Commits on May 22, 2023
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* basic struct to pybind11 * First draft of python compatible structs * Finished single dicho analysis * Completed DichoMA * cleaned up print statements
Commits on May 23, 2023
Commits on May 25, 2023
Commits on May 31, 2023
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* model src and test cpp * added python hooks for continuous models
Commits on Jun 7, 2023
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* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * added BMD print statements and reformatted py scripts * added bypass of format print statement rule
Commits on Jun 21, 2023
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* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * 1st stage of mscombo stub * code cleanup * completed multitumor stub * added nested model stubs * updated format for python script * more lint fixes
Commits on Jun 23, 2023
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* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * 1st stage of mscombo stub * code cleanup * completed multitumor stub * added nested model stubs * updated format for python script * more lint fixes * forgot to add python scripts
Commits on Sep 6, 2023
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Fix for confidence level bug (#20)
* Fix for confidence level bug * code cleanup
Commits on Sep 19, 2023
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* fixed continuous individual data runs * Fixed bug in isIncreasing parameter * added default missing values for BMD, BMDL, and BMDU
Commits on Nov 1, 2023
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* finished BMD calcs * 1st stage of mscombo development * intermediate commit for mscombo calculates BMD, but not BMDL or BMDU * added handling of removed datasets * debug attempt * added combo loglike calc * updated bmdl & bmdu methods * Added slopeFactor
Commits on Nov 2, 2023
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* finished BMD calcs * 1st stage of mscombo development * intermediate commit for mscombo calculates BMD, but not BMDL or BMDU * added handling of removed datasets * debug attempt * added combo loglike calc * updated bmdl & bmdu methods * Added slopeFactor * bug fix for windows compilation * removed unused prG and prB in struct. * bug fix for previous commit
Commits on Mar 19, 2024
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* finished BMD calcs * 1st stage of mscombo development * intermediate commit for mscombo calculates BMD, but not BMDL or BMDU * added handling of removed datasets * debug attempt * added combo loglike calc * updated bmdl & bmdu methods * Added slopeFactor * bug fix for windows compilation * removed unused prG and prB in struct. * bug fix for previous commit * fixed bmdl/bmdu multitumor convergence. Fixed cmake build files. * Added multitumor selection routines * Added setSlopeFactor methods * completed beta version of multitumor model code * Addressed comments in PR
Commits on May 7, 2024
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Add github action for windows (#13)
* here * setup paths * check eigen env * gsl? * use built-in? * again! * install nlopt? * try cmake command * install gsl * set some envs * add eigen * split up deps * updates * update path * get both * more updates * try conda gsl? * try? * enviro variables * more enviro * progress * conda? * continue * do again * test * pathfinding * use conda? * more updates * conda env list * ls some things * add path variable? * add msbuild tools * fix version? * try cloning gsl instead of anaconda * change dir to search for each library * remove versions * go back to debug gsl * fix path * fix gsl build * try to cache eigen/nlopt/gsl * adjust syntax * try fixing syntax again * try different syntax again * revert to earlier method/fix typo * get rid of .. in dependency dir * set dirs even when cache is hit * continue testing * save pybmds linux wheel * add back enviro settings --------- Co-authored-by: munnsmunns <[email protected]>
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add python type stubs to bmdscore (#26)
* add notes describing type annotation creation * update python package libraries * add stubfile generation to build commands and wheel
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