├── .Rbuildignore ├── .gitattributes ├── .github └── workflows │ ├── builds.yml │ ├── clang-check.yml │ ├── cran-check.yml │ ├── mac-check.yml │ ├── releases.yml │ ├── rhub.yaml │ └── sanitizer.yml ├── .gitignore ├── CHANGELOG.md ├── DESCRIPTION ├── NAMESPACE ├── R ├── .Rhistory ├── Build_Priors.R ├── MAdensity_plot.R ├── NTP.R ├── RcppExports.R ├── TOXICR_GLOBALS.R ├── cleveland_plot.R ├── cont_functions.R ├── continuous_clean.R ├── continuous_plots.R ├── continuous_pvalue.R ├── continuous_wrappers.R ├── data_checks.R ├── dicho_functions.R ├── dichotomous_plots.R ├── dichotomous_wrappers.R ├── model_averaging_fits.R ├── opening_messages.R ├── predict.R ├── prior_classes.R ├── summary_continuous.R ├── summary_dichotomous.R ├── sysdata.rda └── update_ToxicR.R ├── README.md ├── cleanup ├── configure ├── configure.ac ├── cran-comments.md ├── data ├── data.RData ├── hemotology.RData └── ntp_599.RData ├── inst └── COPYRIGHTS ├── man ├── MAdensity_plot.Rd ├── cauchyprior.Rd ├── cleveland_plot.Rd ├── create_continuous_prior.Rd ├── create_dichotomous_prior.Rd ├── create_prior_list.Rd ├── dichotomousDR.Rd ├── gammaprior.Rd ├── lnormprior.Rd ├── ma_build_priors.Rd ├── ma_continuous_fit.Rd ├── ma_dichotomous_fit.Rd ├── normprior.Rd ├── ntp_599_female.Rd ├── ntp_599_hemotology.Rd ├── ntp_dunn.Rd ├── ntp_dunnett.Rd ├── ntp_jonckeere.Rd ├── ntp_polyk.Rd ├── ntp_shirley.Rd ├── ntp_weight_data.Rd ├── ntp_williams.Rd ├── pertprior.Rd ├── prep.Rd ├── single_continuous_fit.Rd ├── single_dichotomous_fit.Rd └── update_ToxicR.Rd ├── src ├── Makevars.in ├── Makevars.ucrt ├── Makevars.win ├── RcppExports.cpp ├── cmake-3.31.0.tar.gz ├── code_base │ ├── .DS_Store │ ├── DichGammaBMD_NC.cpp │ ├── DichLogProbitBMD_NC.cpp │ ├── DichLogisticBMD_NC.cpp │ ├── DichProbitBMD_NC.cpp │ ├── DichQlinearBMD_NC.cpp │ ├── DichWeibullBMD_NC.cpp │ ├── IDPrior.cpp │ ├── IDPriorMCMC.cpp │ ├── Makefile.am │ ├── analysis_of_deviance.cpp │ ├── analysis_of_deviance.h │ ├── bmdStruct.cpp │ ├── bmdStruct.h │ ├── continuous_clean_aux.cpp │ ├── continuous_clean_aux.h │ ├── continuous_entry_code.cpp │ ├── continuous_entry_code.h │ ├── continuous_model_functions.cpp │ ├── continuous_model_functions.h │ ├── dichotomous_entry_code.cpp │ ├── dichotomous_entry_code.h │ ├── gradient.cpp │ ├── gradient.h │ ├── helperfunctions.cpp │ ├── list_r_conversion.h │ ├── lognormalModels.cpp │ ├── lognormal_EXP_NC.cpp │ ├── lognormal_EXP_aerts_NC.cpp │ ├── lognormal_GAMMA_aerts_NC.cpp │ ├── lognormal_GAMMA_efsa_NC.cpp │ ├── lognormal_HILL_NC.cpp │ ├── lognormal_HILL_aerts_NC.cpp │ ├── lognormal_IEXP_aerts_NC.cpp │ ├── lognormal_IGAMMA_aerts_NC.cpp │ ├── lognormal_ILOGSKEW_aerts_NC.cpp │ ├── lognormal_ILOMAX_aerts_NC.cpp │ ├── lognormal_LMS_NC.cpp │ ├── lognormal_LOGISTIC_aerts_NC.cpp │ ├── lognormal_LOGNORMAL_aerts_NC.cpp │ ├── lognormal_LOGSKEW_aerts_NC.cpp │ ├── lognormal_LOMAX_aerts_NC.cpp │ ├── lognormal_POLYNOMIAL_NC.cpp │ ├── lognormal_POWER_NC.cpp │ ├── lognormal_PROBIT_aerts_NC.cpp │ ├── normalModels.cpp │ ├── normal_EXP_NC.cpp │ ├── normal_EXP_aerts_NC.cpp │ ├── normal_FUNL_NC.cpp │ ├── normal_GAMMA_aerts_NC.cpp │ ├── normal_GAMMA_efsa_NC.cpp │ ├── normal_HILL_NC.cpp │ ├── normal_HILL_aerts_NC.cpp │ ├── normal_IEXP_aerts_NC.cpp │ ├── normal_IGAMMA_aerts_NC.cpp │ ├── normal_ILOGSKEW_aerts_NC.cpp │ ├── normal_ILOMAX_aerts_NC.cpp │ ├── normal_LMS_NC.cpp │ ├── normal_LOGISTIC_aerts_NC.cpp │ ├── normal_LOGNORMAL_aerts_NC.cpp │ ├── normal_LOGSKEW_aerts_NC.cpp │ ├── normal_LOMAX_aerts_NC.cpp │ ├── normal_POLYNOMIAL_NC.cpp │ ├── normal_POWER_NC.cpp │ ├── normal_PROBIT_aerts_NC.cpp │ ├── normal_likelihoods.cpp │ ├── owenst_asa076.cpp │ ├── owenst_asa076.h │ ├── seeder.cpp │ ├── skewnorm_optim.cpp │ ├── stdafx.cpp │ ├── stdafx.h │ └── targetver.h ├── include │ ├── DichGammaBMD_NC.h │ ├── DichHillBMD_NC.h │ ├── DichLogLogisticBMD_NC.h │ ├── DichLogProbitBMD_NC.h │ ├── DichLogisticBMD_NC.h │ ├── DichMultistageBMD_NC.h │ ├── DichProbitBMD_NC.h │ ├── DichQlinearBMD_NC.h │ ├── DichWeibullBMD_NC.h │ ├── IDPrior.h │ ├── IDPriorMCMC.h │ ├── binomModels.h │ ├── binomialTests.h │ ├── bmd_calculate.h │ ├── bmds_entry.h │ ├── cBMDstatmod.h │ ├── cmodeldefs.h │ ├── dBMDstatmod.h │ ├── log_likelihoods.h │ ├── lognormalModels.h │ ├── lognormalTests.h │ ├── lognormal_EXP_NC.h │ ├── lognormal_EXP_aerts_NC.h │ ├── lognormal_GAMMA_aerts_NC.h │ ├── lognormal_GAMMA_efsa_NC.h │ ├── lognormal_HILL_NC.h │ ├── lognormal_HILL_aerts_NC.h │ ├── lognormal_IEXP_aerts_NC.h │ ├── lognormal_IGAMMA_aerts_NC.h │ ├── lognormal_ILOGSKEW_aerts_NC.h │ ├── lognormal_ILOMAX_aerts_NC.h │ ├── lognormal_LMS_NC.h │ ├── lognormal_LOGISTIC_aerts_NC.h │ ├── lognormal_LOGNORMAL_aerts_NC.h │ ├── lognormal_LOGSKEW_aerts_NC.h │ ├── lognormal_LOMAX_aerts_NC.h │ ├── lognormal_POLYNOMIAL_NC.h │ ├── lognormal_POWER_NC.h │ ├── lognormal_PROBIT_aerts_NC.h │ ├── lognormal_likelihoods.h │ ├── mcmc_anal.h │ ├── mcmc_analysis.h │ ├── mcmc_struct.h │ ├── normalModels.h │ ├── normalTests.h │ ├── normal_EXP_NC.h │ ├── normal_EXP_aerts_NC.h │ ├── normal_FUNL_NC.h │ ├── normal_GAMMA_aerts_NC.h │ ├── normal_GAMMA_efsa_NC.h │ ├── normal_HILL_NC.h │ ├── normal_HILL_aerts_NC.h │ ├── normal_IEXP_aerts_NC.h │ ├── normal_IGAMMA_aerts_NC.h │ ├── normal_ILOGSKEW_aerts_NC.h │ ├── normal_ILOMAX_aerts_NC.h │ ├── normal_LMS_NC.h │ ├── normal_LOGISTIC_aerts_NC.h │ ├── normal_LOGNORMAL_aerts_NC.h │ ├── normal_LOGSKEW_aerts_NC.h │ ├── normal_LOMAX_aerts_NC.h │ ├── normal_POLYNOMIAL_NC.h │ ├── normal_POWER_NC.h │ ├── normal_PROBIT_aerts_NC.h │ ├── normal_likelihoods.h │ ├── normal_lomax_NC.h │ ├── probit_hill_NC.h │ ├── seeder.h │ ├── skewnorm_optim.h │ ├── statisticalmodel.h │ └── statmod.h ├── main_entry.cpp ├── main_entry_ma.cpp ├── main_entry_mcmc.cpp ├── main_polyk.cpp ├── main_seeder.cpp ├── nlopt-src.tar.gz ├── polyK │ ├── polyK.cpp │ ├── polyK.h │ ├── polyK_animal.h │ ├── polyK_setup.cpp │ └── polyK_setup.h ├── scripts │ ├── cmake_config.sh │ ├── cmake_install.sh │ ├── nlopt_cleanup.sh │ ├── nlopt_download.sh │ ├── nlopt_install.sh │ └── r_config.sh └── set_omp_threads.cpp ├── tests ├── comprehensive_tests │ ├── all_tests.R │ ├── datasets │ │ ├── intermediate_control_mean.txt │ │ ├── intermediate_control_stdev.txt │ │ ├── negative_control_mean.txt │ │ ├── negative_control_stdev.txt │ │ ├── positive_control_A2M_7932_results.csv │ │ ├── positive_control_ABCC3_7941_results.csv │ │ ├── positive_control_ACOT1_7968_results.csv │ │ ├── positive_control_ACOT2_7969_results.csv │ │ ├── positive_control_ALDH1A1_8022_results.csv │ │ ├── positive_control_ANXA7_8051_results.csv │ │ ├── positive_control_APOA1_33150_results.csv │ │ ├── positive_control_BTG3_33276_results.csv │ │ ├── positive_control_CCNG1_32302_results.csv │ │ ├── positive_control_EPHX1_8567_results.csv │ │ ├── positive_control_GDF15_33113_results.csv │ │ ├── positive_control_HSPB1_8847_results.csv │ │ ├── positive_control_MGLL_9227_results.csv │ │ ├── positive_control_STAC3_9953_results.csv │ │ ├── positive_control_TM7SF2_10031_results.csv │ │ ├── positive_control_mean.txt │ │ └── positive_control_stdev.txt │ └── helper.R ├── testthat.R └── testthat │ ├── helper.R │ ├── test-bounds.R │ ├── test-ma_continuous.R │ ├── test-ma_dichotomous.R │ ├── test-omp.R │ ├── test-seeder.R │ ├── test-single_continuous_laplace.R │ ├── test-single_continuous_mcmc.R │ ├── test-single_continuous_mle.R │ ├── test-single_dichotomous_laplace.R │ ├── test-single_dichotomous_mcmc.R │ ├── test-single_dichotomous_mle.R │ └── test-single_dichotomous_mle_2.R ├── tools ├── cmake_call.sh └── winlibs.R └── vignettes ├── .DS_Store ├── .gitignore └── Continuous.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NIEHS/ToxicR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | 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