Files in W-Mohammed/calibrater
Calibration of Decision-Analytic Models
.Rbuildignore
.gitignore
CRS_scripts/CR.qmd
CRS_scripts/Chapter_2_plots.R
CRS_scripts/Chapter_3_case_1.R
CRS_scripts/Chapter_3_case_2.R
CRS_scripts/Chapter_3_case_3.R
CRS_scripts/Chapter_3_case_4.R
CRS_scripts/Chapter_3_case_5.R
CRS_scripts/Chapter_3_plots.R
CRS_scripts/Chapter_4_plots.R
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/CRS_MarkovModel.R
R/HID_MarkovModel.R
R/IMIS_.R
R/PSA_helpers.R
R/RcppExports.R
R/SickSicker_MarkovModel.R
R/bayesian_helpers.R
R/calibR-package.R
R/calibR_R6.R
R/global_helpers.R
R/goodness_of_fit.R
R/optim_helpers.R
R/optim_test_helpers.R
R/plot_fitness_helpers.R
R/plot_priors_posterior_helpers.R
R/plot_targets_helpers.R
R/sample_prior.R
R/sysdata.rda
R/utils-fonts.R
R/utils-pipe.R
calibR.Rproj
data-raw/CRS_data.R
data-raw/CR_CRS_data_1t.R
data-raw/CR_CRS_data_1t_2.R
data-raw/CR_CRS_data_1t_lp.R
data-raw/CR_CRS_data_2t.R
data-raw/CR_CRS_data_2t_2.R
data-raw/CR_CRS_data_2t_lp.R
data-raw/CR_HID_data_1p.R
data-raw/CR_HID_data_2p.R
data-raw/CR_HID_data_3p.R
data-raw/CR_HID_data_4p.R
data-raw/CR_HID_data_5p.R
data-raw/CR_HID_data_6p.R
data-raw/CR_HID_data_7p.R
data-raw/HID_data.R
data-raw/HID_data2.R
data-raw/HID_data2_flat.R
data-raw/HID_data2_flat_2p.R
data-raw/HID_data2_flat_2p2.R
data-raw/HID_data_2.R
data-raw/HID_data_flat.R
data-raw/HID_data_flat_2p.R
data-raw/HID_data_flat_2p2.R
data-raw/ROSEN_data.R
data-raw/sickSicker_data.R
data/CRS_data.rda
data/CRS_data_1.rda
data/CRS_data_2.rda
data/CRS_targets.rda
data/CRS_targets_2.rda
data/CR_CRS_data_1t.rda
data/CR_CRS_data_1t_2.rda
data/CR_CRS_data_1t_lp.rda
data/CR_CRS_data_2t.rda
data/CR_CRS_data_2t_2.rda
data/CR_CRS_data_2t_lp.rda
data/CR_HID_data_1p.rda
data/CR_HID_data_2p.rda
data/CR_HID_data_3p.rda
data/CR_HID_data_4p.rda
data/CR_HID_data_5p.rda
data/CR_HID_data_6p.rda
data/CR_HID_data_7p.rda
data/HID_data.rda
data/HID_data2.rda
data/HID_data2_flat.rda
data/HID_data2_flat_2p.rda
data/HID_data2_flat_2p2.rda
data/HID_data_flat.rda
data/HID_data_flat_2p.rda
data/HID_data_flat_2p2.rda
data/PSA tables/Comb_grp_Absolute_bayesian.rds
data/PSA tables/Comb_grp_Absolute_directed.rds
data/PSA tables/Comb_grp_Absolute_random.rds
data/PSA tables/Comb_grp_Relative_bayesian.rds
data/PSA tables/Comb_grp_Relative_directed.rds
data/PSA tables/Comb_grp_Relative_random.rds
data/PSA tables/Combined_Absolute.rds
data/PSA tables/Combined_Relative.rds
data/PSA tables/Full_bayesian_IMIS.rds
data/PSA tables/Full_bayesian_MCMC.rds
data/PSA tables/Full_bayesian_SIR.rds
data/PSA tables/Full_directed_BFGS_LLK_RGS.rds
data/PSA tables/Full_directed_BFGS_SSE_RGS.rds
data/PSA tables/Full_directed_NM_LLK_RGS.rds
data/PSA tables/Full_directed_NM_SSE_RGS.rds
data/PSA tables/Full_directed_SANN_LLK_RGS.rds
data/PSA tables/Full_directed_SANN_SSE_RGS.rds
data/PSA tables/Full_random_LLK_FGS.rds
data/PSA tables/Full_random_LLK_LHS.rds
data/PSA tables/Full_random_LLK_RGS.rds
data/PSA tables/Full_random_SSE_FGS.rds
data/PSA tables/Full_random_SSE_LHS.rds
data/PSA tables/Full_random_SSE_RGS.rds
data/PSA tables/Full_truth.rds
data/PSA tables/Partials_bayesian_IMIS.rds
data/PSA tables/Partials_bayesian_MCMC.rds
data/PSA tables/Partials_bayesian_SIR.rds
data/PSA tables/Partials_directed_BFGS_LLK_RGS.rds
data/PSA tables/Partials_directed_BFGS_SSE_RGS.rds
data/PSA tables/Partials_directed_NM_LLK_RGS.rds
data/PSA tables/Partials_directed_NM_SSE_RGS.rds
data/PSA tables/Partials_directed_SANN_LLK_RGS.rds
data/PSA tables/Partials_directed_SANN_SSE_RGS.rds
data/PSA tables/Partials_random_LLK_FGS.rds
data/PSA tables/Partials_random_LLK_LHS.rds
data/PSA tables/Partials_random_LLK_RGS.rds
data/PSA tables/Partials_random_SSE_FGS.rds
data/PSA tables/Partials_random_SSE_LHS.rds
data/PSA tables/Partials_random_SSE_RGS.rds
data/PSA tables/Partials_truth.rds
data/ROSEN_data.rda
data/sickSicker_data.rda
data/sickSicker_targets.rda
images/HIV_model.JPG
inst/reports/220526.html
inst/reports/220526.qmd
inst/reports/220526_pdf.pdf
inst/reports/220526_pdf.qmd
inst/reports/220602.qmd
man/CRS_markov.Rd
man/CRS_markov_2.Rd
man/HID_markov.Rd
man/HID_markov_2.Rd
man/HID_markov_3.Rd
man/IMIS_.Rd
man/LLK_GOF.Rd
man/PSA_calib_values.Rd
man/SS_MicroSim.Rd
man/SS_markov.Rd
man/assign_extraArgs_.Rd
man/backTransform.Rd
man/calculate_likelihood.Rd
man/calculate_posterior.Rd
man/calculate_posteriors.Rd
man/calculate_prior.Rd
man/calculate_priors.Rd
man/calibR_R6.Rd
man/calibTest_rosen.Rd
man/calibrateModel_beyesian.Rd
man/calibrateModel_beyesian2.Rd
man/calibrateModel_directed.Rd
man/effective_sample_size.Rd
man/fitness_contour_area.Rd
man/get_clean_method_name.Rd
man/get_gof_contour_plot_title.Rd
man/get_target_plot_title.Rd
man/import_plots_fonts.Rd
man/log_likelihood.Rd
man/log_posterior.Rd
man/log_posteriors.Rd
man/log_prior.Rd
man/log_priors.Rd
man/logit_to_prob.Rd
man/name_HID_params.Rd
man/pipe.Rd
man/plot_fitness_contour.Rd
man/plot_fitness_function.Rd
man/plot_pri_post_distributions.Rd
man/plot_targets.Rd
man/prob_to_logit.Rd
man/run_PSA.Rd
man/run_demo_App.Rd
man/sample_prior_FGS.Rd
man/sample_prior_FGS_.Rd
man/sample_prior_IMIS.Rd
man/sample_prior_LHS.Rd
man/sample_prior_RGS.Rd
man/sample_prior_RGS_.Rd
man/summ_optim.Rd
man/wSSE_GOF.Rd
misc/220405.Rmd
misc/220405_2.Rmd
misc/220421_calibration_results.Rmd
misc/220421_calibration_results.docx
misc/220519.Rmd
misc/Bayesian_calibration.Rmd
misc/CRS_markov_2 PSA.R
misc/CRS_markov_2 scenario_2P2T.R
misc/CRS_markov_2 targets plots.R
misc/CRS_markov_2 targets simulation.R
misc/CR_testing.R
misc/CR_testing_230120.R
misc/Directed_search.Rmd
misc/HID_markov_2 targets simulation.R
misc/Random_search.Rmd
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/SickSickerMicSim.cpp
testing.R
tests/testthat.R
tests/testthat/test-CRS_MarkovModel.R
tests/testthat/test-HID_MarkovModel.R
tests/testthat/test-SickSicker_MarkovModel.R
tests/testthat/test-goodness_of_fit.R
tests/testthat/test-optim_helpers.R
tests/testthat/test-sample_prior.R
