Files in n8thangreen/LTBIscreeningproject

LTBI screening cost-effectiveness analysis

.Rprofile

DESCRIPTION

NAMESPACE

R/CumIncidence.R R/UN_TB_prev_country_years.R R/calc_QALY_tb.R R/calc_num_active_tb.R R/cbind_all_subsets.R R/combine_freq_tables.R R/cost-effectiveness-output-statistics.R R/cost_tb_notif.R R/costeff_stats.R R/count_comprsk_events.R R/create_avoid_tb_list.R R/data-TB_burden_countries.R R/data-WHO_incid_by_country_all_years.R R/decision_tree_cluster.R R/freq_table_for_publication.R R/from_list_to_BCEA.R R/get_2d_CI_level.R R/hist_progression_times.R R/impute_LTBI_status.R R/insert_dectree_cost.R R/is_death.R R/isna_OR_isinf.R R/myToDataFrame_fns.R R/netbenefit_regn.R R/num_subset_dectree.R R/num_subset_tb.R R/oneway_matrix.R R/output-table.R R/plot_care_cascade.R R/policy_cohort.R R/policy_interv.R R/policy_run.R R/prep_cost-eff_constructors.R R/prob_from_cum_incidence.R R/rows_first_n_ids.R R/run_model.R R/sample_subset_pop_dectree.R R/sample_tb.R R/sample_tb_year.R R/save_session_info.R R/scenario_QALY.R R/scenario_cost.R R/screen_discount.R R/screened_cohort_QALYs.R R/screened_cohort_cost.R R/set_branch_uniform_params.R R/sim_tb_times.R R/subpop_by_exituk_year.R R/subset_pop_dectree.R R/subset_pop_dectree_TEST.R R/write_clipboard.R R/write_excel.R README.md

data/IMPUTED_sample.csv

data/LTBI_dectree-QALY.yaml

data/LTBI_dectree-cost.yaml

docs/articles/active-tb-imputation.html

docs/articles/active-tb-imputation_files/figure-html/unnamed-chunk-1-1.png

docs/articles/all_years_tb_sims_histograms.png

docs/articles/basic-example.html

docs/articles/combine_dectree_and_popmodel_output.html

docs/articles/combine_dectree_and_popmodel_output_files/figure-html/unnamed-chunk-6-1.png

docs/articles/combine_dectree_and_popmodel_output_files/figure-html/unnamed-chunk-6-2.png

docs/articles/cost-effectiveness-analysis.html

docs/articles/extrapolated_active_tb.png

docs/articles/index.html

docs/articles/lancet-aldridge-plots.png

docs/articles/scenario-simulation.html

docs/articles/set-up.html

docs/authors.html

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/calc.ICER.html

docs/reference/calc.INMB.html

docs/reference/calc_QALY_tb.html

docs/reference/count_comprsk_events.html

docs/reference/index.html

scripts/000-programme-level-params-scenario-runner.R scripts/01-data-prep_scenario.R scripts/01a-data-prep_interv-constants.R scripts/01b-data-prep_cost-effectiveness.R scripts/01c-data-prep_modelling.R scripts/02-decision-tree-model.R scripts/02-parallel-decision-tree.R scripts/02b-decision-tree-model_indiv-cost-&-QALYloss.R scripts/04-combine_dectree_and_cmprk_model_output.R scripts/04a_1-active-TB-extrapolation.R scripts/04a_1-active-TB-extrapolation_PLOTS.R scripts/04a_2-active-TB-imputation-Horsburgh.R scripts/04a_3-include-new-tb-events.R scripts/04bb-calc_outcomes-GLOBAL.R scripts/04c-cost-effectiveness_QALY-costs.R scripts/05-CE_plane_trajectories.R scripts/05-QALY_cost_distns_by_scenario_plots.R scripts/05-bayesglm_predictions.R scripts/05-ceac-plot.R scripts/05-data_summary_table.R scripts/05-net-benefit.R scripts/05-netbenefit-threshold-analysis.R scripts/05-partial_correlation_coefficients.R scripts/05-plot-pop_QALYloss_over_time.R scripts/05-pop_count_histograms.R scripts/05-ranking-plots.R scripts/05-stan_predictions.R scripts/05-ternary plots.R scripts/05-upper_triangle_contour_INMB.R scripts/05a-output-plots_competing-risks.R scripts/05b-output-plots_cost-effectiveness-HALT.R scripts/05b-output-plots_cost-effectiveness.R scripts/05e-output-plots_cost-effectiveness_active-TB-cases.R scripts/05f-tornado_plots.R scripts/05g-INMB_ICER_histograms.R scripts/05h-CE_summary_stats.R scripts/05i-active-TB-imputation_survival-plots.R scripts/05j-strat_pop_year.R scripts/05k-other-C-E-plots.R scripts/05l-output-plots_twoway-sensitivity-analysis.R scripts/CE_plane_by_scenario.R scripts/QALY_ts_for_Excel.R scripts/STATA_dta_to_RData.R scripts/average_tb_discounts.R scripts/cluster-prep-decisiontree-data-HALT.R scripts/create--single_migrant_cohort.R scripts/create--single_migrant_cohort_Excel_test_cases.R scripts/create-scenario-parameter-value-array.R scripts/create-survival-analysis-arrays.R scripts/create_LTBI_input_workspace.R scripts/create_prev_inc_country_array.R scripts/data-prep_constants-policy.R scripts/data-prep_policies.R scripts/data_incidence_curves.R scripts/e_and_c_totals_by_scenario.R scripts/fit_75pc-upper-bound.R scripts/fit_Sutherland.R scripts/flexsurv-model-fit.R scripts/plot--attack-rate-from-Lancet-paper.R scripts/plot--tb_pop_year.R scripts/plot-care_cascade.R scripts/plot_extrapolated_incidence.R scripts/plot_imputed-extrapolated-times-to-active-tb.R scripts/plots--exit_time_cohort_characteristics.R scripts/plots--strat_pop_year_statusquo.R scripts/plots--time to leave EWNI.R scripts/prep-decisiontree.R scripts/prob_fillin_TODO.R scripts/setup_folders.R scripts/sim_vs_predict_validation.R scripts/tables--combine_costeffectiveness_tables.R scripts/tables--who-inc_vs_cohort-characteristics.R scripts/tables--wide_combined_ce.R scripts/writecsv-dectrees-as-dataframes.R

session_info.txt

tests/04a_2-tests.R tests/ce-tables outputs.R tests/check-dates-fields.R tests/sim_tb_times.R tests/test--04c-cost-effectiveness_QALY-costs.R tests/testthat.R

tests/testthat/LTBI_dtree-QALYloss_01-TEST.yaml

tests/testthat/LTBI_dtree-cost_SIMPLE-TEST.yaml

tests/testthat/excel_use_cases_output.csv

tests/testthat/osNode_cost_2009.Rds

tests/testthat/test-Excel_use_cases.R tests/testthat/test-count_comprsk_events.R tests/testthat/test-make_intervals_pop_list.R tests/testthat/test-make_utilities_pop_list.R tests/testthat/test-sample_tb_year.R tests/testthat/test-scenario_cost.R tests/testthat/test-scenario_qaly.R tests/testthat/test-subset_pop_dectree.R tests/testthat/test-total_scenario.R tests/testthat/tests-calc_QALY_tb.R tests/testthat/tests-decision-tree-model.R tests/testthat/tests-decision_tree_cluster.R tests/variable distns.R

vignettes/LTBI_dtree-cost-symptoms.yaml

vignettes/active-tb-imputation.Rmd

vignettes/active_tb_imputation.bib

vignettes/all_years_tb_sims_histograms.png

vignettes/cohort.Rds

vignettes/combine_dectree_and_popmodel_output.Rmd vignettes/cost-effectiveness-analysis.Rmd

vignettes/decision_tree_output.Rds

vignettes/extrapolated_active_tb.png

vignettes/lancet-aldridge-plots.PNG

vignettes/osNode_cost_2009.Rds

vignettes/osNode_health_2009.Rds

vignettes/scenario-simulation.Rmd vignettes/set-up.Rmd

n8thangreen/LTBIscreeningproject documentation built on May 23, 2019, 12:01 p.m.