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# Python stuff
Pipfile.lock
**/*.pyc
venv/
env/
condaenv/
.pytest_cache
*.cprof
*.egg-info
vic_figures/
# Sphinx docs
_build
docs/examples
# Benchmarking
benchmark.json
.benchmarks/
# IDE stuff
.idea
.spyderworkspace
.vscode
*.ipynb
notebooks/
# Images
*.png
# Data
*.db
# Runtime artifacts
logs/
*.log
*.pkl
*ipynb_checkpoints*
# Track encrypted input database.
!data/inputs/inputs.db
# Website stuff
node_modules/
.next/
website.json
out/
# Python packaging stuff
autumn.egg*
build/
dist/
# R stuff
.Rhistory
# Scripts, secrets
osx_boot.sh
*.secret.*
fil-result/
# Old model runs
data/marshall_islands
data/mongolia
data/covid_*
data/sir_example_*
# Models runs and calibrations
data/outputs
# TeX stuff (all the automatically generated files, except .log which is included above)
*.aux
*.gz
*.blg
*.out
*.bbl
*.toc
apps/*/tex/*.pdf
*.synctex*
docs/papers/master_files/*.pdf
!docs/papers/*/projects/*/methods_figures/*.png
# Policy brief
!docs/papers/covid_19/policy_brief/images/*.png
# Random stuff
*marshall-islands*.pickle
notebooks/user/rragonnet/outputs/
saved_*
*marshall-islands*.pickle
saved_optimisation_analyses/
saved_uncertainty_analyses/
saved_*
autumn_from_summer/databases/outputs*
autumn_from_summer/mongolia/mcmc_chistmas_2019/
dummy/
apps/covid_19/targets/philippines/Philippines_data_2020May20.pdf
apps/covid_19/mixing_optimisation/optimisation_outputs/united-kingdom_config_0_results.csv
apps/covid_19/mixing_optimisation/detection.csv
data/test_get_sample/opti_sample.csv
data/xls/data_liberia.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/results_N_21.tar
apps/covid_19/mixing_optimisation/optimisation_outputs/old/united-kingdom_config_0_results.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_location_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_location_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_location_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_location_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_age_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_age_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_age_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_united-kingdom_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_location_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_location_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_location_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_location_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_age_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_age_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_age_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_sweden_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_location_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_location_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_location_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_location_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_age_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_age_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_age_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_italy_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_location_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_location_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_location_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_location_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_age_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_age_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_age_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_france_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_location_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_location_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_location_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_location_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_age_3_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_age_3_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_age_2_yoll.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/21July2020/results_belgium_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/opti_plots/dumped_dict_param_posteriors.yml
apps/covid_19/mixing_optimisation/opti_plots/dumped_dict.yml
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_3_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_2_deaths.pdf
apps/covid_19/mixing_optimisation/optimisation_outputs/22July2020/results_italy_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/22July2020/results_italy_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/optimisation_outputs/22July2020/results_italy_by_age_2_deaths.csv
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_2_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_3_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_location_config_2_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_location_config_2_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_location_config_3_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_location_config_3_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/hospitals/rainbow_by_location_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/hospitals/rainbow_by_age_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/hospitals/rainbow_by_location_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/hospitals/rainbow_by_age_deaths.pdf
/.vs
/AuTuMN.sln
/AuTuMN.pyproj.user
/AuTuMN.pyproj
apps/covid_19/mixing_optimisation/opti_plots/figures/age_specific_attack_rates/age_specific_attack_rates_by_age.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/hospital_occupancy_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/hospitals/hospital_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/hospitals/hospital_uncertainty_by_location_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/icu_occupancy_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/infection_deaths_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/new_hospital_admissions_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/new_icu_admissions_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/multiscenario_uncertainty/proportion_seropositive_uncertainty_by_age_fully_immune.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/optimal_plans/optimal_plan_by_age.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/optimal_plans/optimal_plan_by_location.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/optimised_matrices/matrices_by_age.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/hospital_occupancy.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/icu_occupancy.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/infection_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/new_hospital_admissions.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/new_icu_admissions.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/notifications.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/percentiles/proportion_seropositive.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_2_yoll_cropped.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/rainbows/rainbow_by_age_config_3_yoll_cropped.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/sensitivity_min_mixing/sensitivity_min_mixing.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic no config name/waning_immunity_by_age_config_2_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic no config name/waning_immunity_by_age_config_2_yoll_.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic no config name/waning_immunity_by_age_config_3_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic no config name/waning_immunity_by_age_config_3_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic with config name/waning_immunity_by_age_config_2_deaths_pessimistic.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic with config name/waning_immunity_by_age_config_2_yoll_pessimistic.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic with config name/waning_immunity_by_age_config_3_deaths_pessimistic.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/pessimistic with config name/waning_immunity_by_age_config_3_yoll_pessimistic.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/with config name/waning_immunity_by_age_config_2_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/with config name/waning_immunity_by_age_config_2_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/with config name/waning_immunity_by_age_config_3_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/with config name/waning_immunity_by_age_config_3_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/without config name/waning_immunity_by_age_config_2_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/without config name/waning_immunity_by_age_config_2_yoll.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/without config name/waning_immunity_by_age_config_3_deaths.pdf
apps/covid_19/mixing_optimisation/opti_plots/figures/waning_immunity/without config name/waning_immunity_by_age_config_3_yoll.pdf
apps/covid_19/mixing_optimisation/optimisation_outputs/sensitivity_min_mixing/results.yml
apps/covid_19/mixing_optimisation/optimisation_outputs/sensitivity_min_mixing/results_test.yml
apps/covid_19/params/belgium/scenario-1.yml
apps/covid_19/params/belgium/scenario-2.yml
apps/covid_19/params/belgium/scenario-3.yml
apps/covid_19/params/belgium/scenario-4.yml
apps/covid_19/params/france/scenario-1.yml
apps/covid_19/params/france/scenario-2.yml
apps/covid_19/params/france/scenario-3.yml
apps/covid_19/params/france/scenario-4.yml
apps/covid_19/params/italy/scenario-1.yml
apps/covid_19/params/italy/scenario-2.yml
apps/covid_19/params/italy/scenario-3.yml
apps/covid_19/params/italy/scenario-4.yml
apps/covid_19/params/spain/scenario-1.yml
apps/covid_19/params/spain/scenario-2.yml
apps/covid_19/params/spain/scenario-3.yml
apps/covid_19/params/spain/scenario-4.yml
apps/covid_19/params/sweden/scenario-1.yml
apps/covid_19/params/sweden/scenario-2.yml
apps/covid_19/params/sweden/scenario-3.yml
apps/covid_19/params/sweden/scenario-4.yml
apps/covid_19/params/united-kingdom/scenario-1.yml
apps/covid_19/params/united-kingdom/scenario-2.yml
apps/covid_19/params/united-kingdom/scenario-3.yml
apps/covid_19/params/united-kingdom/scenario-4.yml
data/pbi_outputs_for_opti/by_age/fully_immune/output_table_fully_immune_by_age.csv
data/pbi_outputs_for_opti/by_location/fully_immune/output_table_fully_immune_by_location.csv
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/meta.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/baseline.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/scenario-1.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/scenario-2.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/scenario-3.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/scenario-4.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/models/scenario-5.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/belgium/2020-08-18--09-50-45/params.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/france/2020-08-18--10-01-41/meta.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/france/2020-08-18--10-01-41/models/baseline.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/france/2020-08-18--10-01-41/models/scenario-1.yml
data/scenario_outputs_waning_immunity/by_age_2_deaths/france/2020-08-18--10-01-41/models/scenario-2.yml
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data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/spain/2020-08-19--14-19-50/params.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/meta.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/models/baseline.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/models/scenario-1.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/models/scenario-2.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/models/scenario-3.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/models/scenario-4.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/sweden/2020-08-19--14-15-58/params.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/meta.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/models/baseline.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/models/scenario-1.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/models/scenario-2.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/models/scenario-3.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/models/scenario-4.yml
data/scenario_outputs_waning_immunity/by_age_3_yoll_pessimistic/united-kingdom/2020-08-19--14-11-58/params.yml
apps/pycharm.py
apps/tuberculosis/regions/marshall_islands/figures/calibration_targets/targets.pdf
apps/tuberculosis/regions/marshall_islands/figures/main_outputs/main_outputs.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_france.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_belgium.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_italy.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_spain.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_sweden.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/dumped_files/dumped_detection_percentiles_united-kingdom.npy
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/detection_posteriors.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/param_posteriors.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/model_fits.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/model_fits_seroprevalence.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/seroprevalence_by_age/sero_by_age_belgium.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/seroprevalence_by_age/sero_by_age_spain.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/seroprevalence_by_age/sero_by_age_united-kingdom.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/param_traces.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/seroprevalence_by_age/sero_by_age_france.pdf
apps/covid_19/mixing_optimisation/outputs/plots/calibration/figures/seroprevalence_by_age/sero_by_age_sweden.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/optimal_plan/optimal_plan_by_age.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/optimal_plan/optimal_plan_by_location.pdf
apps/covid_19/mixing_optimisation/sensitivity_analyses/min_mixing_results.yml
apps/covid_19/mixing_optimisation/outputs/plots/input_plots/figures/mobility_inputs.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/optimised_matrices/optimal_matrices_by_age.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/optimised_matrices/optimal_matrices_by_location.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_age_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_age_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-02--11-21-32/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-02--11-21-32/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/france/2020-11-02--11-22-52/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/france/2020-11-02--11-22-52/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/italy/2020-11-02--11-24-03/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/italy/2020-11-02--11-24-03/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/spain/2020-11-02--11-25-13/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/spain/2020-11-02--11-25-13/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/sweden/2020-11-02--11-28-58/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/sweden/2020-11-02--11-28-58/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/united-kingdom/2020-11-02--11-26-23/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/united-kingdom/2020-11-02--11-26-23/params.yml
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/attack_rate_by_age/age_specific_attack_rates_by_age.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/attack_rate_by_age/age_specific_attack_rates_by_location.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_location_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_age_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_age_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_location_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_location_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/rainbow_by_location_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-02--20-16-43/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-02--20-16-43/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/france/2020-11-02--20-18-16/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/france/2020-11-02--20-18-16/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/italy/2020-11-02--20-19-42/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/italy/2020-11-02--20-19-42/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/spain/2020-11-02--20-21-13/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/spain/2020-11-02--20-21-13/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/sweden/2020-11-02--20-22-42/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/sweden/2020-11-02--20-22-42/params.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/united-kingdom/2020-11-02--20-24-05/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/united-kingdom/2020-11-02--20-24-05/params.yml
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/hospital_uncertainty/hospital_occupancy_uncertainty_by_age.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/hospital_uncertainty/hospital_occupancy_uncertainty_by_location.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/hospital_uncertainty/proportion_seropositive_uncertainty_by_age.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/hospital_uncertainty/proportion_seropositive_uncertainty_by_location.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/tables/output_table_by_location.csv
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/tables/output_table_by_age.csv
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_six_months_deaths_down.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_six_months_yoll_up.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_six_months_yoll_down.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_six_months_deaths_down.yml
debug.log
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/sensitivity_min_mixing/sensitivity_min_mixing.pdf
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_six_months_yoll_down.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_twelve_months_deaths_down.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_twelve_months_yoll_down.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_twelve_months_yoll_up.yml
apps/covid_19/mixing_optimisation/optimised_variables/optimal_plan_sensitivity/belgium_by_age_twelve_months_yoll_down.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-04--21-11-02/meta.yml
apps/covid_19/mixing_optimisation/outputs/pbi_databases/manual_runs_full_immunity/belgium/2020-11-04--21-11-02/params.yml
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/all_wi_scenarios/waning_immunity_by_age_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/all_wi_scenarios/waning_immunity_by_age_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/all_wi_scenarios/waning_immunity_by_age_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/all_wi_scenarios/waning_immunity_by_age_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/input_plots/figures/microdistancing.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_age_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_age_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_age_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_age_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_location_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_location_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_location_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/no_config_name/rainbow_by_location_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_age_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_age_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_age_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_age_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_location_six_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_location_six_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_location_twelve_months_deaths.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/rainbows/with_config_name/rainbow_by_location_twelve_months_yoll.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/tables/output_table_by_location_per_capita.csv
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_six_months_deaths_pessimistic.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_six_months_yoll_pessimistic.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_twelve_months_deaths_pessimistic.pdf
apps/covid_19/mixing_optimisation/outputs/plots/outputs/figures/wi_figures/pessimistic/waning_immunity_by_age_twelve_months_yoll_pessimistic.pdf
apps/tuberculosis/regions/marshall_islands/outputs/figures/counterfactual/counterfactual.pdf
apps/tuberculosis/regions/marshall_islands/outputs/desktop.ini
apps/tuberculosis/regions/marshall_islands/outputs/figures/elimination/elimination.pdf
apps/tuberculosis/regions/marshall_islands/outputs/figures/calibration/model_fits.pdf
apps/tuberculosis/regions/marshall_islands/outputs/figures/diabetes/diabetes.pdf
apps/tuberculosis/regions/marshall_islands/outputs/figures/elimination/elimination_logscale.pdf
apps/tuberculosis/regions/marshall_islands/outputs/parameter_posteriors/posterior_centiles.csv
apps/tuberculosis/regions/marshall_islands/outputs/figures/posterior_table/posterior_ranges.csv
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/counterfactual/counterfactual.pdf
apps/tuberculosis/regions/marshall_islands/outputs/figures/priors_table/priors.csv
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/calibration/model_fits.pdf
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/diabetes/diabetes.pdf
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/elimination/elimination.pdf
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/elimination/elimination_logscale.pdf
apps/tuberculosis/regions/marshall_islands/outputs/old_figures/posterior_table/posterior_ranges.csv
apps/tuberculosis/regions/marshall_islands/outputs/figures/output_numbers.txt
apps/tuberculosis/regions/marshall_islands/outputs/figures/calibration/screening_rate.pdf
# ignore vic figures automatically generated
vic_figures/
notebooks/user/rragonnet/lhs_start_traces_median.pdf
notebooks/user/rragonnet/posterior_against_params.pdf
# ignoring marshall islands figures and databases
autumn/projects/tuberculosis/marshall_islands/outputs/all_outputs/*