├── .DS_Store ├── .gitignore ├── LICENSE ├── README.md ├── compare_contact_matrices ├── .DS_Store ├── codes │ ├── .DS_Store │ ├── 0_master.r │ ├── 1_loadContactSurveys.r │ ├── 1_loadSyntheticContacts.r │ ├── 2_getHomeContactMatrix.r │ ├── 2_normalise.r │ ├── 2_normalise_urbanrural.r │ ├── 3_calculateSymmetry.r │ ├── 3_plotComparisonOthers.r │ ├── 3_plotComparison_2017.r │ ├── 3_plotComparison_otherlocations.r │ ├── 3_plotComparison_urbanrural.r │ ├── 4_plotImpact_R0_urbanrural.r │ ├── 5_plotImpact_infectionAttackRate.r │ ├── 5_plotImpact_interventionEffectiveness.r │ ├── functions_plot.r │ └── functions_processing.r ├── compare_contact_matrices.Rproj ├── input │ ├── .DS_Store │ ├── africanagematrices.rdata │ ├── africanmatrices.rdata │ ├── contact_datasets.rdata │ ├── contacts.Rdata │ ├── popRural.rdata │ ├── popUrban.rdata │ ├── poptotal.rdata │ ├── synthetic_contacts.rdata │ └── workpopage.rdata ├── output │ ├── .DS_Store │ ├── cases_byscenario_202201.rdata │ ├── cases_reduction_202201.rdata │ ├── data_byage_202201.rdata │ ├── data_effectiveness_202201.rdata │ ├── hhsize_empirical.rdata │ └── home_contacts_empirical.rdata └── plots │ ├── .DS_Store │ ├── case_reduction_absolute.png │ ├── case_reduction_relative.png │ ├── change_in_attack_rate.png │ ├── contacts_compare_2021_urbanrural.png │ ├── contacts_otherlocations.png │ ├── infectionattackrate.png │ └── r0contacts_urbanrural.png ├── generate_synthetic_matrices ├── .DS_Store ├── codes │ ├── .DS_Store │ ├── 0_master.r │ ├── contact_2_world.r │ ├── contact_2_world_rural.r │ ├── contact_2_world_urban.r │ ├── contact_3_world_plot.r │ ├── contact_3_world_plot_rural.r │ ├── contact_3_world_plot_urban.r │ ├── contact_4_world_storage.r │ ├── functions_plotContactmatrices.r │ ├── functions_processContactmatrices.r │ ├── home_0_getDHSsummary.r │ ├── home_0_getHamDHS.r │ ├── home_0_getHamDHS_urbanrural.r │ ├── home_0_getHamPOLYMOD.r │ ├── home_0_plotHamDHS_urbanrural.r │ ├── home_1_popRatioModel.r │ ├── home_1_popRatioModel_urbanrural.r │ ├── home_2_getHAMweightsBootstrapsamples.r │ ├── home_3_getHAMweights.r │ ├── home_3_getHAMweights_urbanrural.r │ ├── home_4_getHAMworld.r │ ├── home_4_getHAMworld_urbanrural.r │ ├── home_validation_getHHsizebyage.r │ ├── home_validation_internal_HAM.r │ ├── pop_getPopAge.r │ ├── pop_getPopAgeUrbanRural.r │ ├── pop_getWBindicators.r │ ├── school_0_enrolment.r │ ├── school_0_numberSecTeachers.r │ ├── school_0_pupilToTeacherRatio.r │ ├── school_0_pupilToTeacherRatio_urbanrural.r │ ├── school_0_teacherAgeLevel.r │ ├── school_1_calculateStudents.r │ ├── school_1_calculateStudents_urbanrural.r │ ├── school_2_calculateTeachers.r │ ├── school_2_calculateTeachers_urbanrural.r │ ├── school_3_buildSchoolPopulation.r │ ├── school_3_buildSchoolPopulation_urbanrural.r │ ├── work_1_buildWorkingPopulation.r │ └── work_1_buildWorkingPopulation_urbanrural.r ├── generate_synthetic_matrices.Rproj ├── input │ ├── .DS_Store │ ├── pop │ │ ├── URPAS_2014_ALL.xlsx │ │ ├── WPP2019_POP_F07_1_POPULATION_BY_AGE_BOTH_SEXES.xlsx │ │ ├── WPP2019_POP_F07_2_POPULATION_BY_AGE_MALE.xlsx │ │ ├── WPP2019_POP_F07_3_POPULATION_BY_AGE_FEMALE.xlsx │ │ ├── calculateWorldPop.xlsx │ │ ├── popRural.rdata │ │ ├── popUrban.rdata │ │ ├── popage_female2020.csv │ │ ├── popage_male2020.csv │ │ ├── popage_ruralurban2015.csv │ │ ├── popage_total2020.csv │ │ ├── popfemale.rdata │ │ ├── popmale.rdata │ │ ├── popratio.rdata │ │ ├── popratio_female.rdata │ │ ├── popratio_male.rdata │ │ ├── poptotal.rdata │ │ └── urbanicity.rdata │ ├── school │ │ ├── 9789264306707-graph12-en.xlsx │ │ ├── DP_LIVE_18052020104832036.csv │ │ ├── addpartime_teachers.rdata │ │ ├── end_age_school.rdata │ │ ├── enrolment.rdata │ │ ├── enrolment_levels.rdata │ │ ├── oecd_diff_pupiltoteacherratio_urbanrural.csv │ │ ├── proportion_teacheragelevel.rdata │ │ ├── pupiltoteacherratio.rdata │ │ ├── pupiltoteacherratio_rural.rdata │ │ ├── pupiltoteacherratio_urban.rdata │ │ ├── schoolage.rdata │ │ ├── schoolage_rural.rdata │ │ ├── schoolage_secondary.rdata │ │ ├── schoolage_urban.rdata │ │ ├── secteachers.rdata │ │ ├── start_age_school.rdata │ │ ├── students.rdata │ │ ├── students_rural.rdata │ │ ├── students_urban.rdata │ │ ├── teachers.rdata │ │ ├── teachers_primary.rdata │ │ ├── teachers_rural.rdata │ │ ├── teachers_secondary.rdata │ │ ├── teachers_urban.rdata │ │ └── teacherssecondary.rdata │ └── work │ │ ├── LFEP_AGE.xlsx │ │ ├── ilostat_ubranrural.csv │ │ ├── labour_force_participation_rate_ILO_modelled_estimates.csv │ │ ├── work_prop.csv │ │ ├── workpopage.rdata │ │ ├── workpopage_rural.rdata │ │ └── workpopage_urban.rdata ├── output │ ├── .DS_Store │ ├── HAMweights.rdata │ ├── HAMweights_rural.rdata │ ├── HAMweights_urban.rdata │ ├── agedhs.rdata │ ├── agedhs_rural.rdata │ ├── agedhs_urban.rdata │ ├── deltas.rdata │ ├── hamdhs.rdata │ ├── hamdhs_rural.rdata │ ├── hamdhs_urban.rdata │ ├── hampolymod.rdata │ ├── hampolymoddhs.rdata │ ├── hamworld.rdata │ ├── hamworld_rural.rdata │ ├── hamworld_urban.rdata │ ├── hhagedhs.rdata │ ├── hhagedhs_rural.rdata │ ├── hhagedhs_urban.rdata │ ├── hhsizebyage.rdata │ ├── hhsizebyage_rural.rdata │ ├── hhsizebyage_urban.rdata │ ├── lambdas.rdata │ ├── popratio_polymoddhs.rdata │ ├── popratio_polymoddhs_rural.rdata │ ├── popratio_polymoddhs_urban.rdata │ ├── posterior_uncertainty_interval.rdata │ ├── syntheticmatrices │ │ ├── contact_all.rdata │ │ ├── contact_home.rdata │ │ ├── contact_others.rdata │ │ ├── contact_school.rdata │ │ ├── contact_work.rdata │ │ ├── rural │ │ │ ├── contact_all_rural.rdata │ │ │ ├── contact_home_rural.rdata │ │ │ ├── contact_others_rural.rdata │ │ │ ├── contact_school_rural.rdata │ │ │ └── contact_work_rural.rdata │ │ ├── synthetic_contacts_2021.csv │ │ └── urban │ │ │ ├── contact_all_urban.rdata │ │ │ ├── contact_home_urban.rdata │ │ │ ├── contact_others_urban.rdata │ │ │ ├── contact_school_urban.rdata │ │ │ └── contact_work_urban.rdata │ └── workpopage.rdata └── plots │ ├── 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