Files in dd-harp/MicroMoB

Discrete Time Systems for Robust Analytics for Malaria Policy (RAMP), and Transmission Dynamics and Control of Mosquito-Borne Pathogens Transmission

CODE_OF_CONDUCT.md LICENSE.md NEWS.md R/abiotic.R R/adult-ENBRQ.R R/adult-Gtrace.R R/adult-RM.R R/adult-Ztrace.R R/adult-basicM.R R/adult-bionomics.R R/adult-interface.R R/adult-lumpy.R R/aquatic-basic.R R/aquatic-interface.R R/aquatic-trace.R R/area_spray.R R/available_blood.R R/available_habitat.R R/available_sugar.R R/bednet-interface.R R/bednet-lemenach.R R/bednet-null.R R/behavior.R R/bionomics.R R/blood_feeding.R R/care_seeking.R R/civil.R R/clinic.R R/compute_terms.R R/compute_variables.R R/control.R R/demography-births.R R/demography-dH.R R/demography-interface.R R/development.R R/dts_equations.R R/dts_setup.R R/dts_solve.R R/dts_utils.R R/egg_laying.R R/eip.R R/eip_fixed.R R/eip_null.R R/emerge.R R/exposure.R R/habitat_dynamics.R R/human-SIP.R R/human-SIS.R R/human-interface.R R/human-trace.R R/hydrology.R R/irs-interface.R R/irs-null.R R/local_fraction.R R/lsm-interface.R R/lsm-null.R R/mass_medical.R R/metrics.R R/mosquito-dispersal.R R/other_blood_hosts.R R/ovitrap.R R/plot-MYZ.R R/plot-terms.R R/resources.R R/shock.R R/sugar_baits-interface.R R/sugar_baits-null.R R/sugar_dynamics.R R/time_spent.R R/transmission.R R/travel_malaria-eir.R R/travel_malaria-foi.R R/travel_malaria-interface.R R/travel_malaria-static.R R/vector_control-control.R R/vector_control-interface.R R/vector_control-null.R R/visitors.R R/weather.R README.md man/Abiotic.Rd man/Abiotic.forced.Rd man/Abiotic.null.Rd man/AreaSpray.Rd man/AreaSpray.null.Rd man/AreaSprayEffectSizes.Rd man/AreaSprayEffectSizes.null.Rd man/AreaSprayEffects.Rd man/AreaSprayEffects.null.Rd man/AvailableBlood.Rd man/AvailableBlood.forced.Rd man/AvailableBlood.setup.Rd man/AvailableBlood.static.Rd man/AvailableHabitat.Rd man/AvailableHabitat.forced.Rd man/AvailableHabitat.simple.Rd man/AvailableHabitat.static.Rd man/AvailableSugar.Rd man/AvailableSugar.forced.Rd man/AvailableSugar.static.Rd man/BedNetEffectSizes.Rd man/BedNetEffectSizes.lemenach.Rd man/BedNetEffectSizes.null.Rd man/BedNetEffects.Rd man/BedNetEffects.lemenach.Rd man/BedNetEffects.null.Rd man/Behavior.Rd man/Behavior.forced.Rd man/Behavior.null.Rd man/Bionomics.Ldynamic.Rd man/Bionomics.Mdynamic.Rd man/Bionomics.Rd man/Bionomics.dynamic.Rd man/Bionomics.setup.Rd man/Bionomics.static.Rd man/Births.Rd man/Births.zero.Rd man/CareSeeking.Rd man/CareSeeking.null.Rd man/Civil.Rd man/Civil.forced.Rd man/Civil.null.Rd man/Clinic.Rd man/Clinic.null.Rd man/Control.Rd man/Control.forced.Rd man/Control.null.Rd man/Control.static.Rd man/DTS_step.Rd man/DTS_step_aquatic.Rd man/DTS_step_cohort.Rd man/DTS_step_human.Rd man/DTS_step_mosy.Rd man/Development.Rd man/Development.null.Rd man/DistributeBedNets.Rd man/DistributeBedNets.null.Rd man/EIP.Rd man/EIP.fixed.Rd man/EIP.null.Rd man/EggLaying.Rd man/EggLaying.dynamic.Rd man/EggLaying.setup.Rd man/EggLaying.simple.Rd man/EggLaying.static.Rd man/Emergence.Rd man/Exposure.Rd man/F_EIR.Rd man/F_H.Rd man/F_H.SIP.Rd man/F_H.SIS.Rd man/F_H.trace.Rd man/F_X.Rd man/F_X.SIP.Rd man/F_X.SIS.Rd man/F_X.trace.Rd man/F_alpha.Rd man/F_alpha.basic.Rd man/F_alpha.trace.Rd man/F_b.Rd man/F_b.SIP.Rd man/F_b.SIS.Rd man/F_b.trace.Rd man/F_beta.Rd man/F_eggs.ENBRQ.Rd man/F_eggs.Gtrace.Rd man/F_eggs.RM.Rd man/F_eggs.RMlumpy.Rd man/F_eggs.Rd man/F_eggs.Ztrace.Rd man/F_eggs.basicM.Rd man/F_f.Rd man/F_f.dddn.Rd man/F_f.static.Rd man/F_f.type2.Rd man/F_foi.Rd man/F_foi.nb.Rd man/F_foi.pois.Rd man/F_fqM.ENBRQ.Rd man/F_fqM.Gtrace.Rd man/F_fqM.RM.Rd man/F_fqM.RMlumpy.Rd man/F_fqM.Rd man/F_fqM.Ztrace.Rd man/F_fqM.basicM.Rd man/F_fqZ.ENBRQ.Rd man/F_fqZ.Gtrace.Rd man/F_fqZ.RM.Rd man/F_fqZ.RMlumpy.Rd man/F_fqZ.Rd man/F_fqZ.Ztrace.Rd man/F_fqZ.basicM.Rd man/F_kappa.Rd man/F_nu.Rd man/F_nu.dddn.Rd man/F_nu.static.Rd man/F_nu.type2.Rd man/F_p.Rd man/F_p.dddn.Rd man/F_p.static.Rd man/F_pr.Rd man/F_pr.SIP.Rd man/F_pr.SIS.Rd man/F_pr.trace.Rd man/F_q.Rd man/F_q.dddn.Rd man/F_q.dynamic.Rd man/F_q.static.Rd man/F_sigma.Rd man/F_sigma.dddn.Rd man/F_sigma.static.Rd man/F_tau.Rd man/HTC.Rd man/HTC.SIP.Rd man/HTC.SIS.Rd man/HabitatDynamics.Rd man/HabitatDynamics.static.Rd man/Hydrology.Rd man/Hydrology.null.Rd man/IRS_EffectSizes.Rd man/IRS_EffectSizes.null.Rd man/IRS_Effects.Rd man/IRS_Effects.null.Rd man/LBionomics.Rd man/LBionomics.basic.Rd man/LBionomics.trace.Rd man/LSM_EffectSizes.Rd man/LSM_EffectSizes.null.Rd man/LSM_Effects.Rd man/LSM_Effects.null.Rd man/LocalFrac.Rd man/LocalFrac.dynamic.Rd man/LocalFrac.static.Rd man/MBionomics.ENBRQ.Rd man/MBionomics.Gtrace.Rd man/MBionomics.RM.Rd man/MBionomics.RMlumpy.Rd man/MBionomics.Rd man/MBionomics.Ztrace.Rd man/MBionomics.basicM.Rd man/MassMedical.Rd man/MassMedical.forced.Rd man/MassMedical.null.Rd man/OtherBloodHosts.Rd man/OtherBloodHosts.static.Rd man/OviTraps.Rd man/OviTraps.null.Rd man/OwnBedNet.Rd man/OwnBedNet.null.Rd man/Rainfall.Rd man/Rainfall.null.Rd man/Relative_Humidity.Rd man/Relative_Humidity.null.Rd man/Resources.Rd man/Resources.forced.Rd man/Resources.setup.Rd man/Resources.static.Rd man/Shock.Rd man/Shock.null.Rd man/SprayHouses.Rd man/SprayHouses.null.Rd man/SugarBaitEffectSizes.Rd man/SugarBaitEffectSizes.null.Rd man/SugarBaitEffects.Rd man/SugarBaitEffects.null.Rd man/SugarBaits.Rd man/SugarBaits.null.Rd man/SugarDynamics.Rd man/SugarDynamics.static.Rd man/Temperature.Rd man/Temperature.null.Rd man/Transmission.Rd man/Transmission.dynamic.Rd man/Transmission.setup.Rd man/Transmission.static.Rd man/TreatHabitats.Rd man/TreatHabitats.null.Rd man/UseBedNet.Rd man/UseBedNet.null.Rd man/VectorControl.Rd man/VectorControl.control.Rd man/VectorControl.null.Rd man/VectorControlEffectSizes.Rd man/VectorControlEffectSizes.control.Rd man/VectorControlEffectSizes.null.Rd man/VectorControlEffects.Rd man/VectorControlEffects.control.Rd man/VectorControlEffects.null.Rd man/Visitors.Rd man/Visitors.basic.Rd man/Visitors.static.Rd man/Weather.Rd man/Weather.forced.Rd man/Weather.null.Rd man/approx_equal.Rd man/checkIt.Rd man/check_abiotic.Rd man/check_abiotic.forced.Rd man/check_abiotic.null.Rd man/check_civil.Rd man/check_civil.forced.Rd man/check_civil.null.Rd man/compute_AvailableHabitat.Rd man/compute_AvailableHosts.Rd man/compute_EIR.Rd man/compute_EIR_full.Rd man/compute_EggsLaid.Rd man/compute_NI.Rd man/compute_NI_ix.Rd man/compute_beta.Rd man/compute_calU.Rd man/compute_kappa.Rd man/compute_local_frac.Rd man/compute_terms.Rd man/compute_terms.cohort.Rd man/compute_terms.dts.Rd man/compute_terms.human.Rd man/compute_terms.na.Rd man/compute_terms_steady.Rd man/compute_vars_aqua.Rd man/compute_vars_cohort.Rd man/compute_vars_full.Rd man/compute_vars_human.Rd man/compute_vars_mosy.Rd man/dHdt.Rd man/dHdt.zero.Rd man/dLdt.Rd man/dLdt.basic.Rd man/dLdt.trace.Rd man/dMYZdt.ENBRQ.Rd man/dMYZdt.Gtrace.Rd man/dMYZdt.RM.Rd man/dMYZdt.RMlumpy.Rd man/dMYZdt.Rd man/dMYZdt.Ztrace.Rd man/dMYZdt.basicM.Rd man/dXdt.Rd man/dXdt.SIP.Rd man/dXdt.SIS.Rd man/dXdt.trace.Rd man/diag_inverse.Rd man/dts_lines_EIR.Rd man/dts_lines_M.Rd man/dts_lines_PR.Rd man/dts_lines_X_SIP.Rd man/dts_lines_X_SIS.Rd man/dts_lines_YZ.Rd man/dts_lines_YZ_fracs.Rd man/dts_lines_Z_fracs.Rd man/dts_lines_aEIR.Rd man/dts_plot_EIR.Rd man/dts_plot_M.Rd man/dts_plot_PR.Rd man/dts_plot_X.Rd man/dts_plot_X.SIP.Rd man/dts_plot_X.SIS.Rd man/dts_plot_YZ.Rd man/dts_plot_YZ_fracs.Rd man/dts_plot_Z_fracs.Rd man/dts_plot_aEIR.Rd man/dts_setup.Rd man/dts_setup_aquatic.Rd man/dts_setup_cohort.Rd man/dts_setup_human.Rd man/dts_setup_mosy.Rd man/dts_solve.Rd man/dts_solve.aqua.Rd man/dts_solve.cohort.Rd man/dts_solve.dts.Rd man/dts_solve.human.Rd man/dts_solve.mosy.Rd man/dts_stable_orbit.Rd man/dts_steady.Rd man/get_inits.Rd man/get_inits_L.Rd man/get_inits_L.basic.Rd man/get_inits_L.trace.Rd man/get_inits_MYZ.ENBRQ.Rd man/get_inits_MYZ.Gtrace.Rd man/get_inits_MYZ.RM.Rd man/get_inits_MYZ.RMlumpy.Rd man/get_inits_MYZ.Rd man/get_inits_MYZ.Ztrace.Rd man/get_inits_MYZ.basicM.Rd man/get_inits_X.Rd man/get_inits_X.SIP.Rd man/get_inits_X.SIS.Rd man/get_inits_X.trace.Rd man/last_to_inits.Rd man/list_MYZvars.ENBRQ.Rd man/list_MYZvars.RM.Rd man/list_MYZvars.RMlumpy.Rd man/list_MYZvars.Rd man/list_MYZvars.basicM.Rd man/list_Xvars.Rd man/list_Xvars.SIP.Rd man/list_Xvars.SIS.Rd man/make_Linits_basic.Rd man/make_Lpar_basic.Rd man/make_Lpar_trace.Rd man/make_MYZinits_ENBRQ.Rd man/make_MYZinits_RM.Rd man/make_MYZinits_RMlumpy.Rd man/make_MYZinits_basicM.Rd man/make_MYZpar_ENBRQ.Rd man/make_MYZpar_Gtrace.Rd man/make_MYZpar_RM.Rd man/make_MYZpar_RMlumpy.Rd man/make_MYZpar_Ztrace.Rd man/make_MYZpar_basicM.Rd man/make_Omega.Rd man/make_TaR.Rd man/make_TimeSpent.Rd man/make_TimeSpent.as_matrix.Rd man/make_TimeSpent.athome.Rd man/make_TimeSpent.xy.Rd man/make_TimeSpent_athome.Rd man/make_TimeSpent_xy.Rd man/make_Xinits_SIP.Rd man/make_Xinits_SIS.Rd man/make_Xpar_SIP.Rd man/make_Xpar_SIS.Rd man/make_Xpar_trace.Rd man/make_calK.Rd man/make_calK.as_matrix.Rd man/make_calK.herethere.Rd man/make_calK.xy.Rd man/make_calK_xy.Rd man/make_calN.Rd man/make_calU.Rd man/make_calU_s.Rd man/make_indices.Rd man/make_indices_L.Rd man/make_indices_L.basic.Rd man/make_indices_L.trace.Rd man/make_indices_MYZ.ENBRQ.Rd man/make_indices_MYZ.Gtrace.Rd man/make_indices_MYZ.RM.Rd man/make_indices_MYZ.RMlumpy.Rd man/make_indices_MYZ.Rd man/make_indices_MYZ.Ztrace.Rd man/make_indices_MYZ.basicM.Rd man/make_indices_X.Rd man/make_indices_X.SIP.Rd man/make_indices_X.SIS.Rd man/make_indices_X.trace.Rd man/make_inits_L_basic.Rd man/make_inits_L_trace.Rd man/make_inits_MYZ_ENBRQ.Rd man/make_inits_MYZ_Gtrace.Rd man/make_inits_MYZ_RM.Rd man/make_inits_MYZ_RMlumpy.Rd man/make_inits_MYZ_Ztrace.Rd man/make_inits_MYZ_basicM.Rd man/make_inits_X_SIP.Rd man/make_inits_X_SIS.Rd man/make_inits_X_trace.Rd man/make_parameters_L_basic.Rd man/make_parameters_L_trace.Rd man/make_parameters_MYZ_ENBRQ.Rd man/make_parameters_MYZ_Gtrace.Rd man/make_parameters_MYZ_RM.Rd man/make_parameters_MYZ_RMlumpy.Rd man/make_parameters_MYZ_Ztrace.Rd man/make_parameters_MYZ_basicM.Rd man/make_parameters_X_SIP.Rd man/make_parameters_X_SIS.Rd man/make_parameters_X_trace.Rd man/make_parameters_demography_null.Rd man/make_parameters_dts.Rd man/metric_calD.Rd man/metric_calR.Rd man/metric_calV.Rd man/metric_calZ.Rd man/parse_dts_out.Rd man/parse_dts_out_L.Rd man/parse_dts_out_L.basic.Rd man/parse_dts_out_L.trace.Rd man/parse_dts_out_MYZ.ENBRQ.Rd man/parse_dts_out_MYZ.Gtrace.Rd man/parse_dts_out_MYZ.RM.Rd man/parse_dts_out_MYZ.RMlumpy.Rd man/parse_dts_out_MYZ.Rd man/parse_dts_out_MYZ.Ztrace.Rd man/parse_dts_out_MYZ.basicM.Rd man/parse_dts_out_X.Rd man/parse_dts_out_X.SIP.Rd man/parse_dts_out_X.SIS.Rd man/parse_dts_out_X.trace.Rd man/parse_dts_out_vec.Rd man/setup_BFpar_static.Rd man/setup_BloodFeeding.Rd man/setup_EGGpar_static.Rd man/setup_EIP.Rd man/setup_EIP.fixed.Rd man/setup_EIP.null.Rd man/setup_EggLaying_simple.Rd man/setup_EggLaying_static.Rd man/setup_Hpar_static.Rd man/setup_Linits.Rd man/setup_Linits.basic.Rd man/setup_Linits.trace.Rd man/setup_Lpar.Rd man/setup_Lpar.basic.Rd man/setup_Lpar.trace.Rd man/setup_MYZinits.ENBRQ.Rd man/setup_MYZinits.Gtrace.Rd man/setup_MYZinits.RM.Rd man/setup_MYZinits.RMlumpy.Rd man/setup_MYZinits.Rd man/setup_MYZinits.Ztrace.Rd man/setup_MYZinits.basicM.Rd man/setup_MYZpar.ENBRQ.Rd man/setup_MYZpar.Gtrace.Rd man/setup_MYZpar.RM.Rd man/setup_MYZpar.RMlumpy.Rd man/setup_MYZpar.Rd man/setup_MYZpar.Ztrace.Rd man/setup_MYZpar.basicM.Rd man/setup_Xinits.Rd man/setup_Xinits.SIP.Rd man/setup_Xinits.SIS.Rd man/setup_Xinits.trace.Rd man/setup_Xpar.Rd man/setup_Xpar.SIP.Rd man/setup_Xpar.SIS.Rd man/setup_Xpar.trace.Rd man/setup_abiotic_forced.Rd man/setup_abiotic_null.Rd man/setup_area_spray_null.Rd man/setup_behavior.Rd man/setup_behavior.forced.Rd man/setup_behavior.null.Rd man/setup_behavior_forced.Rd man/setup_behavior_null.Rd man/setup_bionomics_static.Rd man/setup_care_seeking_null.Rd man/setup_civil_forced.Rd man/setup_civil_null.Rd man/setup_clinic_forced.Rd man/setup_clinic_null.Rd man/setup_control.Rd man/setup_control.forced.Rd man/setup_control.null.Rd man/setup_control_forced.Rd man/setup_control_null.Rd man/setup_development_null.Rd man/setup_eip_fixed.Rd man/setup_eip_null.Rd man/setup_exposure_nb.Rd man/setup_exposure_pois.Rd man/setup_habitat_dynamics_static.Rd man/setup_hydrology_null.Rd man/setup_irs_null.Rd man/setup_itn_lemenach.Rd man/setup_itn_null.Rd man/setup_local_fraction_simple.Rd man/setup_lsm_null.Rd man/setup_mass_medical_forced.Rd man/setup_mass_medical_null.Rd man/setup_other_blood_hosts_static.Rd man/setup_ovitraps_null.Rd man/setup_rainfall_null.Rd man/setup_relative_humidity_null.Rd man/setup_resources_forced.Rd man/setup_resources_null.Rd man/setup_resources_static.Rd man/setup_shock_null.Rd man/setup_sugar_baits_null.Rd man/setup_sugar_static.Rd man/setup_temperature_null.Rd man/setup_travel_eir.Rd man/setup_travel_foi.Rd man/setup_travel_static.Rd man/setup_vc_control.Rd man/setup_vc_null.Rd man/setup_visitors_basic.Rd man/setup_visitors_static.Rd man/setup_weather_forced.Rd man/setup_weather_null.Rd man/shapeIt.Rd man/travel_malaria.Rd man/travel_malaria.eir.Rd man/travel_malaria.foi.Rd man/travel_malaria.static.Rd man/update_inits.Rd man/update_inits_L.Rd man/update_inits_L.basic.Rd man/update_inits_L.trace.Rd man/update_inits_MYZ.ENBRQ.Rd man/update_inits_MYZ.Gtrace.Rd man/update_inits_MYZ.RM.Rd man/update_inits_MYZ.RMlumpy.Rd man/update_inits_MYZ.Rd man/update_inits_MYZ.Ztrace.Rd man/update_inits_MYZ.basicM.Rd man/update_inits_X.Rd man/update_inits_X.SIP.Rd man/update_inits_X.SIS.Rd man/update_inits_X.trace.Rd tests/testthat.R tests/testthat/test-test.R vignettes/Behavioral-States.R vignettes/Behavioral-States.Rmd vignettes/Contributing.Rmd vignettes/RM-Mosquito.R vignettes/RM-Mosquito.Rmd vignettes/Ross-Macdonald.R vignettes/Ross-Macdonald.Rmd vignettes/Understanding_exDE.R vignettes/Understanding_ramp_dts.R vignettes/Understanding_ramp_dts.Rmd vignettes/bloodmeal.R vignettes/bloodmeal.Rmd