_pkgdown.yml

url: https://dd-harp.github.io/exDE/
template:
  bootstrap: 5
navbar:
  left:
  - text: Functions
    href: reference/index.html
  - text: Articles
    menu:
    - text: Understanding exDE
      href: articles/Understanding_exDE.html
    - text: Modular Forms for Disease Dynamics
      href: articles/modularity.html
    - text: 5-3-4 Spatial Example
      href: articles/ex_534.html
    - text: Spatial Metrics
      href: articles/spat_metric.html
    - text: Vector Control Example
      href: articles/vc_lemenach.html
    - text: Contributing
      href: articles/Contributing.html
  - text: Concepts
    menu:
    - text: Heterogeneous Transmission
      href: articles/heterogeneous_transmission.html
    - text: Heterogeneous Biting
      href: articles/heterogeneous_biting.html
    - text: Heterogeneous Mixing
      href: articles/heterogeneous_mixing.html
    - text: Environmental Heterogeneity
      href: articles/environmental_heterogeneity.html
  - text: Adult Mosquito Dynamics
    menu:
    - text: Ross-Macdonald model
      href: articles/adult_RM.html
    - text: Generalized Ross-Macdonald model
      href: articles/adult_GeRM.html
  - text: Aquatic Mosquito Dynamics
    menu:
    - text: Trace (forced) model
      href: articles/aqua_trace.html
    - text: Basic competition model
      href: articles/aqua_basic.html
  - text: Human Infection Dynamics
    menu:
    - text: SIS model
      href: articles/human_sis.html
    - text: SIP model
      href: articles/human_sip.html
    - text: MoI hybrid model
      href: articles/human_hmoi.html
  right:
  - icon: fa-github
    href: https://github.com/dd-harp/exDE/
home:
  sidebar:
    structure:
    - links
    - license
    - community
    - citation
    - authors
    - dev
    - custom_news
    components:
      custom_news:
        title: Changelog
        text: <a href="news/index.html">News</a>
reference:
- title: Blood Feeding and Transmission
  desc: |
    Methods to compute the transmission terms
  contents:
  - Transmission
  - LocalFrac
  - AvailableBlood
- subtitle: Transmision
  desc: |
    Specialized methods to compute the transmission terms
  contents:
  - Transmission.static
  - Transmission.dynamic
  - Transmission.setup
  - F_beta
  - compute_beta
  - F_EIR
  - compute_EIR
  - compute_EIR_full
  - F_kappa
  - compute_kappa
- subtitle: Blood Feeding
  desc: |
    Method to set up the blood feeding model
  contents:
  - setup_BFpar_static
  - setup_BloodFeeding
  - make_TaR
- subtitle: Time Spent and Time at Risk
  desc: |
    Method to set up time spent and time at risk (TaR) matrices
  contents:
  - make_TimeSpent
  - make_TimeSpent.athome
  - make_TimeSpent_athome
  - make_TimeSpent.as_matrix
  - make_TimeSpent.xy
  - make_TimeSpent_xy
- subtitle: Availability of humans / hosts
  desc: |
    Specialized methods to compute available humans / hosts
  contents:
  - AvailableBlood.static
  - AvailableBlood.setup
  - AvailableBlood.forced
  - compute_AvailableHosts
- title: Exposure
  desc: |
    Methods to model the force of infection
  contents:
  - Exposure
  - F_foi
- subtitle: Poisson Exposure
  desc: |
    Specialized methods the Poisson exposure model
  contents:
  - F_foi.pois
  - setup_exposure_pois
- subtitle: Negative Binomial Exposure
  desc: |
    Specialized methods the Negative Binomial exposure model
  contents:
  - F_foi.nb
  - setup_exposure_nb
- subtitle: Local Fraction
  desc: |
    Specialized methods for  NULL dynamics: a funtion generates values of Z to force human infection dynamics
  contents:
  - LocalFrac.static
  - LocalFrac.dynamic
  - compute_local_frac
  - setup_local_fraction_simple
- title: Egg Laying & Emergence
  desc: |
    Generic methods for the aquatic (immature) mosquito component.
  contents:
  - Emergence
  - make_calN
  - EggLaying
  - EggLaying.static
  - EggLaying.dynamic
  - EggLaying.simple
  - EggLaying.setup
  - compute_calU
  - compute_EggsLaid
  - make_calU
  - make_calU_s
  - setup_EggLaying_static
  - setup_EggLaying_simple
  - setup_EGGpar_static
- title: Adult Mosquito Dynamics
  desc: |
    Generic methods for the adult mosquito dynamics component.
  contents:
  - MBionomics
  - F_fqZ
  - F_fqM
  - F_tau
  - F_eggs
  - dMYZdt
  - setup_MYZpar
  - setup_MYZinits
  - make_indices_MYZ
  - parse_deout_MYZ
  - get_inits_MYZ
  - update_inits_MYZ
  - make_Omega
  - dde2ode_MYZ
  - dde2ode_MYZ.dde
  - dde2ode_MYZ.ode
  - xde_plot_M
  - xde_lines_M
  - xde_plot_YZ
  - xde_lines_YZ
  - xde_plot_YZ_fracs
  - xde_lines_YZ_fracs
  - xde_plot_Z_fracs
  - xde_lines_Z_fracs
- subtitle: EIP
  desc: |
    Specialized methods for  NULL dynamics: a funtion generates values of Z to force human infection dynamics
  contents:
  - EIP
  - EIP.static
  - dEIPdt
  - dEIPdt.static
  - setup_EIP
  - setup_EIP.static
  - setup_eip_static
- subtitle: Ztrace
  desc: |
    Specialized methods for  NULL dynamics: a funtion generates values of Z to force human infection dynamics
  contents:
  - MBionomics.Ztrace
  - F_fqZ.Ztrace
  - F_fqM.Ztrace
  - F_eggs.Ztrace
  - dMYZdt.Ztrace
  - setup_MYZpar.Ztrace
  - setup_MYZinits.Ztrace
  - make_MYZpar_Ztrace
  - make_indices_MYZ.Ztrace
  - parse_deout_MYZ.Ztrace
  - make_inits_MYZ_Ztrace
  - get_inits_MYZ.Ztrace
  - update_inits_MYZ.Ztrace
  - make_parameters_MYZ_Ztrace
- subtitle: Gtrace
  desc: |
    Specialized methods for NULL dynamics: a funtion generates values for eggs laid to aquatic ecology
  contents:
  - MBionomics.Gtrace
  - F_fqZ.Gtrace
  - F_fqM.Gtrace
  - F_eggs.Gtrace
  - dMYZdt.Gtrace
  - setup_MYZpar.Gtrace
  - setup_MYZinits.Gtrace
  - setup_MYZpar.Gtrace
  - setup_MYZinits.Gtrace
  - make_MYZpar_Gtrace
  - make_indices_MYZ.Gtrace
  - parse_deout_MYZ.Gtrace
  - make_inits_MYZ_Gtrace
  - get_inits_MYZ.Gtrace
  - update_inits_MYZ.Gtrace
  - make_parameters_MYZ_Gtrace
- subtitle: basicM
  desc: |
    Specialized methods for basicM, a model of adult mosquito dynamics with no parasite infection dynamics.
  contents:
  - MBionomics.basicM
  - F_fqZ.basicM
  - F_fqM.basicM
  - F_eggs.basicM
  - dMYZdt.basicM
  - setup_MYZpar.basicM
  - setup_MYZinits.basicM
  - make_MYZpar_basicM
  - make_MYZinits_basicM
  - make_indices_MYZ.basicM
  - parse_deout_MYZ.basicM
  - make_inits_MYZ_basicM
  - get_inits_MYZ.basicM
  - update_inits_MYZ.basicM
  - make_parameters_MYZ_basicM
- subtitle: RM
  desc: |
    Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982).
  contents:
  - MBionomics.RM
  - F_fqZ.RM
  - F_fqM.RM
  - F_eggs.RM
  - dMYZdt.RM_ode
  - dMYZdt.RM_dde
  - setup_MYZpar.RM
  - setup_MYZinits.RM
  - make_MYZpar_RM
  - make_MYZinits_RM_ode
  - make_MYZinits_RM_dde
  - make_indices_MYZ.RM_ode
  - make_indices_MYZ.RM_dde
  - parse_deout_MYZ.RM
  - make_inits_MYZ_RM_ode
  - make_inits_MYZ_RM_dde
  - get_inits_MYZ.RM_ode
  - get_inits_MYZ.RM_dde
  - update_inits_MYZ.RM_ode
  - update_inits_MYZ.RM_dde
  - make_parameters_MYZ_RM
- subtitle: GeRM
  desc: |
    Specialized methods for a generalized Ross-Macdonald model for adult mosquito ecology and parasite infection dynamics, first published by Sean L Wu, et al.(2023).
  contents:
  - MBionomics.GeRM
  - F_fqZ.GeRM
  - F_fqM.GeRM
  - F_eggs.GeRM
  - dMYZdt.GeRM_ode
  - dMYZdt.GeRM_dde
  - setup_MYZpar.GeRM
  - setup_MYZinits.GeRM
  - make_MYZpar_GeRM
  - make_MYZinits_GeRM_ode
  - make_MYZinits_GeRM_dde
  - make_indices_MYZ.GeRM_ode
  - make_indices_MYZ.GeRM_dde
  - parse_deout_MYZ.GeRM
  - make_inits_MYZ_GeRM_ode
  - make_inits_MYZ_GeRM_dde
  - get_inits_MYZ.GeRM_ode
  - get_inits_MYZ.GeRM_dde
  - update_inits_MYZ.GeRM_ode
  - update_inits_MYZ.GeRM_dde
  - make_parameters_MYZ_GeRM
- title: Aquatic Mosquito Dynamics
  desc: |
    Generic methods for the aquatic (immature) mosquito component.
  contents:
  - LBionomics
  - F_alpha
  - dLdt
  - setup_Lpar
  - setup_Linits
  - make_indices_L
  - parse_deout_L
  - get_inits_L
  - update_inits_L
- subtitle: trace
  desc: |
    Specialized methods for the exogeneously forced trace model of aquatic mosquito dynamics.
  contents:
  - LBionomics.trace
  - F_alpha.trace
  - dLdt.trace
  - setup_Lpar.trace
  - setup_Linits.trace
  - make_Lpar_trace
  - make_indices_L.trace
  - parse_deout_L.trace
  - make_inits_L_trace
  - get_inits_L.trace
  - update_inits_L.trace
  - make_parameters_L_trace
- subtitle: basic
  desc: |
    Specialized methods for a basic competition model of aquatic mosquito dynamics.
  contents:
  - LBionomics.basic
  - F_alpha.basic
  - dLdt.basic
  - setup_Lpar.basic
  - setup_Linits.basic
  - make_Lpar_basic
  - make_Linits_basic
  - make_indices_L.basic
  - parse_deout_L.basic
  - make_inits_L_basic
  - get_inits_L.basic
  - update_inits_L.basic
  - make_parameters_L_basic
- title: Mosquito Bionomics
  desc: |
    Methods to compute or update mosquito bionomic parameters
  contents:
  - Bionomics
  - Bionomics.static
  - Bionomics.dynamic
  - Bionomics.Ldynamic
  - Bionomics.Mdynamic
  - Bionomics.setup
  - setup_bionomics_static
- subtitle:  Functional Responses
  desc: |
    Compute bionomic parameters as functional responses to resource availability
  contents:
  - F_sigma
  - F_sigma.static
  - F_sigma.BQS
  - F_nu
  - F_nu.static
  - F_nu.type2
  - F_f
  - F_f.static
  - F_f.type2
  - F_q
  - F_q.static
  - F_q.dynamic
  - F_g
  - F_g.static
- subtitle: Mosquito Dispersal
  desc: |
    Specialized methods to set up mosquito dispersal matrices
  contents:
  - make_calK
  - make_calK.herethere
  - make_calK.as_matrix
  - make_calK.xy
  - make_calK_xy
- title: Human Infection Dynamics
  desc: |
    Generic methods for the dynamical component that handles human infection dynamics, immunity, disease and transmission
  contents:
  - F_X
  - F_H
  - F_pr
  - F_b
  - dXdt
  - setup_Xpar
  - setup_Xinits
  - make_indices_X
  - parse_deout_X
  - get_inits_X
  - update_inits_X
  - HTC
  - xde_plot_X
- subtitle: trace
  desc: |
    Specialized methods for a human trace model to pass kappa as a parameter
  contents:
  - F_X.trace
  - F_H.trace
  - F_pr.trace
  - F_b.trace
  - dXdt.trace
  - setup_Xpar.trace
  - setup_Xinits.trace
  - make_Xpar_trace
  - make_indices_X.trace
  - parse_deout_X.trace
  - make_inits_X_trace
  - get_inits_X.trace
  - update_inits_X.trace
  - make_parameters_X_trace
- subtitle: hMoI
  desc: |
    Specialized methods for a hybrid model of MoI (Multiplicity of Infection) for human infection dynamics.
  contents:
  - F_X.hMoI
  - F_H.hMoI
  - F_pr.hMoI
  - F_b.hMoI
  - dXdt.hMoI
  - setup_Xpar.hMoI
  - setup_Xinits.hMoI
  - make_Xpar_hMoI
  - make_Xinits_hMoI
  - make_indices_X.hMoI
  - parse_deout_X.hMoI
  - make_inits_X_hMoI
  - get_inits_X.hMoI
  - update_inits_X.hMoI
  - make_parameters_X_hMoI
  - HTC.hMoI
- subtitle: SIS
  desc: |
    Specialized methods for the SIS (Susceptible-Infected-Susceptible) model of human dynamics.
  contents:
  - F_X.SIS
  - F_H.SIS
  - F_pr.SIS
  - F_b.SIS
  - dXdt.SIS
  - setup_Xpar.SIS
  - setup_Xinits.SIS
  - make_Xpar_SIS
  - make_Xinits_SIS
  - make_indices_X.SIS
  - parse_deout_X.SIS
  - make_inits_X_SIS
  - get_inits_X.SIS
  - update_inits_X.SIS
  - make_parameters_X_SIS
  - HTC.SIS
  - xde_plot_X.SIS
  - xde_lines_X_SIS
- subtitle: SIP
  desc: |
    Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics.
  contents:
  - F_X.SIP
  - F_H.SIP
  - F_pr.SIP
  - F_b.SIP
  - dXdt.SIP
  - setup_Xpar.SIP
  - setup_Xinits.SIP
  - make_Xpar_SIP
  - make_Xinits_SIP
  - make_indices_X.SIP
  - parse_deout_X.SIP
  - make_inits_X_SIP
  - get_inits_X.SIP
  - update_inits_X.SIP
  - make_parameters_X_SIP
  - HTC.SIP
  - xde_plot_X.SIP
  - xde_lines_X_SIP
- title: Human Population Dynamics
  desc: |
    Generic methods for the human demography and aging
  contents:
  - dHdt
  - setup_Hpar_static
  - Births
  - make_parameters_demography_null
- subtitle: static
  desc: |
    Specialized methods for the static (constant) demographic model
  contents:
  - Births.zero
  - dHdt.zero
- title: Human and Mosquito Behaviors
  desc: |
    Methods to implement human and Mosquito Behaviorsbehaviors
  contents:
  - Behavior
  - Behavior.null
  - Behavior.forced
  - setup_behavior_null
  - setup_behavior_forced
  - setup_behavior
  - setup_behavior.null
  - setup_behavior.forced
- subtitle: Care Seeking
  desc: |
    Methods to implement care seeking
  contents:
  - CareSeeking
  - CareSeeking.null
  - setup_care_seeking_null
- title: Imported Malaria
  desc: |
    Methods to implement imported malaria
  contents:
  - travel_malaria
  - Visitors
- subtitle: Travel Malaria
  desc: |
    Specialized methods for travel malaria
  contents:
  - travel_malaria.static
  - setup_travel_static
  - travel_malaria.foi
  - setup_travel_foi
  - travel_malaria.eir
  - setup_travel_eir
- subtitle: Visitors
  desc: |
    Methods for the availability and infectiousness of a visitor population
  contents:
  - Visitors.static
  - setup_visitors_static
  - Visitors.basic
  - setup_visitors_basic
- title: Exogeneous Forcing
  desc: |
    Methods to implement exogeneous forcing.
  contents:
  - Abiotic
  - Civil
  - Shock
  - Control
  - Clinic
  - Development
  - MassMedical
- subtitle: Models
  desc: |
    Specialized methods the null model (no exogenous forcing)
  contents:
  - Abiotic.null
  - setup_abiotic_null
  - Civil.null
  - setup_civil_null
  - Shock.null
  - setup_shock_null
  - Control.null
  - Control.static
  - setup_control
  - setup_control_null
  - setup_control.null
  - setup_control.forced
  - Clinic.null
  - setup_clinic_null
  - setup_clinic_forced
  - Development.null
  - setup_development_null
  - MassMedical.null
  - setup_mass_medical_null
- subtitle: forced
  desc: |
    Specialized methods to call forcing
  contents:
  - Abiotic.forced
  - setup_abiotic_forced
  - check_abiotic
  - check_abiotic.null
  - check_abiotic.forced
  - Civil.forced
  - setup_civil_forced
  - check_civil
  - check_civil.null
  - check_civil.forced
  - Control.forced
  - setup_control_forced
  - MassMedical.forced
  - setup_mass_medical_forced
- subtitle: Weather
  desc: |
    Specialized methods for weather
  contents:
  - Weather
  - Weather.null
  - Weather.forced
  - setup_weather_null
  - setup_weather_forced
  - setup_rainfall_null
  - Rainfall
  - Rainfall.null
  - setup_temperature_null
  - Temperature
  - Temperature.null
  - setup_relative_humidity_null
  - Relative_Humidity
  - Relative_Humidity.null
- subtitle: Hydrology
  desc: |
    Specialized methods for hydrology
  contents:
  - Hydrology
  - Hydrology.null
  - setup_hydrology_null
- title: Resource Dynamics
  desc: |
    Methods to implement resource availability
  contents:
  - Resources
  - Resources.static
  - Resources.setup
  - Resources.forced
  - setup_resources_null
  - setup_resources_static
  - setup_resources_forced
- subtitle: Other Blood Hosts
  desc: |
    Methods to simulate availability of other blood hosts
  contents:
  - OtherBloodHosts
  - OtherBloodHosts.static
  - setup_other_blood_hosts_static
- subtitle: Habitat Dynamics and Availability
  desc: |
    Specialized methods for weather
  contents:
  - AvailableHabitat
  - AvailableHabitat.static
  - AvailableHabitat.simple
  - AvailableHabitat.forced
  - compute_AvailableHabitat
  - HabitatDynamics
  - HabitatDynamics.static
  - setup_habitat_dynamics_static
- subtitle: Sugar
  desc: |
    Methods to simulate availability of sugar
  contents:
  - SugarDynamics
  - SugarDynamics.static
  - setup_sugar_static
  - AvailableSugar
  - AvailableSugar.static
  - AvailableSugar.forced
- title: Vector Control
  desc: |
    Methods to implement vector control.
  contents:
  - VectorControl
  - VectorControlEffects
  - VectorControlEffectSizes
- subtitle: null model
  desc: |
    Specialized methods for the null model (no vector control)
  contents:
  - VectorControl.null
  - VectorControlEffects.null
  - VectorControlEffectSizes.null
  - setup_vc_null
- subtitle: Implement Control
  desc: |
    Specialized methods to implement vector control
  contents:
  - VectorControl.control
  - VectorControlEffects.control
  - VectorControlEffectSizes.control
  - setup_vc_control
- subtitle: Bed Nets
  desc: |
    Methods to implement bed nets
  contents:
  - DistributeBedNets
  - OwnBedNet
  - UseBedNet
  - BedNetEffects
  - BedNetEffectSizes
  - DistributeBedNets.null
  - OwnBedNet.null
  - UseBedNet.null
  - BedNetEffects.null
  - BedNetEffectSizes.null
  - setup_itn_null
  - BedNetEffects.lemenach
  - BedNetEffectSizes.lemenach
  - setup_itn_lemenach
- subtitle: Indoor Residual Spraying
  desc: |
    Methods to implement IRS
  contents:
  - SprayHouses
  - IRS_Effects
  - IRS_EffectSizes
  - SprayHouses.null
  - IRS_Effects.null
  - IRS_EffectSizes.null
  - setup_irs_null
- subtitle: Area Spraying
  desc: |
    Methods to implement area spraying
  contents:
  - AreaSpray
  - AreaSprayEffects
  - AreaSprayEffectSizes
  - AreaSpray.null
  - AreaSprayEffects.null
  - AreaSprayEffectSizes.null
  - setup_area_spray_null
- subtitle: Sugar Baits
  desc: |
    Methods to implement sugar baits
  contents:
  - SugarBaits
  - SugarBaitEffects
  - SugarBaitEffectSizes
  - SugarBaits.null
  - SugarBaitEffects.null
  - SugarBaitEffectSizes.null
  - setup_sugar_baits_null
- subtitle: Larval Source Management
  desc: |
    Methods to implement LSM
  contents:
  - TreatHabitats
  - LSM_Effects
  - LSM_EffectSizes
  - TreatHabitats.null
  - LSM_Effects.null
  - LSM_EffectSizes.null
  - setup_lsm_null
- subtitle: Ovitraps
  desc: |
    Specialized methods for ovitraps
  contents:
  - OviTraps
  - OviTraps.null
  - setup_ovitraps_null

- title: Setup
  desc: |
    Basic setup for models
  contents:
  - make_parameters_xde
  - make_indices
- subtitle: Setting Up
  desc: |
    Methods to set up basic models
  contents:
  - xde_setup
  - xde_setup_aquatic
  - xde_setup_mosy
  - xde_setup_human
  - xde_setup_cohort
- subtitle: Initial Values
  desc: |
    Methods to set up basic models
  contents:
  - get_inits
  - update_inits
  - last_to_inits
- title: Solving
  desc: |
    Methods to compute the derivatives and solve the equat
- subtitle: Derivatives
  contents:
  - xDE_diffeqn
  - xDE_diffeqn_aquatic
  - xDE_diffeqn_mosy
  - xDE_diffeqn_human
  - xDE_diffeqn_cohort
- subtitle: Solving
  desc: |
    Wrappers around the derivatives functions that handle time and parse outputs
  contents:
  - xde_solve
  - xde_solve.dde
  - xde_solve.ode
  - xde_solve.aqua
  - xde_solve.aqua_dde
  - xde_solve.mosy
  - xde_solve.mosy_dde
  - xde_solve.human
  - xde_solve.cohort
  - xde_stable_orbit
  - xde_steady
- title: Analysis and Visualization
  desc: |
    Methods to compute and output terms
- subtitle: Spatial metrics
  contents:
  - metric_calV
  - metric_calD
  - metric_calR
  - metric_calZ
- subtitle: Compute terms
  desc: |
    Methods to compute and transmission terms
  contents:
  - parse_deout
  - parse_deout_vec
  - compute_terms
  - compute_terms.xde
  - compute_terms.cohort
  - compute_terms.human
  - compute_terms.na
  - compute_terms_steady
  - compute_NI
  - compute_NI_ix
  - compute_vars_full
  - compute_vars_human
  - compute_vars_aqua
  - compute_vars_mosy
  - compute_vars_cohort
- subtitle: Plot terms
  desc: |
    Basic visualization of the transmission terms
  contents:
  - xde_plot_EIR
  - xde_lines_EIR
  - xde_plot_aEIR
  - xde_lines_aEIR
  - xde_plot_PR
  - xde_lines_PR
- title: Utilities
  contents:
  - diag_inverse
  - approx_equal
  - checkIt
  - shapeIt