Function reference • exDE

Exogeneous Forcing

Methods to implement exogeneous forcing.

ExogenousForcing(): Modify parameters due to exogenous forcing

ExogenousForcing(<null>): Modify parameters due to exogenous forcing

make_parameters_exogenous_null(): Make parameters for the null model of exogenous forcing (do nothing)

Malaria Importation

Methods to implement malaria importation.

MalariaImportation(): Malaria importation through infected visitors, etc.

kappa_with_visitors(): Compute kappa with visitors

loc_fqZ(): Compute the local fraction, with visitors

Malaria importation null model

Specialized methods for a null model of malaria importation.

MalariaImportation(<null>): Malaria importation, the null model

kappa_with_visitors(<null>): kappa with visitors, the null model

loc_fqZ(<null>): fqZ with visitors, the null model

make_parameters_mi_null(): Make parameters for the null model for malaria importation

malaria importation basic model

Specialized methods for a basic model of malaria importation.

MalariaImportation(<basic>): Malaria importation, the basic model

kappa_with_visitors(<basic>): kappa with visitors, the basic model

loc_fqZ(<basic>): fqZ with visitors, the basic model

make_parameters_mi_basic(): Make parameters for the basic model for malaria importation

Vector Control

Methods to implement vector control.

VectorControl(): Modify baseline values due to vector control

VectorControl(<null>): Modify baseline values due to vector control

make_parameters_vc_null(): Make parameters for the null model of vector control (do nothing)

VectorControl(<lemenach>): Modify baseline values due to vector control

make_parameters_vc_lemenach(): Make parameters for Le Menach ITN model of vector control

Adult mosquito component

Generic methods for the adult mosquito component.

MosquitoBehavior(): Compute bloodfeeding and mortality rates

F_tau(): Time spent host seeking/feeding and resting/ovipositing

F_Z(): Density of infectious mosquitoes

F_Z_lag(): Density of lagged infectious mosquitoes

F_eggs(): Number of eggs laid by adult mosquitoes

dMYZdt(): Derivatives for adult mosquitoes

make_indices_MYZ(): Add indices for adult mosquitoes to parameter list

get_inits_MYZ(): Return initial values as a vector

make_Omega(): Make the mosquito demography matrix

A Ross-Macdonald mosquito model

Specialized methods for a Ross-Macdonald model of adult mosquito dynamics.

MosquitoBehavior(<RM>): Compute bloodfeeding and mortality rates

F_tau(<RM>): Time spent host seeking/feeding and resting/ovipositing

F_Z(<RM>): Density of infectious mosquitoes

F_Z_lag(<RM>): Density of lagged infectious mosquitoes

F_eggs(<RM>): Number of eggs laid by adult mosquitoes

dMYZdt(<RM_ode>): Derivatives for adult mosquitoes

dMYZdt(<RM_dde>): Derivatives for adult mosquitoes

make_indices_MYZ(<RM>): Add indices for adult mosquitoes to parameter list

make_parameters_MYZ_RM(): Make parameters for generalized RM ODE adult mosquito model

make_inits_MYZ_RM(): Make inits for generalized RM ODE adult mosquito model

get_inits_MYZ(<RM>): Return initial values as a vector

Generalized Ross-Macdonald mosquito model

Specialized methods for the generalized Ross-Macdonald model of adult mosquito dynamics.

MosquitoBehavior(<GeRM_base>): Compute bloodfeeding and mortality rates

MosquitoBehavior(<GeRM_exo>): Compute bloodfeeding and mortality rates

F_tau(<GeRM>): Time spent host seeking/feeding and resting/ovipositing

F_Z(<GeRM>): Density of infectious mosquitoes

F_Z_lag(<GeRM>): Density of lagged infectious mosquitoes

F_eggs(<GeRM>): Number of eggs laid by adult mosquitoes

dMYZdt(<GeRM_ode>): Derivatives for adult mosquitoes

dMYZdt(<GeRM_dde>): Derivatives for adult mosquitoes

make_indices_MYZ(<GeRM>): Add indices for adult mosquitoes to parameter list

make_parameters_MYZ_GeRM(): Make parameters for generalized GeRM ODE adult mosquito model

make_parameters_MYZ_GeRM_exo(): Make parameters for generalized GeRM ODE adult mosquito model

make_inits_MYZ_GeRM(): Make inits for generalized GeRM ODE adult mosquito model

get_inits_MYZ(<GeRM>): Return initial values as a vector

specialized methods for the adult mosquito Ztrace model

Specialized methods for the Z-trace of adult mosquito dynamics.

MosquitoBehavior(<Ztrace>): Compute bloodfeeding and mortality rates

F_Z(<Ztrace>): Number of infective adults in each patch

F_Z_lag(<Ztrace>): Number of infective adults in each patch

F_eggs(<Ztrace>): Number of eggs laid by adult mosquitoes

dMYZdt(<Ztrace>): Derivatives for aquatic stage mosquitoes

make_indices_MYZ(<Ztrace>): Add indices for aquatic stage mosquitoes to parameter list

make_parameters_MYZ_Ztrace(): Make parameters for Ztrace aquatic mosquito model

make_inits_MYZ_Ztrace(): Make parameters for Ztrace aquatic mosquito model

get_inits_MYZ(<Ztrace>): Return initial values as a vector

Aquatic mosquito component

Generic methods for the aquatic (immature) mosquito component.

F_alpha(): Number of newly emerging adults from each larval habitat

dLdt(): Derivatives for aquatic stage mosquitoes

make_indices_L(): Add indices for aquatic stage mosquitoes to parameter list

get_inits_L(): Return initial values as a vector

Trace (forced) aquatic mosquito model

Specialized methods for the exogeneously forced trace model of aquatic mosquito dynamics.

F_alpha(<trace>): Number of newly emerging adults from each larval habitat

dLdt(<trace>): Derivatives for aquatic stage mosquitoes

make_indices_L(<trace>): Add indices for aquatic stage mosquitoes to parameter list

make_parameters_L_trace(): Make parameters for trace aquatic mosquito model

make_inits_L_trace(): Make parameters for trace aquatic mosquito model

get_inits_L(<trace>): Return initial values as a vector

Basic competition aquatic mosquito model

Specialized methods for the basic competition model of aquatic mosquito dynamics.

F_alpha(<basic>): Number of newly emerging adults from each larval habitat

dLdt(<basic>): Derivatives for aquatic stage mosquitoes

make_indices_L(<basic>): Add indices for aquatic stage mosquitoes to parameter list

make_parameters_L_basic(): Make parameters for basic competition aquatic mosquito model

make_inits_L_basic(): Make inits for basic competition aquatic mosquito model

get_inits_L(<basic>): Return initial values as a vector

Transmission

Generic methods for transmission.

F_beta(): Biting distribution matrix

F_EIR(): Entomological inoculation rate on human strata

F_kappa(): Net infectiousness of human population to mosquitoes

Transmission for ODEs

Specialized methods for transmission for ODEs

F_kappa(<ode>): Net infectiousness of human population to mosquitoes

F_EIR(<ode>): Entomological inoculation rate on human strata

F_beta(<ode>): Net infectiousness of human population to mosquitoes

Transmission for DDEs

Specialized methods for transmission for ODEs

F_kappa(<dde>): Net infectiousness of human population to mosquitoes

F_EIR(<dde>): Entomological inoculation rate on human strata

F_beta(<dde>): Net infectiousness of human population to mosquitoes

Transmission for trace models

Specialized methods for transmission for trace models

F_kappa(<trace>): Net infectiousness of human population to mosquitoes

F_EIR(<trace>): Entomological inoculation rate on human strata

F_beta(<trace>): Net infectiousness of human population to mosquitoes

Mixing matrix

Generic methods to compute the mixing matrix mixing.

make_beta(): Call compute_beta as needed

make_beta_lag(): Call compute_beta with lagged variables, as needed

compute_beta(): Compute beta, the biting distribution matrix

static

Specialized methods for static denominators

make_beta(<static>): Biting distribution matrix

make_beta_lag(<static>): Biting distribution matrix

dynamic

Specialized methods for dynamic denominators

make_beta(<dynamic>): Biting distribution matrix

make_beta_lag(<dynamic>): Lagged biting distribution matrix

Human disease component

Generic methods for the human disease component.

F_x(): Size of effective infectious human population

F_x_lag(): Size of lagged effective infectious human population

dXdt(): Derivatives for human population

make_indices_X(): Add indices for human population to parameter list

get_inits_X(): Return initial values as a vector

hybrid MoI model

Specialized methods for a hybrid model of MoI (Multiplicity of Infection) for human infection dynamics.

F_x(<hMoI>): Size of effective infectious human population

F_x_lag(<hMoI>): Size of lagged effective infectious human population

dXdt(<hMoI>): Derivatives for human population

make_indices_X(<hMoI>): Add indices for human population to parameter list

make_parameters_X_hMoI(): Make parameters for hybrid MoI human model

make_inits_X_hMoI(): Make inits for hybrid MoI human model

get_inits_X(<hMoI>): Return initial values as a vector

SIS human model

Specialized methods for the SIS (Susceptible-Infected-Susceptible) model of human dynamics.

F_x(<SIS>): Size of effective infectious human population

F_x_lag(<SIS>): Size of lagged effective infectious human population

dXdt(<SIS>): Derivatives for human population

make_indices_X(<SIS>): Add indices for human population to parameter list

make_parameters_X_SIS(): Make parameters for SIS human model

make_inits_X_SIS(): Make inits for SIS human model

get_inits_X(<SIS>): Return initial values as a vector

SIP human model

Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics.

F_x(<SIP>): Size of effective infectious human population

F_x_lag(<SIP>): Size of lagged effective infectious human population

dXdt(<SIP>): Derivatives for human population

make_indices_X(<SIP>): Add indices for human population to parameter list

make_parameters_X_SIP(): Make parameters for SIP human model

make_inits_X_SIP(): Make inits for SIP human model

get_inits_X(<SIP>): Return initial values as a vector

Human demography component

Generic methods for the human demography component.

F_H(): Size of human population denominators

F_H_lag(): Size of lagged human population denominators

Births(): A function that computes the birth rate for human populations

dHdt(): Derivatives of demographic changes in human populations

make_indices_H(): Add indices for human population denominators to parameter list

get_inits_H(): Return initial values as a vector

F_births(): The human population birth rate

make_parameters_demography_null(): Make parameters for null human demography model

Static demography model

Specialized methods for the static (constant) demographic model

F_H(<static>): Size of human population denominators

F_H_lag(<static>): Size of lagged human population denominators

Births(<static>): Derivatives of demographic changes in human populations

dHdt(<static>): Derivatives of demographic changes in human populations

make_indices_H(<static>): Add indices for human population denominators to parameter list

get_inits_H(<static>): Return initial values as a vector

make_parameters_demography_static(): Make parameters for static human demography model

Dynamic demography model

Specialized methods for the demographic model with dynamic denominators

F_H(<dynamic>): Size of human population denominators

F_H_lag(<dynamic>): Size of lagged human population denominators

Births(<numeric>): Derivatives of demographic changes in human populations

dHdt(<numeric>): Derivatives of demographic changes in human populations

make_indices_H(<dynamic>): Add indices for human population denominators to parameter list

get_inits_H(<dynamic>): Return initial values as a vector

make_parameters_demography_dynamic(): Make parameters for forced (dynamic) human demography model

Births

Specialized methods to compute population birth rates

F_births(<null>): Null human population births

F_births(<constant>): Constant human population birth rate (forced)

F_births(<forced>): Growing human population birth rate (forced)

F_births(<exp>): Constant per-capita human population birth rate (endogenous)

Generalized spatial differential equations

xDE_diffeqn(): Generalized spatial differential equation model

xDE_diffeqn_mosy(): Generalized spatial differential equation model (mosquito only)

Spatial metrics

metric_calV(): Parasite dispersal by mosquitoes

metric_calD(): Parasite dispersal by humans

metric_calR(): Parasite Dispersal through one Parasite Generation (Humans)

metric_calZ(): Parasite Dispersal through one Parasite Generation (Mosquitoes)

Utilities

make_parameters_xde(): Make base parameters

make_indices(): Set indices for generalized spatial model

get_inits(): Get the initial values as a vector

diag_inverse(): Invert a diagonal matrix

approx_equal(): Check if two numeric values are approximately equal