Function reference

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)

MalariaImportation()
 Malaria importation through infected visitors, etc.

kappa_with_visitors()
 Compute kappa with visitors

loc_fqZ()
 Compute the local fraction, with visitors

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

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

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

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 RossMacdonald mosquito model
Specialized methods for a RossMacdonald 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 RossMacdonald mosquito model
Specialized methods for the generalized RossMacdonald 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 Ztrace 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

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

F_beta()
 Biting distribution matrix

F_EIR()
 Entomological inoculation rate on human strata

F_kappa()
 Net infectiousness of human population to mosquitoes

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

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

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

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

make_beta(<static>)
 Biting distribution matrix

make_beta_lag(<static>)
 Biting distribution matrix

make_beta(<dynamic>)
 Biting distribution matrix

make_beta_lag(<dynamic>)
 Lagged biting distribution matrix

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 (SusceptibleInfectedSusceptible) 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 (SusceptibleInfectedProphylaxis) 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

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

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

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

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 percapita human population birth rate (endogenous)

xDE_diffeqn()
 Generalized spatial differential equation model

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

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)

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