| Abiotic | Set up exogenous variables for abiotic forcing |
| Abiotic.forced | Set up exogenous variables for abiotic forcing |
| Abiotic.null | Set up exogenous variables for abiotic forcing |
| approx_equal | Check if two numeric values are approximately equal |
| AreaSpray | Methods for mass spraying |
| AreaSprayEffects | Methods for mass spraying |
| AreaSprayEffectSizes | Methods for mass spraying |
| AreaSprayEffectSizes.null | Set up mass spraying |
| AreaSprayEffects.null | Set up mass spraying |
| AreaSpray.null | Set up mass spraying |
| AvailableBlood | Update the availability of blood hosts |
| AvailableBlood.forced | Compute availability of local humans for blood feeding |
| AvailableBlood.setup | Compute availability of local humans for blood feeding |
| AvailableBlood.static | Compute availability of local humans for blood feeding |
| AvailableHabitat | Update the availability of aquatic habitats |
| AvailableHabitat.forced | Compute total availability of aquatic habitats |
| AvailableHabitat.simple | Compute total availability of aquatic habitats |
| AvailableHabitat.static | Compute total availability of aquatic habitats |
| AvailableSugar | Update the availability of sugar |
| AvailableSugar.forced | Compute total availability of sugar |
| AvailableSugar.static | Compute total availability of sugar |
| BedNetEffects | Modify variables or parameters, called from... |
| BedNetEffectSizes | Modify baseline bionomic parameters, called from... |
| BedNetEffectSizes.lemenach | Modify baseline values due to vector control |
| BedNetEffectSizes.null | Bed net ownership |
| BedNetEffects.lemenach | Modify baseline values due to vector control |
| BedNetEffects.null | Bed net ownership |
| Behavior | Methods for dynamic human and mosquito behaviors |
| Behavior.forced | Methods for dynamic human and mosquito behaviors |
| Behavior.null | Methods for dynamic human and mosquito behaviors |
| Bionomics | Set bionomic parameter rates relative to baseline |
| Bionomics.dynamic | Set bionomic parameter rates relative to baseline |
| Bionomics.Ldynamic | Set bionomic parameter rates relative to baseline |
| Bionomics.Mdynamic | Set bionomic parameter rates relative to baseline |
| Bionomics.setup | Set bionomic parameter rates relative to baseline |
| Bionomics.static | Set bionomic parameter rates relative to baseline |
| Births | A function that computes the birth rate for human populations |
| Births.zero | Derivatives of demographic changes in human populations |
| CareSeeking | Set the values of exogenous variables describing care seeking |
| CareSeeking.null | Set the values of exogenous variables describing care seeking |
| check_abiotic | Check abiotic |
| check_abiotic.forced | Check abiotic |
| check_abiotic.null | Check abiotic |
| check_civil | Check civil |
| check_civil.forced | Check civil |
| check_civil.null | Check civil |
| checkIt | Check the length of an input value |
| Civil | Set up exogenous variables for civil forcing |
| Civil.forced | Set up exogenous variables for civil forcing |
| Civil.null | Set up exogenous variables for civil forcing |
| Clinic | Methods for distributing interventions during clinical visits |
| Clinic.null | Methods for distributing interventions during clinical visits |
| compute_AvailableHabitat | Compute total availability of aquatic habitats |
| compute_AvailableHosts | Compute availability blood hosts of the i^th species |
| compute_beta | Compute beta |
| compute_calU | Compute calU |
| compute_EggsLaid | Compute eggs laid |
| compute_EIR | Compute EIR |
| compute_EIR_full | Compute EIR for each vector-host pair |
| compute_kappa | Compute kappa |
| compute_local_frac | Compute the local fraction |
| compute_NI | Compute the NI |
| compute_NI_ix | Compute NI once |
| compute_terms | Compute dynamical terms |
| compute_terms.cohort | Compute dynamical terms |
| compute_terms.dts | Compute dynamical terms |
| compute_terms.human | Compute dynamical terms |
| compute_terms.na | Compute dynamical terms |
| compute_terms_steady | Compute dynamical terms |
| compute_vars_aqua | Differential equation models for aquatic mosquito populations |
| compute_vars_cohort | Differential equation models for human cohorts |
| compute_vars_full | Compute other variables at time t |
| compute_vars_human | Compute other variables at time t |
| compute_vars_mosy | Compute other variables at time t |
| Control | Modify parameters due to exogenous forcing by all kinds of... |
| Control.forced | Modify parameters due to exogenous forcing by all kinds of... |
| Control.null | Modify parameters due to exogenous forcing by all kinds of... |
| Control.static | Modify parameters due to exogenous forcing by all kinds of... |
| Development | Set up developments |
| Development.null | Set up developments |
| dHdt | Derivatives of demographic changes in human populations |
| dHdt.zero | Derivatives of demographic changes in human populations |
| diag_inverse | Invert a diagonal matrix |
| DistributeBedNets | Distribute bed nets, called from Control(VectorControl) |
| DistributeBedNets.null | Distribute bed nets |
| dLdt | Derivatives for aquatic stage mosquitoes |
| dLdt.basic | Derivatives for aquatic stage mosquitoes |
| dLdt.trace | Derivatives for aquatic stage mosquitoes |
| dMYZdt | Derivatives for adult mosquitoes |
| dMYZdt.basicM | Derivatives for adult mosquitoes |
| dMYZdt.ENBRQ | Derivatives for adult mosquitoes |
| dMYZdt.Gtrace | Derivatives for aquatic stage mosquitoes |
| dMYZdt.RM | Derivatives for adult mosquitoes |
| dMYZdt.RMlumpy | Derivatives for adult mosquitoes |
| dMYZdt.Ztrace | Derivatives for aquatic stage mosquitoes |
| dts_lines_aEIR | Add lines for the annualized EIR _vs._ t |
| dts_lines_EIR | Add lines for the EIR _vs._ time |
| dts_lines_M | Add lines for adult mosquito population density |
| dts_lines_PR | Add lines for the prevalence / parasite rate (PR) from a... |
| dts_lines_X_SIP | Add lines for the density of infected individuals for the SIP... |
| dts_lines_X_SIS | Add lines for the density of infected individuals for the SIS... |
| dts_lines_YZ | Add lines for the density of infected and infective... |
| dts_lines_YZ_fracs | Add lines for the fraction of infected and infective... |
| dts_lines_Z_fracs | Add lines for the fraction of infected and infective... |
| dts_plot_aEIR | Plot the annualized EIR _vs._ time |
| dts_plot_EIR | Plot the EIR _vs._ time |
| dts_plot_M | Plot adult mosquito population density |
| dts_plot_PR | Plot the prevalence / parasite rate (PR) from a model of... |
| dts_plot_X | Basic plotting for epidemiological models |
| dts_plot_X.SIP | Plot the density of infected individuals for the SIP model |
| dts_plot_X.SIS | Plot the density of infected individuals for the SIS model |
| dts_plot_YZ | Plot the density of infected and infective mosquitoes |
| dts_plot_YZ_fracs | Plot the fraction of infected and infective mosquitoes |
| dts_plot_Z_fracs | Plot the fraction of infected and infective mosquitoes |
| dts_setup | Set up a model for dts_diffeqn |
| dts_setup_aquatic | Set up a model for dts_diffeqn_aqua |
| dts_setup_cohort | Set up a model for dts_diffeqn_cohort |
| dts_setup_human | Set up a model for dts_diffeqn_human |
| dts_setup_mosy | Set up a model for dts_diffeqn_mosy |
| dts_solve | Solve a system of equations |
| dts_solve.aqua | Solve a system of equations for aquatic dynamics, forced by... |
| dts_solve.cohort | Solve a system of equations with dts_diffeqn_cohort |
| dts_solve.dts | Solve a system of equations as an ode |
| dts_solve.human | Solve a system of equations with dts_diffeqn_human |
| dts_solve.mosy | Solve a system of equations for mosquito ecology using... |
| dts_stable_orbit | Solve for the steady state or stable orbit of a system of... |
| dts_steady | Solve for the steady state of a system of equations |
| DTS_step | Generalized spatial differential equation model |
| DTS_step_aquatic | Difference equation models for aquatic mosquito populations |
| DTS_step_cohort | Difference equation models for human cohorts |
| DTS_step_human | Difference equations isolating the humans, forced with Ztrace |
| DTS_step_mosy | Generalized spatial differential equation model (mosquito... |
| dXdt | Derivatives for human population |
| dXdt.SIP | Derivatives for human population |
| dXdt.SIS | Derivatives for human population |
| dXdt.trace | Derivatives for human population |
| EggLaying | Compute eggs laid |
| EggLaying.dynamic | Compute eggs laid |
| EggLaying.setup | Compute eggs laid |
| EggLaying.simple | Compute eggs laid |
| EggLaying.static | Compute eggs laid |
| EIP | Compute the EIP |
| EIP.fixed | Modify parameters due to exogenous forcing by all kinds of... |
| EIP.null | Modify parameters due to exogenous forcing by all kinds of... |
| Emergence | Compute emerging adults |
| Exposure | Exposure and Infection |
| F_alpha | Number of newly emerging adults from each larval habitat |
| F_alpha.basic | Number of newly emerging adults from each larval habitat |
| F_alpha.trace | Number of newly emerging adults from each larval habitat |
| F_b | Infection blocking pre-erythrocytic immunity |
| F_beta | Compute beta, the biting distribution matrix |
| F_b.SIP | Infection blocking pre-erythrocytic immunity |
| F_b.SIS | Infection blocking pre-erythrocytic immunity |
| F_b.trace | Infection blocking pre-erythrocytic immunity |
| F_eggs | Number of eggs laid by adult mosquitoes |
| F_eggs.basicM | Number of eggs laid by adult mosquitoes |
| F_eggs.ENBRQ | Number of eggs laid by adult mosquitoes |
| F_eggs.Gtrace | Number of eggs laid by adult mosquitoes |
| F_eggs.RM | Number of eggs laid by adult mosquitoes |
| F_eggs.RMlumpy | Number of eggs laid by adult mosquitoes |
| F_eggs.Ztrace | Number of eggs laid by adult mosquitoes |
| F_EIR | Entomological inoculation rate on human strata |
| F_f | Compute the blood feeding rate, f |
| F_f.dddn | Dawn, day, dusk, night model for the blood feeding rate |
| F_foi | A model for daily FoI as a function of the daily EIR. |
| F_foi.nb | The daily FoI as a function of the daily EIR under a negative... |
| F_foi.pois | A Poisson model for the daily local FoI as a function of the... |
| F_fqM | Blood feeding rate of the mosquito population |
| F_fqM.basicM | The net blood feeding rate of the infective mosquito... |
| F_fqM.ENBRQ | The net blood feeding rate of the infective mosquito... |
| F_fqM.Gtrace | Blood feeding rate of the infective mosquito population |
| F_fqM.RM | The net blood feeding rate of the infective mosquito... |
| F_fqM.RMlumpy | The net blood feeding rate of the infective mosquito... |
| F_fqM.Ztrace | Blood feeding rate of the infective mosquito population |
| F_fqZ | Blood feeding rate of the infective mosquito population |
| F_fqZ.basicM | The net blood feeding rate of the infective mosquito... |
| F_fqZ.ENBRQ | The net blood feeding rate of the infective mosquito... |
| F_fqZ.Gtrace | Blood feeding rate of the infective mosquito population |
| F_fqZ.RM | The net blood feeding rate of the infective mosquito... |
| F_fqZ.RMlumpy | The net blood feeding rate of the infective mosquito... |
| F_fqZ.Ztrace | Blood feeding rate of the infective mosquito population |
| F_f.static | Static model for the blood feeding rate |
| F_f.type2 | Type 2 functional response for the blood feeding rate |
| F_H | Size of human population denominators |
| F_H.SIP | Size of effective infectious human population |
| F_H.SIS | Size of effective infectious human population |
| F_H.trace | Size of the human population |
| F_kappa | Net infectiousness of human population to mosquitoes |
| F_nu | Compute the egg laying rate |
| F_nu.dddn | Dawn, day, dusk, night model for the human fraction |
| F_nu.static | Static model for the egg laying rate |
| F_nu.type2 | Type 2 functional response for the blood feeding rate |
| F_p | Compute mosguito survival |
| F_p.dddn | Dawn, day, dusk, night model for the human fraction |
| F_pr | Compute the "true" prevalence of infection / parasite rate |
| F_pr.SIP | Compute the "true" prevalence of infection / parasite rate |
| F_pr.SIS | Compute the "true" prevalence of infection / parasite rate |
| F_pr.trace | Compute the "true" prevalence of infection / parasite rate |
| F_p.static | Static model for mosquito survival |
| F_q | Compute the human blood fraction |
| F_q.dddn | Dawn, day, dusk, night model for the human fraction |
| F_q.dynamic | Static model for human blood fraction |
| F_q.static | Static model for human blood fraction |
| F_sigma | Compute mosquito emigration rates |
| F_sigma.dddn | Dawn, day, dusk, night model for the human fraction |
| F_sigma.static | Static model for mosquito emigration |
| F_tau | Time spent host seeking/feeding and resting/ovipositing |
| F_X | Size of effective infectious human population |
| F_X.SIP | Size of effective infectious human population |
| F_X.SIS | Size of effective infectious human population |
| F_X.trace | Size of effective infectious human population |
| get_inits | Get the initial values as a vector |
| get_inits_L | Return initial values as a vector |
| get_inits_L.basic | Return initial values as a vector |
| get_inits_L.trace | Return initial values as a vector |
| get_inits_MYZ | Return initial values as a vector |
| get_inits_MYZ.basicM | Return initial values as a vector |
| get_inits_MYZ.ENBRQ | Return initial values as a vector |
| get_inits_MYZ.Gtrace | Return initial values as a vector |
| get_inits_MYZ.RM | Return initial values as a vector |
| get_inits_MYZ.RMlumpy | Return initial values as a vector |
| get_inits_MYZ.Ztrace | Return initial values as a vector |
| get_inits_X | Return initial values as a vector |
| get_inits_X.SIP | Return initial values as a vector |
| get_inits_X.SIS | Return initial values as a vector |
| get_inits_X.trace | Return initial values as a vector |
| HabitatDynamics | Habitat Dynamics and Searching |
| HabitatDynamics.static | Set the values of habitat search weights and other exogenous... |
| HTC | Compute the human transmitting capacity |
| HTC.SIP | Compute the HTC for the SIP model |
| HTC.SIS | Compute the HTC for the SIS model |
| Hydrology | Set the values of exogenous variables describing hydrology |
| Hydrology.null | Set the values of exogenous variables describing hydrology |
| IRS_Effects | Model the effects of IRS |
| IRS_EffectSizes | Model IRS effect sizes |
| IRS_EffectSizes.null | Model IRS effect sizes |
| IRS_Effects.null | Model the effects of IRS |
| last_to_inits | Set the initial values to the last values of the last... |
| LBionomics | Set aquatic bionomic parameter rates relative to baseline |
| LBionomics.basic | Reset aquatic parameters to baseline |
| LBionomics.trace | Reset aquatic parameters to baseline |
| list_MYZvars | Return the variables as a list |
| list_MYZvars.basicM | Return the variables as a list |
| list_MYZvars.ENBRQ | Return the variables as a list |
| list_MYZvars.RM | Return the variables as a list |
| list_MYZvars.RMlumpy | Return the variables as a list |
| list_Xvars | Return the variables as a list |
| list_Xvars.SIP | Return the variables as a list |
| list_Xvars.SIS | Return the variables as a list |
| LocalFrac | Compute the local fraction |
| LocalFrac.dynamic | Compute transmission terms dynamically, no update required |
| LocalFrac.static | Compute transmission terms dynamically, no update required |
| LSM_Effects | Modify effects of LSM |
| LSM_EffectSizes | Compute effect sizes of LSM |
| LSM_EffectSizes.null | Modify effects of LSM, the null model |
| LSM_Effects.null | Modify effects of LSM, the null model |
| make_calK | Make a mosquito dispersal matrix, called calK |
| make_calK.as_matrix | Pass a pre-configured calK |
| make_calK.herethere | Dispersal to every other patch, with equal probability |
| make_calK_xy | Develop a mosquito dispersal matrix from a kernel and... |
| make_calK.xy | Develop a mosquito dispersal matrix from a kernel and... |
| make_calN | Make the habitat membership matrix, calN |
| make_calU | Make the egg distribution matrix, calU |
| make_calU_s | Make the egg distribution matrix, calU |
| make_indices | Set indices for generalized spatial model |
| make_indices_L | Add indices for aquatic stage mosquitoes to parameter list |
| make_indices_L.basic | Add indices for aquatic stage mosquitoes to parameter list |
| make_indices_L.trace | Add indices for aquatic stage mosquitoes to parameter list |
| make_indices_MYZ | Add indices for adult mosquitoes to parameter list |
| make_indices_MYZ.basicM | Add indices for adult mosquitoes to parameter list |
| make_indices_MYZ.ENBRQ | Add indices for adult mosquitoes to parameter list |
| make_indices_MYZ.Gtrace | Add indices for aquatic stage mosquitoes to parameter list |
| make_indices_MYZ.RM | Add indices for adult mosquitoes to parameter list |
| make_indices_MYZ.RMlumpy | Add indices for adult mosquitoes to parameter list |
| make_indices_MYZ.Ztrace | Add indices for aquatic stage mosquitoes to parameter list |
| make_indices_X | Add indices for human population to parameter list |
| make_indices_X.SIP | Add indices for human population to parameter list |
| make_indices_X.SIS | Add indices for human population to parameter list |
| make_indices_X.trace | Add indices for human population to parameter list |
| make_inits_L_basic | Make inits for basic competition aquatic mosquito model |
| make_inits_L_trace | Make parameters for trace aquatic mosquito model |
| make_inits_MYZ_basicM | Make inits for basicM adult mosquito model |
| make_inits_MYZ_ENBRQ | Make inits for ENBRQ adult mosquito model |
| make_inits_MYZ_Gtrace | Make parameters for Gtrace aquatic mosquito model |
| make_inits_MYZ_RM | Make inits for RM adult mosquito model |
| make_inits_MYZ_RMlumpy | Make inits for RMlumpy adult mosquito model |
| make_inits_MYZ_Ztrace | Make parameters for Ztrace aquatic mosquito model |
| make_inits_X_SIP | Make inits for SIP human model |
| make_inits_X_SIS | Make inits for SIS human model |
| make_inits_X_trace | Make inits for trace human model |
| make_Linits_basic | Make inits for basic competition aquatic mosquito model |
| make_Lpar_basic | Make parameters for basic competition aquatic mosquito model |
| make_Lpar_trace | Make parameters for trace aquatic mosquito model |
| make_MYZinits_basicM | Make inits for basicM adult mosquito model |
| make_MYZinits_ENBRQ | Make inits for ENBRQ adult mosquito model |
| make_MYZinits_RM | Make inits for RM adult mosquito model |
| make_MYZinits_RMlumpy | Make inits for RMlumpy adult mosquito model |
| make_MYZpar_basicM | Make parameters for basicM adult mosquito model |
| make_MYZpar_ENBRQ | Make parameters for ENBRQ adult mosquito model |
| make_MYZpar_Gtrace | Make parameters for Gtrace aquatic mosquito model |
| make_MYZpar_RM | Make parameters for RM adult mosquito model |
| make_MYZpar_RMlumpy | Make parameters for RMlumpy ODE adult mosquito model |
| make_MYZpar_Ztrace | Make parameters for Ztrace aquatic mosquito model |
| make_Omega | Make the mosquito demography matrix |
| make_parameters_demography_null | Make parameters for null human demography model |
| make_parameters_dts | Make base parameters, assuming nVectors = nHosts = 1 |
| make_parameters_L_basic | Make parameters for basic competition aquatic mosquito model |
| make_parameters_L_trace | Make parameters for trace aquatic mosquito model |
| make_parameters_MYZ_basicM | Make parameters for basicM adult mosquito model |
| make_parameters_MYZ_ENBRQ | Make parameters for ENBRQ adult mosquito model |
| make_parameters_MYZ_Gtrace | Make parameters for Gtrace aquatic mosquito model |
| make_parameters_MYZ_RM | Make parameters for RM adult mosquito model |
| make_parameters_MYZ_RMlumpy | Make parameters for RMlumpy ODE adult mosquito model |
| make_parameters_MYZ_Ztrace | Make parameters for Ztrace aquatic mosquito model |
| make_parameters_X_SIP | Make parameters for SIP human model |
| make_parameters_X_SIS | Make parameters for SIS human model |
| make_parameters_X_trace | Make parameters for trace human model |
| make_TaR | Make TaR |
| make_TimeSpent | Make a time spent matrix, called TimeSpent |
| make_TimeSpent.as_matrix | Pass a pre-configured TimeSpent |
| make_TimeSpent_athome | Make a mosquito dispersal matrix, called TimeSpent |
| make_TimeSpent.athome | Make a mosquito dispersal matrix, called TimeSpent with a... |
| make_TimeSpent_xy | Make a mosquito dispersal matrix, called TimeSpent |
| make_TimeSpent.xy | Develop a mosquito dispersal matrix from a kernel and... |
| make_Xinits_SIP | Make initial values for the SIP human model, with defaults |
| make_Xinits_SIS | Make initial values for the SIS human model, with defaults |
| make_Xpar_SIP | Make parameters for SIP human model, with defaults |
| make_Xpar_SIS | Make parameters for SIS human model, with defaults |
| make_Xpar_trace | Make parameters for human null model |
| MassMedical | Methods for mass medical interventions |
| MassMedical.forced | Methods for mass medical |
| MassMedical.null | Methods for mass medical |
| MBionomics | Set bloodfeeding and mortality rates to baseline |
| MBionomics.basicM | Reset bloodfeeding and mortality rates to baseline |
| MBionomics.ENBRQ | Reset bloodfeeding and mortality rates to baseline |
| MBionomics.Gtrace | Compute bloodfeeding and mortality rates |
| MBionomics.RM | Reset bloodfeeding and mortality rates to baseline |
| MBionomics.RMlumpy | Reset bloodfeeding and mortality rates to baseline |
| MBionomics.Ztrace | Compute bloodfeeding and mortality rates |
| metric_calD | Parasite dispersal by humans |
| metric_calR | Parasite Dispersal through one Parasite Generation (Humans) |
| metric_calV | Parasite dispersal by mosquitoes |
| metric_calZ | Parasite Dispersal through one Parasite Generation... |
| OtherBloodHosts | Set the values of exogenous variables describing other blood... |
| OtherBloodHosts.static | Set the values of exogenous variables describing other blood... |
| OviTraps | Methods for oviposition traps |
| OviTraps.null | Methods for oviposition traps |
| OwnBedNet | Model bed net loss, called from Control(VectorControl) |
| OwnBedNet.null | Bed net ownership |
| parse_dts_out | Parse the output of an object returned by deSolve |
| parse_dts_out_L | Parse the output of deSolve and return the variables by name... |
| parse_dts_out_L.basic | Parse the variable names for the basic model |
| parse_dts_out_L.trace | Parse the variable names for the trace model |
| parse_dts_out_MYZ | Parse the output of deSolve and return the variables by name... |
| parse_dts_out_MYZ.basicM | Parse the output of deSolve and return variables for the... |
| parse_dts_out_MYZ.ENBRQ | Parse the output of deSolve and return variables for the... |
| parse_dts_out_MYZ.Gtrace | Parse the output of deSolve and return variables for the... |
| parse_dts_out_MYZ.RM | Parse the output of deSolve and return variables for the RM... |
| parse_dts_out_MYZ.RMlumpy | Parse the output of deSolve and return variables for the... |
| parse_dts_out_MYZ.Ztrace | Parse the output of deSolve and return variables for the... |
| parse_dts_out_vec | Parse the output of an object returned by deSolve |
| parse_dts_out_X | Parse the output of deSolve and return the variables by name... |
| parse_dts_out_X.SIP | Parse the output of deSolve and return variables for the SIP... |
| parse_dts_out_X.SIS | Parse the output of deSolve and return variables for the SIS... |
| parse_dts_out_X.trace | Parse the output of deSolve and return variables for the... |
| Rainfall | Methods for exogenous variables describing rainfall |
| Rainfall.null | Methods for exogenous variables describing rainfall |
| Relative_Humidity | Methods for exogenous variables describing relative humidity |
| Relative_Humidity.null | Methods for exogenous variables describing relative humidity |
| Resources | Set the values of exogenous variables describing available... |
| Resources.forced | Methods for resources |
| Resources.setup | Modify resources and resource availability |
| Resources.static | Modify resources and resource availability |
| setup_abiotic_forced | Make parameters for the null model of abiotic forcing (do... |
| setup_abiotic_null | Set up the null model for exogenous forcing (do nothing) |
| setup_area_spray_null | Set up the null model for area spraying (do nothing) |
| setup_behavior | Setup behavior |
| setup_behavior_forced | Make parameters for the forced model for resource... |
| setup_behavior.forced | Setup behavior |
| setup_behavior_null | Make parameters for the null model for resource availability... |
| setup_behavior.null | Setup behavior |
| setup_BFpar_static | Set up the blood feeding model |
| setup_bionomics_static | Make parameters for the static model bionomics |
| setup_BloodFeeding | Set up blood feeding |
| setup_care_seeking_null | Make parameters for the null model for care seeking (do... |
| setup_civil_forced | Make parameters for the null model of civil forcing (do... |
| setup_civil_null | Set up the null model for exogenous forcing (do nothing) |
| setup_clinic_forced | Set up a model for clinic |
| setup_clinic_null | Set up the null model for clinical distribution (do nothing) |
| setup_control | Setup CONTROL with forcing |
| setup_control_forced | Set up a model with some control |
| setup_control.forced | Setup control |
| setup_control_null | Set up the null model for control forcing (do nothing) |
| setup_control.null | Setup control |
| setup_development_null | Set up the null model for developments (do nothing) |
| setup_EggLaying_simple | Setup egg laying for most models |
| setup_EggLaying_static | Setup egg laying for most models |
| setup_EGGpar_static | Setup the structures required for egg laying |
| setup_EIP | Set up the fixed model for control forcing (do nothing) |
| setup_eip_fixed | Set up a fixed model for the EIP |
| setup_EIP.fixed | Set up a fixed model for the EIP |
| setup_eip_null | Set up a null model for the EIP |
| setup_EIP.null | Set up a null model for the EIP |
| setup_exposure_nb | Make parameters for the null model of exposure |
| setup_exposure_pois | Make parameters for the null model of exposure |
| setup_habitat_dynamics_static | Setup the egg laying object |
| setup_Hpar_static | A utility to set up Hpar |
| setup_hydrology_null | Make parameters for the null model for hydrology (do nothing) |
| setup_irs_null | Make parameters for the null model of IRS (do nothing) |
| setup_itn_lemenach | Make parameters for Le Menach ITN model of vector control |
| setup_itn_null | Make parameters for the null model of bed nets (do nothing) |
| setup_Linits | A function to set up adult mosquito models |
| setup_Linits.basic | Setup the basic model |
| setup_Linits.trace | Setup the trace model |
| setup_local_fraction_simple | Set up the local_fraction for static models |
| setup_Lpar | A function to set up adult mosquito models |
| setup_Lpar.basic | Setup Lpar for the basic model |
| setup_Lpar.trace | Setup Lpar for the trace model |
| setup_lsm_null | Make parameters for the null model of LSM (do nothing) |
| setup_mass_medical_forced | Set up a model for mass medical |
| setup_mass_medical_null | Set up the null model for mass medical (do nothing) |
| setup_MYZinits | A function to set up adult mosquito models |
| setup_MYZinits.basicM | Setup initial values for the basicM model |
| setup_MYZinits.ENBRQ | Setup initial values for the ENBRQ model |
| setup_MYZinits.Gtrace | Setup the Gtrace model |
| setup_MYZinits.RM | Setup initial values for the RM model |
| setup_MYZinits.RMlumpy | Setup initial values for the RMlumpy model |
| setup_MYZinits.Ztrace | Setup the Ztrace model |
| setup_MYZpar | A function to set up adult mosquito models |
| setup_MYZpar.basicM | Setup MYZpar for the basicM model |
| setup_MYZpar.ENBRQ | Setup MYZpar for the ENBRQ model |
| setup_MYZpar.Gtrace | Setup the Gtrace |
| setup_MYZpar.RM | Setup MYZpar for the RM model |
| setup_MYZpar.RMlumpy | Setup MYZpar for the RMlumpy model |
| setup_MYZpar.Ztrace | Setup the Ztrace model |
| setup_other_blood_hosts_static | Make parameters for the static model for other blood hosts... |
| setup_ovitraps_null | Set up the null model for oviposition traps (do nothing) |
| setup_rainfall_null | Set up the null model for RAINFALL |
| setup_relative_humidity_null | Set up the null model for HUMIDITY |
| setup_resources_forced | Set up a model for mass medical |
| setup_resources_null | Set up parameters for the null model for resource... |
| setup_resources_static | Set up parameters for the null model for resource... |
| setup_shock_null | Set up the null model for shocks (do nothing) |
| setup_sugar_baits_null | Set up the null model for sugar baits (do nothing) |
| setup_sugar_static | Make parameters for the static model for sugar (do nothing) |
| setup_temperature_null | Set up the null model for temperature |
| setup_travel_eir | Set up parameters and function for an eir-based... |
| setup_travel_foi | Set up parameters and function for the FoI-based... |
| setup_travel_static | A function to set up malaria importation |
| setup_vc_control | Make parameters for the control model of vector control (do... |
| setup_vc_null | Distribute vector control, the null model |
| setup_visitors_basic | Make parameters and functions for the basic model for... |
| setup_visitors_static | Make parameters for the static model visitors (no visitors) |
| setup_weather_forced | Set up the forced model for weather |
| setup_weather_null | Set up the null model for weather |
| setup_Xinits | A function to set up Xpar |
| setup_Xinits.SIP | Setup Xinits.SIP |
| setup_Xinits.SIS | Setup Xinits.SIS |
| setup_Xinits.trace | Setup Xinits.trace |
| setup_Xpar | A function to set up Xpar |
| setup_Xpar.SIP | Setup Xpar.SIP |
| setup_Xpar.SIS | Setup Xpar.SIS |
| setup_Xpar.trace | Setup Xpar.trace |
| shapeIt | Check the shape and dimensions of an object |
| Shock | Set up shocks |
| Shock.null | Set up shocks |
| SprayHouses | Do mass house spraying (IRS) |
| SprayHouses.null | Do mass house spraying (IRS) |
| SugarBaitEffects | Methods for the durability and effects of the sugar baits |
| SugarBaitEffectSizes | Methods for the effect sizes of the sugar baits |
| SugarBaitEffectSizes.null | Methods for the effect sizes of the sugar baits |
| SugarBaitEffects.null | Methods for the effects of the sugar baits |
| SugarBaits | Methods for distributing sugar baits |
| SugarBaits.null | Methods for sugar baits |
| SugarDynamics | Set the values of exogenous variables describing sugar |
| SugarDynamics.static | Set the values of exogenous variables describing sugar |
| Temperature | Methods for exogenous variables describing temperature |
| Temperature.null | Methods for exogenous variables describing temperature |
| Transmission | Compute the mixing matrix and transmission terms |
| Transmission.dynamic | Compute transmission terms, the dynamic case |
| Transmission.setup | Compute transmission terms, the dynamic case |
| Transmission.static | Compute transmission terms dynamically, no update required |
| travel_malaria | Simulate travel malaria |
| travel_malaria.eir | A model for travel malaria based on the eir in destinations |
| travel_malaria.foi | A model for the travel FoI |
| travel_malaria.static | travel, a static model |
| TreatHabitats | Modify values due to treat habitats as part of LSM, called by... |
| TreatHabitats.null | Set up the null model for LSM |
| update_inits | Set the initial values to the last values of the last... |
| update_inits_L | Set the initial values from a vector of model states |
| update_inits_L.basic | Update inits for the basic aquatic mosquito competition model |
| update_inits_L.trace | Update inits for the basic aquatic mosquito competition model |
| update_inits_MYZ | Set the initial values as a vector |
| update_inits_MYZ.basicM | Make inits for basicM adult mosquito model |
| update_inits_MYZ.ENBRQ | Make inits for ENBRQ adult mosquito model |
| update_inits_MYZ.Gtrace | Update inits for Gtrace |
| update_inits_MYZ.RM | Make inits for RM adult mosquito model |
| update_inits_MYZ.RMlumpy | Make inits for RMlumpy adult mosquito model |
| update_inits_MYZ.Ztrace | Update inits for Ztrace |
| update_inits_X | Set the initial values from a vector of states |
| update_inits_X.SIP | Update inits for the SIP human model from a vector of states |
| update_inits_X.SIS | Update inits for the SIS human model from a vector of states |
| update_inits_X.trace | Update inits for the trace human model from a vector of... |
| UseBedNet | Model bed net usage, called from Behavior |
| UseBedNet.null | Bed net ownership |
| VectorControl | Distribute vector control |
| VectorControl.control | Distribute vector control, the null model |
| VectorControlEffects | Vector control: durability & effects |
| VectorControlEffects.control | Vector control durability and effects |
| VectorControlEffectSizes | Vector control effect sizes |
| VectorControlEffectSizes.control | Distribute vector control, the null model |
| VectorControlEffectSizes.null | Vector control effect sizes |
| VectorControlEffects.null | Vector control: durability & effects |
| VectorControl.null | Distribute vector control |
| Visitors | Visitors |
| Visitors.basic | Visitors, the basic model |
| Visitors.static | Visitors, a static model |
| Weather | Methods for exogenous variables describing weather |
| Weather.forced | Methods for exogenous variables describing weather |
| Weather.null | Methods for exogenous variables describing weather |
