Extensible Differential Equations for Mosquito-Borne Pathogen Modeling


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Documentation for package ‘exDE’ version 1.0.0

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approx_equal Check if two numeric values are approximately equal
diag_inverse Invert a diagonal matrix
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.RM_dde Derivatives for adult mosquitoes
dMYZdt.RM_ode Derivatives for adult mosquitoes
dXdt Derivatives for human population
dXdt.hMoI Derivatives for human population
dXdt.SIP Derivatives for human population
dXdt.SIS Derivatives for human population
ExogenousForcing Modify parameters due to exogenous forcing
ExogenousForcing.null Modify parameters due to exogenous forcing
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_beta Biting distribution matrix
F_beta.hMoI Biting distribution matrix
F_beta.SIP Biting distribution matrix
F_beta.SIS Biting distribution matrix
F_beta_lag Lagged biting distribution matrix
F_beta_lag.hMoI Lagged biting distribution matrix
F_beta_lag.SIP Lagged biting distribution matrix
F_beta_lag.SIS Lagged biting distribution matrix
F_eggs Number of eggs laid by adult mosquitoes
F_eggs.RM Number of eggs laid by adult mosquitoes
F_EIR Entomological inoculation rate on human strata
F_EIR.hMoI Entomological inoculation rate on human strata
F_EIR.SIP Entomological inoculation rate on human strata
F_EIR.SIS Entomological inoculation rate on human strata
F_kappa Net infectiousness of human population to mosquitoes
F_kappa.RM_dde Net infectiousness of human population to mosquitoes
F_kappa.RM_ode Net infectiousness of human population to mosquitoes
F_tau Time spent host seeking/feeding and resting/ovipositing
F_tau.RM Time spent host seeking/feeding and resting/ovipositing
F_x Size of effective infectious human population
F_x.hMoI 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_lag Size of lagged effective infectious human population
F_x_lag.hMoI Size of lagged effective infectious human population
F_x_lag.SIP Size of lagged effective infectious human population
F_x_lag.SIS Size of lagged effective infectious human population
F_Z Density of infectious mosquitoes
F_Z.RM Density of infectious mosquitoes
F_Z_lag Density of lagged infectious mosquitoes
F_Z_lag.RM Density of lagged infectious mosquitoes
make_index_L Add indices for aquatic stage mosquitoes to parameter list
make_index_L.basic Add indices for aquatic stage mosquitoes to parameter list
make_index_L.trace Add indices for aquatic stage mosquitoes to parameter list
make_index_MYZ Add indices for adult mosquitoes to parameter list
make_index_MYZ.RM Add indices for adult mosquitoes to parameter list
make_index_X Add indices for human population to parameter list
make_index_X.hMoI Add indices for human population to parameter list
make_index_X.SIP Add indices for human population to parameter list
make_index_X.SIS Add indices for human population to parameter list
make_indices Set indices for generalized spatial model
make_Omega Make the mosquito demography matrix
make_parameters_exogenous_null Make parameters for the null model of exogenous forcing (do nothing)
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_RM_dde Make parameters for generalized RM DDE adult mosquito model
make_parameters_MYZ_RM_ode Make parameters for generalized RM ODE adult mosquito model
make_parameters_vc_lemenach Make parameters for Le Menach ITN model of vector control
make_parameters_vc_null Make parameters for the null model of vector control (do nothing)
make_parameters_X_hMoI Make parameters for hybrid MoI human model
make_parameters_X_SIP Make parameters for SIP human model
make_parameters_X_SIS Make parameters for SIS human model
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 (Mosquitoes)
MosquitoBehavior Compute bloodfeeding and mortality rates
MosquitoBehavior.RM Compute bloodfeeding and mortality rates
VectorControl Modify baseline values due to vector control
VectorControl.lemenach Modify baseline values due to vector control
VectorControl.null Modify baseline values due to vector control
xDE_diffeqn Generalized spatial differential equation model
xDE_diffeqn_mosy Generalized spatial differential equation model (mosquito only)