Function reference • ramp.dts

Blood Feeding and Transmission Methods to compute the transmission terms
`Transmission()`	Compute the mixing matrix and transmission terms
`LocalFrac()`	Compute the local fraction
`AvailableBlood()`	Update the availability of blood hosts
Transmision Specialized methods to compute the transmission terms
`Transmission(<static>)`	Compute transmission terms dynamically, no update required
`Transmission(<dynamic>)`	Compute transmission terms, the dynamic case
`Transmission(<setup>)`	Compute transmission terms, the dynamic case
`F_beta()`	Compute beta, the biting distribution matrix
`compute_beta()`	Compute beta
`F_EIR()`	Entomological inoculation rate on human strata
`compute_EIR()`	Compute EIR
`compute_EIR_full()`	Compute EIR for each vector-host pair
`F_kappa()`	Net infectiousness of human population to mosquitoes
`compute_kappa()`	Compute kappa
Blood Feeding Method to set up the blood feeding model
`setup_BFpar_static()`	Set up the blood feeding model
`setup_BloodFeeding()`	Set up blood feeding
`make_TaR()`	Make TaR
Time Spent and Time at Risk Method to set up time spent and time at risk (TaR) matrices
`make_TimeSpent()`	Make a time spent matrix, called TimeSpent
`make_TimeSpent(<athome>)`	Make a mosquito dispersal matrix, called TimeSpent with a here / away
`make_TimeSpent_athome()`	Make a mosquito dispersal matrix, called TimeSpent
`make_TimeSpent(<as_matrix>)`	Pass a pre-configured TimeSpent
`make_TimeSpent(<xy>)`	Develop a mosquito dispersal matrix from a kernel and xy-coordinates
`make_TimeSpent_xy()`	Make a mosquito dispersal matrix, called TimeSpent
Availability of humans / hosts Specialized methods to compute available humans / hosts
`AvailableBlood(<static>)`	Compute availability of local humans for blood feeding
`AvailableBlood(<setup>)`	Compute availability of local humans for blood feeding
`AvailableBlood(<forced>)`	Compute availability of local humans for blood feeding
`compute_AvailableHosts()`	Compute availability blood hosts of the i^th species
Exposure Methods to model the force of infection
`Exposure()`	Exposure and Infection
`F_foi()`	A model for daily FoI as a function of the daily EIR.
Poisson Exposure Specialized methods the Poisson exposure model
`F_foi(<pois>)`	A Poisson model for the daily local FoI as a function of the daily EIR.
`setup_exposure_pois()`	Make parameters for the null model of exposure
Negative Binomial Exposure Specialized methods the Negative Binomial exposure model
`F_foi(<nb>)`	The daily FoI as a function of the daily EIR under a negative binomial model of exposure.
`setup_exposure_nb()`	Make parameters for the null model of exposure
Local Fraction Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics
`LocalFrac(<static>)`	Compute transmission terms dynamically, no update required
`LocalFrac(<dynamic>)`	Compute transmission terms dynamically, no update required
`compute_local_frac()`	Compute the local fraction
`setup_local_fraction_simple()`	Set up the local_fraction for static models
Egg Laying & Emergence Generic methods for the aquatic (immature) mosquito component.
`Emergence()`	Compute emerging adults
`make_calN()`	Make the habitat membership matrix, calN
`EggLaying()`	Compute eggs laid
`EggLaying(<static>)`	Compute eggs laid
`EggLaying(<dynamic>)`	Compute eggs laid
`EggLaying(<simple>)`	Compute eggs laid
`EggLaying(<setup>)`	Compute eggs laid
`compute_calU()`	Compute calU
`compute_EggsLaid()`	Compute eggs laid
`make_calU()`	Make the egg distribution matrix, calU
`make_calU_s()`	Make the egg distribution matrix, calU
`setup_EggLaying_static()`	Setup egg laying for most models
`setup_EggLaying_simple()`	Setup egg laying for most models
`setup_EGGpar_static()`	Setup the structures required for egg laying
Adult Mosquito Dynamics Generic methods for the adult mosquito dynamics component.
`MBionomics()`	Set bloodfeeding and mortality rates to baseline
`F_fqZ()`	Blood feeding rate of the infective mosquito population
`F_fqM()`	Blood feeding rate of the mosquito population
`F_tau()`	Time spent host seeking/feeding and resting/ovipositing
`F_eggs()`	Number of eggs laid by adult mosquitoes
`dMYZdt()`	Derivatives for adult mosquitoes
`setup_MYZpar()`	A function to set up adult mosquito models
`setup_MYZinits()`	A function to set up adult mosquito models
`list_MYZvars()`	Return the variables as a list
`make_indices_MYZ()`	Add indices for adult mosquitoes to parameter list
`parse_dts_out_MYZ()`	Parse the output of deSolve and return the variables by name in a list
`get_inits_MYZ()`	Return initial values as a vector
`update_inits_MYZ()`	Set the initial values as a vector
`make_Omega()`	Make the mosquito demography matrix
`dts_plot_M()`	Plot adult mosquito population density
`dts_lines_M()`	Add lines for adult mosquito population density
`dts_plot_YZ()`	Plot the density of infected and infective mosquitoes
`dts_lines_YZ()`	Add lines for the density of infected and infective mosquitoes
`dts_plot_YZ_fracs()`	Plot the fraction of infected and infective mosquitoes
`dts_lines_YZ_fracs()`	Add lines for the fraction of infected and infective mosquitoes
`dts_plot_Z_fracs()`	Plot the fraction of infected and infective mosquitoes
`dts_lines_Z_fracs()`	Add lines for the fraction of infected and infective mosquitoes
EIP Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics
`EIP()`	Compute the EIP
`setup_EIP()`	Set up the fixed model for control forcing (do nothing)
`EIP(<fixed>)`	Modify parameters due to exogenous forcing by all kinds of control
`setup_EIP(<fixed>)`	Set up a fixed model for the EIP
`setup_eip_fixed()`	Set up a fixed model for the EIP
`EIP(<null>)`	Modify parameters due to exogenous forcing by all kinds of control
`setup_EIP(<null>)`	Set up a null model for the EIP
`setup_eip_null()`	Set up a null model for the EIP
Ztrace Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics
`MBionomics(<Ztrace>)`	Compute bloodfeeding and mortality rates
`F_fqZ(<Ztrace>)`	Blood feeding rate of the infective mosquito population
`F_fqM(<Ztrace>)`	Blood feeding rate of the infective mosquito population
`F_eggs(<Ztrace>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<Ztrace>)`	Derivatives for aquatic stage mosquitoes
`setup_MYZpar(<Ztrace>)`	Setup the Ztrace model
`setup_MYZinits(<Ztrace>)`	Setup the Ztrace model
`make_MYZpar_Ztrace()`	Make parameters for Ztrace aquatic mosquito model
`make_indices_MYZ(<Ztrace>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_MYZ(<Ztrace>)`	Parse the output of deSolve and return variables for the Ztrace model
`make_inits_MYZ_Ztrace()`	Make parameters for Ztrace aquatic mosquito model
`get_inits_MYZ(<Ztrace>)`	Return initial values as a vector
`update_inits_MYZ(<Ztrace>)`	Update inits for Ztrace
`make_parameters_MYZ_Ztrace()`	Make parameters for Ztrace aquatic mosquito model
Gtrace Specialized methods for NULL dynamics: a funtion generates values for eggs laid to aquatic ecology
`MBionomics(<Gtrace>)`	Compute bloodfeeding and mortality rates
`F_fqZ(<Gtrace>)`	Blood feeding rate of the infective mosquito population
`F_fqM(<Gtrace>)`	Blood feeding rate of the infective mosquito population
`F_eggs(<Gtrace>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<Gtrace>)`	Derivatives for aquatic stage mosquitoes
`setup_MYZpar(<Gtrace>)`	Setup the Gtrace
`setup_MYZinits(<Gtrace>)`	Setup the Gtrace model
`make_MYZpar_Gtrace()`	Make parameters for Gtrace aquatic mosquito model
`make_indices_MYZ(<Gtrace>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_MYZ(<Gtrace>)`	Parse the output of deSolve and return variables for the Gtrace model
`make_inits_MYZ_Gtrace()`	Make parameters for Gtrace aquatic mosquito model
`get_inits_MYZ(<Gtrace>)`	Return initial values as a vector
`update_inits_MYZ(<Gtrace>)`	Update inits for Gtrace
`make_parameters_MYZ_Gtrace()`	Make parameters for Gtrace aquatic mosquito model
basicM_dts Specialized methods for basicM_dts, a model of adult mosquito dynamics with no parasite infection dynamics.
`MBionomics(<basicM_dts>)`	Reset bloodfeeding and mortality rates to baseline
`F_fqZ(<basicM_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<basicM_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<basicM_dts>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<basicM_dts>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<basicM_dts>)`	Setup MYZpar for the basicM_dts model
`setup_MYZinits(<basicM_dts>)`	Setup initial values for the basicM_dts model
`make_MYZpar_basicM_dts()`	Make parameters for basicM_dts adult mosquito model
`make_MYZinits_basicM_dts()`	Make inits for basicM_dts adult mosquito model
`list_MYZvars(<basicM_dts>)`	Return the variables as a list
`make_indices_MYZ(<basicM_dts>)`	Add indices for adult mosquitoes to parameter list
`parse_dts_out_MYZ(<basicM_dts>)`	Parse the output of deSolve and return variables for the basicM_dts model
`make_inits_MYZ_basicM_dts()`	Make inits for basicM_dts adult mosquito model
`get_inits_MYZ(<basicM_dts>)`	Return initial values as a vector
`update_inits_MYZ(<basicM_dts>)`	Make inits for basicM_dts adult mosquito model
`make_parameters_MYZ_basicM_dts()`	Make parameters for basicM_dts adult mosquito model
RM_dts Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982).
`MBionomics(<RM_dts>)`	Reset bloodfeeding and mortality rates to baseline
`F_fqZ(<RM_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<RM_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<RM_dts>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<RM_dts>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<RM_dts>)`	Setup MYZpar for the RM_dts model
`setup_MYZinits(<RM_dts>)`	Setup initial values for the RM_dts model
`list_MYZvars(<RM_dts>)`	Return the variables as a list
`make_MYZpar_RM_dts()`	Make parameters for RM_dts adult mosquito model
`make_MYZinits_RM_dts()`	Make inits for RM_dts adult mosquito model
`make_indices_MYZ(<RM_dts>)`	Add indices for adult mosquitoes to parameter list
`parse_dts_out_MYZ(<RM_dts>)`	Parse the output of deSolve and return variables for the RM_dts model
`make_inits_MYZ_RM_dts()`	Make inits for RM_dts adult mosquito model
`get_inits_MYZ(<RM_dts>)`	Return initial values as a vector
`update_inits_MYZ(<RM_dts>)`	Make inits for RM_dts adult mosquito model
`make_parameters_MYZ_RM_dts()`	Make parameters for RM_dts adult mosquito model
ENBRQ_dts Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982).
`MBionomics(<ENBRQ_dts>)`	Reset bloodfeeding and mortality rates to baseline
`F_fqZ(<ENBRQ_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<ENBRQ_dts>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<ENBRQ_dts>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<ENBRQ_dts>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<ENBRQ_dts>)`	Setup MYZpar for the ENBRQ_dts model
`setup_MYZinits(<ENBRQ_dts>)`	Setup initial values for the ENBRQ_dts model
`list_MYZvars(<ENBRQ_dts>)`	Return the variables as a list
`make_MYZpar_ENBRQ_dts()`	Make parameters for ENBRQ_dts adult mosquito model
`make_MYZinits_ENBRQ_dts()`	Make inits for ENBRQ_dts adult mosquito model
`make_indices_MYZ(<ENBRQ_dts>)`	Add indices for adult mosquitoes to parameter list
`parse_dts_out_MYZ(<ENBRQ_dts>)`	Parse the output of deSolve and return variables for the ENBRQ_dts model
`make_inits_MYZ_ENBRQ_dts()`	Make inits for ENBRQ_dts adult mosquito model
`get_inits_MYZ(<ENBRQ_dts>)`	Return initial values as a vector
`update_inits_MYZ(<ENBRQ_dts>)`	Make inits for ENBRQ_dts adult mosquito model
`make_parameters_MYZ_ENBRQ_dts()`	Make parameters for ENBRQ_dts adult mosquito model
RMlumpy Specialized methods for a lumped-days Ross-Macdonald-style model of adult mosquito dynamics
`MBionomics(<RMlumpy>)`	Reset bloodfeeding and mortality rates to baseline
`F_fqZ(<RMlumpy>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<RMlumpy>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<RMlumpy>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<RMlumpy>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<RMlumpy>)`	Setup MYZpar for the RMlumpy model
`setup_MYZinits(<RMlumpy>)`	Setup initial values for the RMlumpy model
`list_MYZvars(<RMlumpy>)`	Return the variables as a list
`make_MYZpar_RMlumpy()`	Make parameters for RMlumpy ODE adult mosquito model
`make_MYZinits_RMlumpy()`	Make inits for RMlumpy adult mosquito model
`make_indices_MYZ(<RMlumpy>)`	Add indices for adult mosquitoes to parameter list
`parse_dts_out_MYZ(<RMlumpy>)`	Parse the output of deSolve and return variables for the RMlumpy model
`make_inits_MYZ_RMlumpy()`	Make inits for RMlumpy adult mosquito model
`get_inits_MYZ(<RMlumpy>)`	Return initial values as a vector
`update_inits_MYZ(<RMlumpy>)`	Make inits for RMlumpy adult mosquito model
`make_parameters_MYZ_RMlumpy()`	Make parameters for RMlumpy ODE adult mosquito model
Aquatic Mosquito Dynamics Generic methods for the aquatic (immature) mosquito component.
`LBionomics()`	Set aquatic bionomic parameter rates relative to baseline
`F_alpha()`	Number of newly emerging adults from each larval habitat
`dLdt()`	Derivatives for aquatic stage mosquitoes
`setup_Lpar()`	A function to set up adult mosquito models
`setup_Linits()`	A function to set up adult mosquito models
`list_Lvars()`	Return the variables as a list
`make_indices_L()`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_L()`	Parse the output of deSolve and return the variables by name in a list
`get_inits_L()`	Return initial values as a vector
`update_inits_L()`	Set the initial values from a vector of model states
trace Specialized methods for the exogeneously forced trace model of aquatic mosquito dynamics.
`LBionomics(<trace>)`	Reset aquatic parameters to baseline
`F_alpha(<trace>)`	Number of newly emerging adults from each larval habitat
`dLdt(<trace>)`	Derivatives for aquatic stage mosquitoes
`setup_Lpar(<trace>)`	Setup Lpar for the trace model
`setup_Linits(<trace>)`	Setup the trace model
`make_Lpar_trace()`	Make parameters for trace aquatic mosquito model
`make_indices_L(<trace>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_L(<trace>)`	Parse the variable names for the trace model
`make_inits_L_trace()`	Make parameters for trace aquatic mosquito model
`get_inits_L(<trace>)`	Return initial values as a vector
`update_inits_L(<trace>)`	Update inits for the basic aquatic mosquito competition model
`make_parameters_L_trace()`	Make parameters for trace aquatic mosquito model
basic_dts Specialized methods for a basic_dts competition model of aquatic mosquito dynamics.
`LBionomics(<basic_dts>)`	Reset aquatic parameters to baseline
`F_alpha(<basic_dts>)`	Number of newly emerging adults from each larval habitat
`dLdt(<basic_dts>)`	Derivatives for aquatic stage mosquitoes
`setup_Lpar(<basic_dts>)`	Setup Lpar for the basic_dts model
`setup_Linits(<basic_dts>)`	Setup the basic_dts model
`list_Lvars(<basic_dts>)`	Return the variables as a list
`make_Lpar_basic_dts()`	Make parameters for basic_dts competition aquatic mosquito model
`make_Linits_basic_dts()`	Make inits for basic_dts competition aquatic mosquito model
`make_indices_L(<basic_dts>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_L(<basic_dts>)`	Parse the variable names for the basic_dts model
`make_inits_L_basic_dts()`	Make inits for basic_dts competition aquatic mosquito model
`get_inits_L(<basic_dts>)`	Return initial values as a vector
`update_inits_L(<basic_dts>)`	Update inits for the basic_dts aquatic mosquito competition model
`make_parameters_L_basic_dts()`	Make parameters for basic_dts competition aquatic mosquito model
stages_dts Specialized methods for a stages_dts competition model of aquatic mosquito dynamics.
`LBionomics(<stages_dts>)`	Reset aquatic parameters to baseline
`F_alpha(<stages_dts>)`	Number of newly emerging adults from each larval habitat
`dLdt(<stages_dts>)`	Derivatives for aquatic stage mosquitoes
`setup_Lpar(<stages_dts>)`	Setup Lpar for the stages_dts model
`setup_Linits(<stages_dts>)`	Setup the stages_dts model
`list_Lvars(<stages_dts>)`	Return the variables as a list
`make_Lpar_stages_dts()`	Make parameters for stages_dts competition aquatic mosquito model
`make_Linits_stages_dts()`	Make inits for stages_dts competition aquatic mosquito model
`make_indices_L(<stages_dts>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_dts_out_L(<stages_dts>)`	Parse the variable names for the stages_dts model
`make_inits_L_stages_dts()`	Make inits for stages_dts competition aquatic mosquito model
`get_inits_L(<stages_dts>)`	Return initial values as a vector
`update_inits_L(<stages_dts>)`	Update inits for the stages_dts aquatic mosquito competition model
`make_parameters_L_stages_dts()`	Make parameters for stages_dts competition aquatic mosquito model
Mosquito Bionomics Methods to compute or update mosquito bionomic parameters
`Bionomics()`	Set bionomic parameter rates relative to baseline
`Bionomics(<static>)`	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
`setup_bionomics_static()`	Make parameters for the static model bionomics
Functional Responses Compute bionomic parameters as functional responses to resource availability
`F_sigma()`	Compute mosquito emigration rates
`F_sigma(<static>)`	Static model for mosquito emigration
`F_sigma(<dddn>)`	Dawn, day, dusk, night model for the human fraction
`F_nu()`	Compute the egg laying rate
`F_nu(<static>)`	Static model for the egg laying rate
`F_nu(<dddn>)`	Dawn, day, dusk, night model for the human fraction
`F_nu(<type2>)`	Type 2 functional response for the blood feeding rate
`F_f()`	Compute the blood feeding rate, f
`F_f(<static>)`	Static model for the blood feeding rate
`F_f(<dddn>)`	Dawn, day, dusk, night model for the blood feeding rate
`F_f(<type2>)`	Type 2 functional response for the blood feeding rate
`F_q()`	Compute the human blood fraction
`F_q(<static>)`	Static model for 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_p()`	Compute mosguito survival
`F_p(<static>)`	Static model for mosquito survival
`F_p(<dddn>)`	Dawn, day, dusk, night model for the human fraction
Mosquito Dispersal Specialized methods to set up mosquito dispersal matrices
`make_calK()`	Make a mosquito dispersal matrix, called calK
`make_calK(<herethere>)`	Dispersal to every other patch, with equal probability
`make_calK(<as_matrix>)`	Pass a pre-configured calK
`make_calK(<xy>)`	Develop a mosquito dispersal matrix from a kernel and xy-coordinates
`make_calK_xy()`	Develop a mosquito dispersal matrix from a kernel and xy-coordinates
Human Infection Dynamics Generic methods for the dynamical component that handles human infection dynamics, immunity, disease and transmission
`dXdt()`	Derivatives for human population
`setup_Xinits()`	A function to set up Xpar
`make_indices_X()`	Add indices for human population to parameter list
`list_Xvars()`	Return the variables as a list
`setup_Xpar()`	A function to set up Xpar
`F_X()`	Size of effective infectious human population
`F_H()`	Size of human population denominators
`F_b()`	Infection blocking pre-erythrocytic immunity
`F_pr()`	Compute the "true" prevalence of infection / parasite rate
`parse_dts_out_X()`	Parse the output of deSolve and return the variables by name in a list
`get_inits_X()`	Return initial values as a vector
`update_inits_X()`	Set the initial values from a vector of states
`HTC()`	Compute the human transmitting capacity
`dts_plot_X()`	Basic plotting for epidemiological models
trace Specialized methods for a human trace model to pass kappa as a parameter
`F_X(<trace>)`	Size of effective infectious human population
`F_H(<trace>)`	Size of the human population
`F_pr(<trace>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<trace>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<trace>)`	Derivatives for human population
`setup_Xpar(<trace>)`	Setup Xpar.trace
`setup_Xinits(<trace>)`	Setup Xinits.trace
`make_Xpar_trace()`	Make parameters for human null model
`make_indices_X(<trace>)`	Add indices for human population to parameter list
`parse_dts_out_X(<trace>)`	Parse the output of deSolve and return variables for the trace model
`make_inits_X_trace()`	Make inits for trace human model
`get_inits_X(<trace>)`	Return initial values as a vector
`update_inits_X(<trace>)`	Update inits for the trace human model from a vector of states
`make_parameters_X_trace()`	Make parameters for trace human model
SIS_dts Specialized methods for the SIS_dts (Susceptible-Infected-Susceptible) model of human dynamics.
`dXdt(<SIS_dts>)`	Derivatives for human population
`make_Xinits_SIS_dts()`	Make initial values for the SIS_dts human model, with defaults
`setup_Xinits(<SIS_dts>)`	Setup Xinits.SIS_dts
`make_indices_X(<SIS_dts>)`	Add indices for human population to parameter list
`list_Xvars(<SIS_dts>)`	Return the variables as a list
`make_Xpar_SIS_dts()`	Make parameters for SIS_dts human model, with defaults
`setup_Xpar(<SIS_dts>)`	Setup Xpar.SIS_dts
`F_X(<SIS_dts>)`	Size of effective infectious human population
`F_H(<SIS_dts>)`	Size of effective infectious human population
`F_pr(<SIS_dts>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SIS_dts>)`	Infection blocking pre-erythrocytic immunity
`parse_dts_out_X(<SIS_dts>)`	Parse the output of deSolve and return variables for the SIS_dts model
`make_inits_X_SIS_dts()`	Make inits for SIS_dts human model
`get_inits_X(<SIS_dts>)`	Return initial values as a vector
`update_inits_X(<SIS_dts>)`	Update inits for the SIS_dts human model from a vector of states
`make_parameters_X_SIS_dts()`	Make parameters for SIS_dts human model
`HTC(<SIS_dts>)`	Compute the HTC for the SIS_dts model
`dts_plot_X(<SIS_dts>)`	Plot the density of infected individuals for the SIS_dts model
`dts_lines_X_SIS_dts()`	Add lines for the density of infected individuals for the SIS_dts model
SIP_dts Specialized methods for the SIP_dts (Susceptible-Infected-Prophylaxis) model of human dynamics.
`dXdt(<SIP_dts>)`	Derivatives for human population
`make_Xinits_SIP_dts()`	Make initial values for the SIP_dts human model, with defaults
`setup_Xinits(<SIP_dts>)`	Setup Xinits.SIP_dts
`make_indices_X(<SIP_dts>)`	Add indices for human population to parameter list
`list_Xvars(<SIP_dts>)`	Return the variables as a list
`make_Xpar_SIP_dts()`	Make parameters for SIP_dts human model, with defaults
`setup_Xpar(<SIP_dts>)`	Setup Xpar.SIP_dts
`F_X(<SIP_dts>)`	Size of effective infectious human population
`F_H(<SIP_dts>)`	Size of effective infectious human population
`F_pr(<SIP_dts>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SIP_dts>)`	Infection blocking pre-erythrocytic immunity
`parse_dts_out_X(<SIP_dts>)`	Parse the output of deSolve and return variables for the SIP_dts model
`make_inits_X_SIP_dts()`	Make inits for SIP_dts human model
`get_inits_X(<SIP_dts>)`	Return initial values as a vector
`update_inits_X(<SIP_dts>)`	Update inits for the SIP_dts human model from a vector of states
`make_parameters_X_SIP_dts()`	Make parameters for SIP_dts human model
`HTC(<SIP_dts>)`	Compute the HTC for the SIP_dts model
`dts_plot_X(<SIP_dts>)`	Plot the density of infected individuals for the SIP_dts model
`dts_lines_X_SIP_dts()`	Add lines for the density of infected individuals for the SIP_dts model
Human Population Dynamics Generic methods for the human demography and aging
`dHdt()`	Derivatives of demographic changes in human populations
`setup_Hpar_static()`	A utility to set up Hpar
`Births()`	A function that computes the birth rate for human populations
`make_parameters_demography_null()`	Make parameters for null human demography model
static Specialized methods for the static (constant) demographic model
`Births(<zero>)`	Derivatives of demographic changes in human populations
`dHdt(<zero>)`	Derivatives of demographic changes in human populations
Human and Mosquito Behaviors Methods to implement human and Mosquito Behaviorsbehaviors
`Behavior()`	Methods for dynamic human and mosquito behaviors
`Behavior(<null>)`	Methods for dynamic human and mosquito behaviors
`Behavior(<forced>)`	Methods for dynamic human and mosquito behaviors
`setup_behavior_null()`	Make parameters for the null model for resource availability (do nothing)
`setup_behavior_forced()`	Make parameters for the forced model for resource availability (do nothing)
`setup_behavior()`	Setup behavior
`setup_behavior(<null>)`	Setup behavior
`setup_behavior(<forced>)`	Setup behavior
Care Seeking Methods to implement care seeking
`CareSeeking()`	Set the values of exogenous variables describing care seeking
`CareSeeking(<null>)`	Set the values of exogenous variables describing care seeking
`setup_care_seeking_null()`	Make parameters for the null model for care seeking (do nothing)
Imported Malaria Methods to implement imported malaria
`travel_malaria()`	Simulate travel malaria
`Visitors()`	Visitors
Travel Malaria Specialized methods for travel malaria
`travel_malaria(<static>)`	travel, a static model
`setup_travel_static()`	A function to set up malaria importation
`travel_malaria(<foi>)`	A model for the travel FoI
`setup_travel_foi()`	Set up parameters and function for the FoI-based travel_malaria model
`travel_malaria(<eir>)`	A model for travel malaria based on the eir in destinations
`setup_travel_eir()`	Set up parameters and function for an eir-based travel_malaria model
Visitors Methods for the availability and infectiousness of a visitor population
`Visitors(<static>)`	Visitors, a static model
`setup_visitors_static()`	Make parameters for the static model visitors (no visitors)
`Visitors(<basic>)`	Visitors, the basic model
`setup_visitors_basic()`	Make parameters and functions for the basic model for visitors
Exogeneous Forcing Methods to implement exogeneous forcing.
`Abiotic()`	Set up exogenous variables for abiotic forcing
`Civil()`	Set up exogenous variables for civil forcing
`Shock()`	Set up shocks
`Control()`	Modify parameters due to exogenous forcing by all kinds of control
`Clinic()`	Methods for distributing interventions during clinical visits
`Development()`	Set up developments
`MassMedical()`	Methods for mass medical interventions
Models Specialized methods the null model (no exogenous forcing)
`Abiotic(<null>)`	Set up exogenous variables for abiotic forcing
`setup_abiotic_null()`	Set up the null model for exogenous forcing (do nothing)
`Civil(<null>)`	Set up exogenous variables for civil forcing
`setup_civil_null()`	Set up the null model for exogenous forcing (do nothing)
`Shock(<null>)`	Set up shocks
`setup_shock_null()`	Set up the null model for shocks (do nothing)
`Control(<null>)`	Modify parameters due to exogenous forcing by all kinds of control
`Control(<static>)`	Modify parameters due to exogenous forcing by all kinds of control
`setup_control()`	Setup CONTROL with forcing
`setup_control_null()`	Set up the null model for control forcing (do nothing)
`setup_control(<null>)`	Setup control
`setup_control(<forced>)`	Setup control
`Clinic(<null>)`	Methods for distributing interventions during clinical visits
`setup_clinic_null()`	Set up the null model for clinical distribution (do nothing)
`setup_clinic_forced()`	Set up a model for clinic
`Development(<null>)`	Set up developments
`setup_development_null()`	Set up the null model for developments (do nothing)
`MassMedical(<null>)`	Methods for mass medical
`setup_mass_medical_null()`	Set up the null model for mass medical (do nothing)
forced Specialized methods to call forcing
`Abiotic(<forced>)`	Set up exogenous variables for abiotic forcing
`setup_abiotic_forced()`	Make parameters for the null model of abiotic forcing (do nothing)
`check_abiotic()`	Check abiotic
`check_abiotic(<null>)`	Check abiotic
`check_abiotic(<forced>)`	Check abiotic
`Civil(<forced>)`	Set up exogenous variables for civil forcing
`setup_civil_forced()`	Make parameters for the null model of civil forcing (do nothing)
`check_civil()`	Check civil
`check_civil(<null>)`	Check civil
`check_civil(<forced>)`	Check civil
`Control(<forced>)`	Modify parameters due to exogenous forcing by all kinds of control
`setup_control_forced()`	Set up a model with some control
`MassMedical(<forced>)`	Methods for mass medical
`setup_mass_medical_forced()`	Set up a model for mass medical
Weather Specialized methods for weather
`Weather()`	Methods for exogenous variables describing weather
`Weather(<null>)`	Methods for exogenous variables describing weather
`Weather(<forced>)`	Methods for exogenous variables describing weather
`setup_weather_null()`	Set up the null model for weather
`setup_weather_forced()`	Set up the forced model for weather
`setup_rainfall_null()`	Set up the null model for RAINFALL
`Rainfall()`	Methods for exogenous variables describing rainfall
`Rainfall(<null>)`	Methods for exogenous variables describing rainfall
`setup_temperature_null()`	Set up the null model for temperature
`Temperature()`	Methods for exogenous variables describing temperature
`Temperature(<null>)`	Methods for exogenous variables describing temperature
`setup_relative_humidity_null()`	Set up the null model for HUMIDITY
`Relative_Humidity()`	Methods for exogenous variables describing relative humidity
`Relative_Humidity(<null>)`	Methods for exogenous variables describing relative humidity
Hydrology Specialized methods for hydrology
`Hydrology()`	Set the values of exogenous variables describing hydrology
`Hydrology(<null>)`	Set the values of exogenous variables describing hydrology
`setup_hydrology_null()`	Make parameters for the null model for hydrology (do nothing)
Resource Dynamics Methods to implement resource availability
`Resources()`	Set the values of exogenous variables describing available mosquito resources
`Resources(<static>)`	Modify resources and resource availability
`Resources(<setup>)`	Modify resources and resource availability
`Resources(<forced>)`	Methods for resources
`setup_resources_null()`	Set up parameters for the null model for resource availability
`setup_resources_static()`	Set up parameters for the null model for resource availability
`setup_resources_forced()`	Set up a model for mass medical
Other Blood Hosts Methods to simulate availability of other blood hosts
`OtherBloodHosts()`	Set the values of exogenous variables describing other blood hosts
`OtherBloodHosts(<static>)`	Set the values of exogenous variables describing other blood hosts
`setup_other_blood_hosts_static()`	Make parameters for the static model for other blood hosts (do nothing)
Habitat Dynamics and Availability Specialized methods for weather
`AvailableHabitat()`	Update the availability of aquatic habitats
`AvailableHabitat(<static>)`	Compute total availability of aquatic habitats
`AvailableHabitat(<simple>)`	Compute total availability of aquatic habitats
`AvailableHabitat(<forced>)`	Compute total availability of aquatic habitats
`compute_AvailableHabitat()`	Compute total availability of aquatic habitats
`HabitatDynamics()`	Habitat Dynamics and Searching
`HabitatDynamics(<static>)`	Set the values of habitat search weights and other exogenous variables describing habitat_dynamics
`setup_habitat_dynamics_static()`	Setup the egg laying object
Sugar Methods to simulate availability of sugar
`SugarDynamics()`	Set the values of exogenous variables describing sugar
`SugarDynamics(<static>)`	Set the values of exogenous variables describing sugar
`setup_sugar_static()`	Make parameters for the static model for sugar (do nothing)
`AvailableSugar()`	Update the availability of sugar
`AvailableSugar(<static>)`	Compute total availability of sugar
`AvailableSugar(<forced>)`	Compute total availability of sugar
Vector Control Methods to implement vector control.
`VectorControl()`	Distribute vector control
`VectorControlEffects()`	Vector control: durability & effects
`VectorControlEffectSizes()`	Vector control effect sizes
null model Specialized methods for the null model (no vector control)
`VectorControl(<null>)`	Distribute vector control
`VectorControlEffects(<null>)`	Vector control: durability & effects
`VectorControlEffectSizes(<null>)`	Vector control effect sizes
`setup_vc_null()`	Distribute vector control, the null model
Implement Control Specialized methods to implement vector control
`VectorControl(<control>)`	Distribute vector control, the null model
`VectorControlEffects(<control>)`	Vector control durability and effects
`VectorControlEffectSizes(<control>)`	Distribute vector control, the null model
`setup_vc_control()`	Make parameters for the control model of vector control (do nothing)
Bed Nets Methods to implement bed nets
`DistributeBedNets()`	Distribute bed nets, called from Control(VectorControl)
`OwnBedNet()`	Model bed net loss, called from Control(VectorControl)
`UseBedNet()`	Model bed net usage, called from Behavior
`BedNetEffects()`	Modify variables or parameters, called from VectorControlEffects
`BedNetEffectSizes()`	Modify baseline bionomic parameters, called from VectorControlEffectSizes
`DistributeBedNets(<null>)`	Distribute bed nets
`OwnBedNet(<null>)`	Bed net ownership
`UseBedNet(<null>)`	Bed net ownership
`BedNetEffects(<null>)`	Bed net ownership
`BedNetEffectSizes(<null>)`	Bed net ownership
`setup_itn_null()`	Make parameters for the null model of bed nets (do nothing)
`BedNetEffects(<lemenach>)`	Modify baseline values due to vector control
`BedNetEffectSizes(<lemenach>)`	Modify baseline values due to vector control
`setup_itn_lemenach()`	Make parameters for Le Menach ITN model of vector control
Indoor Residual Spraying Methods to implement IRS
`SprayHouses()`	Do mass house spraying (IRS)
`IRS_Effects()`	Model the effects of IRS
`IRS_EffectSizes()`	Model IRS effect sizes
`SprayHouses(<null>)`	Do mass house spraying (IRS)
`IRS_Effects(<null>)`	Model the effects of IRS
`IRS_EffectSizes(<null>)`	Model IRS effect sizes
`setup_irs_null()`	Make parameters for the null model of IRS (do nothing)
Area Spraying Methods to implement area spraying
`AreaSpray()`	Methods for mass spraying
`AreaSprayEffects()`	Methods for mass spraying
`AreaSprayEffectSizes()`	Methods for mass spraying
`AreaSpray(<null>)`	Set up mass spraying
`AreaSprayEffects(<null>)`	Set up mass spraying
`AreaSprayEffectSizes(<null>)`	Set up mass spraying
`setup_area_spray_null()`	Set up the null model for area spraying (do nothing)
Sugar Baits Methods to implement sugar baits
`SugarBaits()`	Methods for distributing sugar baits
`SugarBaitEffects()`	Methods for the durability and effects of the sugar baits
`SugarBaitEffectSizes()`	Methods for the effect sizes of the sugar baits
`SugarBaits(<null>)`	Methods for sugar baits
`SugarBaitEffects(<null>)`	Methods for the effects of the sugar baits
`SugarBaitEffectSizes(<null>)`	Methods for the effect sizes of the sugar baits
`setup_sugar_baits_null()`	Set up the null model for sugar baits (do nothing)
Larval Source Management Methods to implement LSM
`TreatHabitats()`	Modify values due to treat habitats as part of LSM, called by Control->VectorControl
`LSM_Effects()`	Modify effects of LSM
`LSM_EffectSizes()`	Compute effect sizes of LSM
`TreatHabitats(<null>)`	Set up the null model for LSM
`LSM_Effects(<null>)`	Modify effects of LSM, the null model
`LSM_EffectSizes(<null>)`	Modify effects of LSM, the null model
`setup_lsm_null()`	Make parameters for the null model of LSM (do nothing)
Ovitraps Specialized methods for ovitraps
`OviTraps()`	Methods for oviposition traps
`OviTraps(<null>)`	Methods for oviposition traps
`setup_ovitraps_null()`	Set up the null model for oviposition traps (do nothing)
Setup Basic setup for models
`make_parameters_dts()`	Make base parameters, assuming nVectors = nHosts = 1
`make_indices()`	Set indices for generalized spatial model
Setting Up Methods to set up basic models
`dts_setup()`	Set up a model for dts_diffeqn
`dts_setup_aquatic()`	Set up a model for dts_diffeqn_aqua
`dts_setup_mosy()`	Set up a model for dts_diffeqn_mosy
`dts_setup_human()`	Set up a model for dts_diffeqn_human
`dts_setup_cohort()`	Set up a model for dts_diffeqn_cohort
Initial Values Methods to set up basic models
`get_inits()`	Get the initial values as a vector
`update_inits()`	Set the initial values to the last values of the last simulation
`last_to_inits()`	Set the initial values to the last values of the last simulation
Solving Methods to compute the derivatives and solve the equat
Derivatives
`DTS_step()`	Generalized spatial differential equation model
`DTS_step_aquatic()`	Difference equation models for aquatic mosquito populations
`DTS_step_mosy()`	Generalized spatial differential equation model (mosquito only)
`DTS_step_human()`	Difference equations isolating the humans, forced with Ztrace
`DTS_step_cohort()`	Difference equation models for human cohorts
Solving Wrappers around the derivatives functions that handle time and parse outputs
`dts_solve()`	Solve a system of equations
`dts_solve(<dts>)`	Solve a system of equations as an ode
`dts_solve(<aqua>)`	Solve a system of equations for aquatic dynamics, forced by egg deposition, using dts_diffeqn_aquatic
`dts_solve(<mosy>)`	Solve a system of equations for mosquito ecology using dts_diffeqn_mosy
`dts_solve(<human>)`	Solve a system of equations with dts_diffeqn_human
`dts_solve(<cohort>)`	Solve a system of equations with dts_diffeqn_cohort
`dts_stable_orbit()`	Solve for the steady state or stable orbit of a system of equations
`dts_steady()`	Solve for the steady state of a system of equations
Analysis and Visualization Methods to compute and output terms
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)
Compute terms Methods to compute and transmission terms
`parse_dts_out()`	Parse the output of an object returned by deSolve
`parse_dts_out_vec()`	Parse the output of an object returned by deSolve
`compute_terms()`	Compute dynamical terms
`compute_terms(<dts>)`	Compute dynamical terms
`compute_terms(<cohort>)`	Compute dynamical terms
`compute_terms(<human>)`	Compute dynamical terms
`compute_terms(<na>)`	Compute dynamical terms
`compute_terms_steady()`	Compute dynamical terms
`compute_NI()`	Compute the NI
`compute_NI_ix()`	Compute NI once
`compute_vars_full()`	Compute other variables at time t
`compute_vars_human()`	Compute other variables at time t
`compute_vars_aqua()`	Differential equation models for aquatic mosquito populations
`compute_vars_mosy()`	Compute other variables at time t
`compute_vars_cohort()`	Differential equation models for human cohorts
Plot terms Basic visualization of the transmission terms
`dts_plot_EIR()`	Plot the EIR vs. time
`dts_lines_EIR()`	Add lines for the EIR vs. time
`dts_plot_aEIR()`	Plot the annualized EIR vs. time
`dts_lines_aEIR()`	Add lines for the annualized EIR vs. t
`dts_plot_PR()`	Plot the prevalence / parasite rate (PR) from a model of human infection and immunity
`dts_lines_PR()`	Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity
Utilities
`diag_inverse()`	Invert a diagonal matrix
`approx_equal()`	Check if two numeric values are approximately equal
`checkIt()`	Check the length of an input value
`shapeIt()`	Check the shape and dimensions of an object

Reference

Blood Feeding and Transmission

Transmision

Blood Feeding

Time Spent and Time at Risk

Availability of humans / hosts

Exposure

Poisson Exposure

Negative Binomial Exposure

Local Fraction

Egg Laying & Emergence

Adult Mosquito Dynamics

EIP

Ztrace

Gtrace

basicM_dts

RM_dts

ENBRQ_dts

RMlumpy

Aquatic Mosquito Dynamics

trace

basic_dts

stages_dts

Mosquito Bionomics

Functional Responses

Mosquito Dispersal

Human Infection Dynamics

trace

SIS_dts

SIP_dts

Human Population Dynamics

static

Human and Mosquito Behaviors

Care Seeking

Imported Malaria

Travel Malaria

Visitors

Exogeneous Forcing

Models

forced

Weather

Hydrology

Resource Dynamics

Other Blood Hosts

Habitat Dynamics and Availability

Sugar

Vector Control

null model

Implement Control

Bed Nets

Indoor Residual Spraying

Area Spraying

Sugar Baits

Larval Source Management

Ovitraps

Setup

Setting Up

Initial Values

Solving

Derivatives

Solving

Analysis and Visualization

Spatial metrics

Compute terms

Plot terms

Utilities