Package index • ramp.library

MYZ - Adult Mosquito The model library for adult mosquito infection dynamics
The Adult Mosquito RMG Model A behavioral state model
`F_eggs(<RMG>)`	Number of eggs laid by adult mosquitoes
`F_fqZ(<RMG>)`	Blood feeding rate of the infective mosquito population
`F_fqM(<RMG>)`	Blood feeding rate of the infective mosquito population
`MBaseline(<RMG>)`	Reset bloodfeeding and mortality rates to baseline
`MBionomics(<RMG>)`	Reset bloodfeeding and mortality rates to baseline
`dMYZdt(<RMG>)`	Derivatives for adult mosquitoes
`get_MYZpars(<RMG>)`	Return the parameters as a list
`set_MYZpars(<RMG>)`	Return the parameters as a list
`get_MYZinits(<RMG>)`	Return initial values as a vector
`set_MYZinits(<RMG>)`	Set new MYZ parameter values
`setup_MYZinits(<RMG>)`	Setup initial values for the RMG model
`setup_MYZpar(<RMG>)`	Setup MYZpar for the RMG model
`make_MYZinits_RMG()`	Make inits for RMG adult mosquito model
`make_MYZpar_RMG()`	Make parameters for RM ODE adult mosquito model
`setup_MYZix(<RMG>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<RMG>)`	Parse the output of deSolve and return variables for the RMG model
`update_MYZinits(<RMG>)`	Make inits for RMG adult mosquito model
`get_g(<RMG>)`	Get the feeding rate
`get_f(<RMG>)`	Get the feeding rate
`get_q(<RMG>)`	Get the feeding rate
`get_sigma(<RMG>)`	Get the feeding rate
The Adult Mosquito SBRQ Model A behavioral state model
`F_eggs(<SBRQ>)`	Number of eggs laid by adult mosquitoes
`F_fqZ(<SBRQ>)`	Blood feeding rate of the infective mosquito population
`F_fqM(<SBRQ>)`	Blood feeding rate of the infective mosquito population
`MBaseline(<SBRQ>)`	Reset bloodfeeding and mortality rates to baseline
`MBionomics(<SBRQ>)`	Reset bloodfeeding and mortality rates to baseline
`dMYZdt(<SBRQ>)`	Derivatives for adult mosquitoes
`get_MYZpars(<SBRQ>)`	Return the parameters as a list
`set_MYZpars(<SBRQ>)`	Return the parameters as a list
`get_MYZinits(<SBRQ>)`	Return initial values as a vector
`set_MYZinits(<SBRQ>)`	Set new MYZ parameter values
`setup_MYZinits(<SBRQ>)`	Setup initial values for the SBRQ model
`setup_MYZpar(<SBRQ>)`	Setup MYZpar for the SBRQ model
`make_MYZinits_SBRQ()`	Make inits for SBRQ adult mosquito model
`make_MYZpar_SBRQ()`	Make parameters for RM ODE adult mosquito model
`setup_MYZix(<SBRQ>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<SBRQ>)`	Parse the output of deSolve and return variables for the SBRQ model
`update_MYZinits(<SBRQ>)`	Make inits for SBRQ adult mosquito model
`get_g(<SBRQ>)`	Get the feeding rate
`get_f(<SBRQ>)`	Get the feeding rate
`get_q(<SBRQ>)`	Get the feeding rate
`get_sigma(<SBRQ>)`	Get the feeding rate
ENBRQ_dts Specialized methods for ENBRQ_dts, a model of adult mosquito dynamics with no parasite infection dynamics.
`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
`make_MYZpar_ENBRQ_dts()`	Make parameters for ENBRQ_dts adult mosquito model
`setup_MYZinits(<ENBRQ_dts>)`	Setup initial values for the ENBRQ_dts model
`make_MYZinits_ENBRQ_dts()`	Make inits for ENBRQ_dts adult mosquito model
`list_MYZvars(<ENBRQ_dts>)`	Return the variables as a list
`setup_MYZix(<ENBRQ_dts>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<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_MYZinits(<ENBRQ_dts>)`	Return initial values as a vector
`update_MYZinits(<ENBRQ_dts>)`	Make inits for ENBRQ_dts adult mosquito model
`make_parameters_MYZ_ENBRQ_dts()`	Make parameters for ENBRQ_dts adult mosquito model
The SEI compartment model Specialized methods for simple infection dynamics for an adult mosquito population
`dMYZdt(<SEI>)`	$\cal MYZ$ Component Derivatives for the `SEI` Mosquito Model
`MBaseline(<SEI>)`	Set mosquito bionomics to baseline
`MBionomics(<SEI>)`	Set mosquito bionomics to baseline
`xde_steady_state_MYZ(<SEI>)`	Steady States: MYZ-SEI
`Update_MYZt(<SEI>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<SEI>)`	Setup MYZpar for the SEI model
`make_MYZpar_SEI()`	Make parameters for SEI ODE adult mosquito model
`F_fqZ(<SEI>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<SEI>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<SEI>)`	Number of eggs laid by adult mosquitoes
`list_MYZvars(<SEI>)`	Return the variables as a list
`get_MYZpars(<SEI>)`	Return the parameters as a list
`set_MYZpars(<SEI>)`	Return the parameters as a list
`put_MYZvars(<SEI>)`	Return the variables as a list
`setup_MYZinits(<SEI>)`	Setup initial values for the SEI model
`make_MYZinits_SEI()`	Make inits for SEI adult mosquito model
`setup_MYZix(<SEI>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<SEI>)`	Parse the output of deSolve and return variables for the SEI model
`get_MYZinits(<SEI>)`	Return initial values as a vector
`set_MYZinits(<SEI>)`	Set new MYZ parameter values
`update_MYZinits(<SEI>)`	Make inits for SEI adult mosquito model
`get_f(<SEI>)`	Get the feeding rate
`get_q(<SEI>)`	Get the feeding rate
`get_g(<SEI>)`	Get the feeding rate
`get_sigma(<SEI>)`	Get the feeding rate
bionomics
`F_sigma(<dddn>)`	Dawn, day, dusk, night model for the human fraction
`F_f(<dddn>)`	Dawn, day, dusk, night model for the blood feeding rate
`F_q(<dddn>)`	Dawn, day, dusk, night model for the human fraction
`F_p(<dddn>)`	Dawn, day, dusk, night model for the human fraction
`F_nu(<dddn>)`	Dawn, day, dusk, night model for the human fraction
L-Aquatic Mosquito Models for parasites infecting human / vertebrate hosts
stages_dts Specialized methods for a stages_dts competition model of aquatic mosquito dynamics.
`LBionomics(<stages_dts>)`	Reset aquatic parameters to baseline
`F_emerge(<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
`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
`setup_Lix(<stages_dts>)`	Add indices for aquatic stage mosquitoes to parameter list
`list_Lvars(<stages_dts>)`	Return the variables as a list
`parse_Lorbits(<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_Linits.stages_dts()`	Return initial values as a vector
`update_Linits(<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
X-Vertebrate Hosts Models for parasites infecting human / vertebrate hosts
The Garki model
`F_X(<garki>)`	Size of effective infectious human population
`F_H(<garki>)`	Size of effective infectious human population
`F_pr(<garki>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<garki>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<garki>)`	Derivatives for human population
`setup_Xpar(<garki>)`	make Xpar for the Garki model
`make_Xpar_garki()`	Make parameters for garki human model
`setup_Xinits(<garki>)`	Setup Xinits.garki
`make_Xinits_garki()`	Make inits for garki human model.
`list_Xvars(<garki>)`	Return the variables as a list
`setup_Xix(<garki>)`	Add indices for human population to parameter list
`parse_Xorbits(<garki>)`	Parse the output of deSolve and return variables for the garki model
`get_Xinits(<garki>)`	Return initial values as a vector for the garki model
`set_Xinits(<garki>)`	Set Xinits.garki
`set_Xpars(<garki>)`	Return the parameters as a list
`update_Xinits(<garki>)`	Update inits for the garki model
`HTC(<garki>)`	Compute the HTC for the garki model
`xds_plot_X(<garki>)`	Plot the density of infected individuals for the garki model
`xds_lines_X_garki()`	Add lines for the density of infected individuals for the garki model
XH Component Models for parasites infecting human / vertebrate hosts
The SIPw model
`dXdt(<SIPw>)`	Derivatives for human population
`Update_Xt(<SIPw>)`	Derivatives for human population
`setup_Xpar(<SIPw>)`	Setup the Xpar for the SIPw_xde model
`make_Xpar_SIPw()`	Make parameters for SIPw_xde human model, with defaults
`F_X(<SIPw>)`	Size of effective infectious human population
`F_H(<SIPw>)`	Size of effective infectious human population
`F_pr(<SIPw>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SIPw>)`	Infection blocking pre-erythrocytic immunity
`setup_Xinits(<SIPw>)`	Setup Xinits.SIPw
`make_Xinits_SIPw()`	Make initial values for a SIPw human model, with defaults
`list_Xvars(<SIPw>)`	Return the SIPw model variables as a list
`put_Xvars(<SIPw>)`	Return the SIPw model variables as a list, returned from Update_Xt.SIPw
`setup_Xix(<SIPw>)`	Add indices for human population to parameter list
`parse_Xorbits(<SIPw>)`	Parse the output of deSolve and return variables for SIPw models
`get_Xinits(<SIPw>)`	Return initial values as a vector from a SIPw model
`update_Xinits(<SIPw>)`	Update inits for SIPw models from a vector of states
`HTC(<SIPw>)`	Compute the HTC for the SIPw_xde model
`xds_plot_X(<SIPw>)`	Plot the density of infected individuals for the SIPw model
`xds_lines_X_SIPw()`	Add lines for the density of infected individuals for the SIP model
`xde_steady_state_X(<SIPw>)`	Compute the steady states for the SIP model as a function of the daily foi
The workhorse model
`F_X(<workhorse>)`	Size of effective infectious human population
`F_H(<workhorse>)`	Size of effective infectious human population
`F_pr(<workhorse>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<workhorse>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<workhorse>)`	Derivatives for human population
`setup_Xinits(<workhorse>)`	Setup Xinits.workhorse
`list_Xvars(<workhorse>)`	Return the variables as a list
`setup_Xpar(<workhorse>)`	make Xpar.workhorse
`make_Xpar_workhorse()`	Make parameters for workhorse human model, with defaults
`make_Xinits_workhorse()`	Make initial values for the workhorse human model, with defaults
`setup_Xix(<workhorse>)`	Add indices for human population to parameter list
`parse_Xorbits(<workhorse>)`	Parse the output of deSolve and return variables for the workhorse model
`get_Xinits(<workhorse>)`	Return initial values as a vector
`update_Xinits(<workhorse>)`	Update inits for the workhorse human model from a vector of states
`HTC(<workhorse>)`	Compute the HTC for the workhorse model
`xds_plot_X(<workhorse>)`	Plot the density of infected individuals for the workhorse model
`xds_lines_X_workhorse()`	Add lines for the density of infected individuals for the workhorse model
The SIR model
`dXdt(<SIR>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_Xpar(<SIR>)`	Setup Xpar.SIR
`make_Xpar_SIR()`	Make parameters for SIR human model, with defaults
`F_X(<SIR>)`	Size of effective infectious human population
`F_H(<SIR>)`	Size of effective infectious human population
`F_pr(<SIR>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SIR>)`	Infection blocking pre-erythrocytic immunity
`setup_Xinits(<SIR>)`	Setup Xinits.SIR
`list_Xvars(<SIR>)`	Return the variables as a list
`make_Xinits_SIR()`	Make initial values for the SIR human model, with defaults
`setup_Xix(<SIR>)`	Add indices for human population to parameter list
`parse_Xorbits(<SIR>)`	Parse the output of deSolve and return variables for the SIR model
`get_Xinits(<SIR>)`	Return initial values as a vector
`set_Xinits(<SIR>)`	Return the parameters as a list
`set_Xpars(<SIR>)`	Return the parameters as a list
`update_Xinits(<SIR>)`	Update inits for the SIR human model from a vector of states
`HTC(<SIR>)`	Compute the HTC for the SIR model
`xds_plot_X(<SIR>)`	Plot the density of infected individuals for the SIR model
`xds_lines_X_SIR()`	Add lines for the density of infected individuals for the SIR model
`xde_steady_state_X(<SIR>)`	Compute the steady states for the SIR model as a function of the daily EIR
`Update_Xt(<SIR>)`	DTS updating for the SIS model for human / vertebrate host infections
`dts_steady_state_X(<SIR>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
The SIRS Model
`F_X(<SIRS>)`	Size of effective infectious human population
`F_H(<SIRS>)`	Size of effective infectious human population
`F_pr(<SIRS>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SIRS>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<SIRS>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_Xpar(<SIRS>)`	Setup Xpar.SIRS
`setup_Xinits(<SIRS>)`	Setup Xinits.SIRS
`list_Xvars(<SIRS>)`	Return the variables as a list
`make_Xpar_SIRS()`	Make parameters for SIRS human model, with defaults
`make_Xinits_SIRS()`	Make initial values for the SIRS human model, with defaults
`setup_Xix(<SIRS>)`	Add indices for human population to parameter list
`parse_Xorbits(<SIRS>)`	Parse the output of deSolve and return variables for the SIRS model
`get_Xinits(<SIRS>)`	Return initial values as a vector
`set_Xinits(<SIRS>)`	Return the parameters as a list
`set_Xpars(<SIRS>)`	Return the parameters as a list
`update_Xinits(<SIRS>)`	Update inits for the SIRS human model from a vector of states
`HTC(<SIRS>)`	Compute the HTC for the SIRS model
`xds_plot_X(<SIRS>)`	Plot the density of infected individuals for the SIRS model
`xds_lines_X_SIRS()`	Add lines for the density of infected individuals for the SIRS model
`xde_steady_state_X(<SIRS>)`	Compute the steady states for the SIRS model as a function of the daily EIR
`Update_Xt(<SIRS>)`	DTS updating for the SIS model for human / vertebrate host infections
`dts_steady_state_X(<SIRS>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
The SEIR model
`F_X(<SEIR>)`	Size of effective infectious human population
`F_H(<SEIR>)`	Size of effective infectious human population
`F_pr(<SEIR>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SEIR>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<SEIR>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_Xpar(<SEIR>)`	Setup Xpar.SEIR
`setup_Xinits(<SEIR>)`	Setup Xinits.SEIR
`list_Xvars(<SEIR>)`	Return the variables as a list
`make_Xpar_SEIR()`	Make parameters for SEIR human model, with defaults
`make_Xinits_SEIR()`	Make initial values for the SEIR human model, with defaults
`setup_Xix(<SEIR>)`	Add indices for human population to parameter list
`parse_Xorbits(<SEIR>)`	Parse the output of deSolve and return variables for the SEIR model
`get_Xinits(<SEIR>)`	Return initial values as a vector
`set_Xinits(<SEIR>)`	Return the parameters as a list
`set_Xpars(<SEIR>)`	Return the parameters as a list
`update_Xinits(<SEIR>)`	Update inits for the SEIR human model from a vector of states
`HTC(<SEIR>)`	Compute the HTC for the SEIR model
`xds_plot_X(<SEIR>)`	Plot the density of infected individuals for the SEIR model
`xds_lines_X_SEIR()`	Add lines for the density of infected individuals for the SEIR model
`xde_steady_state_X(<SEIR>)`	Compute the steady states for the SIRS model as a function of the daily EIR
`Update_Xt(<SEIR>)`	DTS updating for the SIS model for human / vertebrate host infections
`dts_steady_state_X(<SEIR>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
The SEIRV model
`F_X(<SEIRV>)`	Size of effective infectious human population
`F_H(<SEIRV>)`	Size of effective infectious human population
`F_pr(<SEIRV>)`	Compute the "true" prevalence of infection / parasite rate
`F_b(<SEIRV>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<SEIRV>)`	Compute the derivatives for parasite infection dynamics in human population strata
`list_Xvars(<SEIRV>)`	Return the variables as a list
`setup_Xpar(<SEIRV>)`	Setup Xpar.SEIRV
`setup_Xinits(<SEIRV>)`	Setup Xinits.SEIRV
`make_Xpar_SEIRV()`	Make parameters for SEIRV human model, with defaults
`make_Xinits_SEIRV()`	Make initial values for the SEIRV human model, with defaults
`setup_Xix(<SEIRV>)`	Add indices for human population to parameter list
`parse_Xorbits(<SEIRV>)`	Parse the output of deSolve and return variables for the SEIRV model
`get_Xinits(<SEIRV>)`	Return initial values as a vector
`set_Xinits(<SEIRV>)`	Return the parameters as a list
`set_Xpars(<SEIRV>)`	Return the parameters as a list
`update_Xinits(<SEIRV>)`	Update inits for the SEIRV human model from a vector of states
`HTC(<SEIRV>)`	Compute the HTC for the SEIRV model
`xds_plot_X(<SEIRV>)`	Plot the density of infected individuals for the SEIRV model
`xds_lines_X_SEIRV()`	Add lines for the density of infected individuals for the SEIRV model
`xde_steady_state_X(<SEIRV>)`	Compute the steady states for the SEIRV model as a function of the daily EIR
`Update_Xt(<SEIRV>)`	DTS updating for the SIS model for human / vertebrate host infections
`dts_steady_state_X(<SEIRV>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
SEIS Specialized methods for the SEIS (Susceptible-Infected-Susceptible) model of human dynamics.
`dXdt(<SEIS>)`	$\cal X$ Component Derivatives for the `SEIS` Model
`Update_Xt(<SEIS>)`	DTS updating for the SEIS model for human / vertebrate host infections
`setup_Xpar(<SEIS>)`	Setup Xpar.SEIS
`make_Xpar_SEIS()`	Make parameters for SEIS xde human model, with defaults
`setup_Xinits(<SEIS>)`	Setup Xinits.SEIS
`make_Xinits_SEIS()`	Make initial values for the SEIS xde human model, with defaults
`setup_Xix(<SEIS>)`	Add indices for human population to parameter list
`list_Xvars(<SEIS>)`	Return the variables as a list
`get_Xpars(<SEIS>)`	Return the parameters as a list
`put_Xvars(<SEIS>)`	Return the SEIS model variables as a list, returned from Update_Xt.SISd
`F_X(<SEIS>)`	Size of effective infectious human population
`F_H(<SEIS>)`	Size of effective infectious human population
`F_pr(<SEIS>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<SEIS>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<SEIS>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<SEIS>)`	Compute the prevalence of infection by pcr
`F_ni(<SEIS>)`	Compute the NI
`F_b(<SEIS>)`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits(<SEIS>)`	Parse the output of deSolve and return variables for the SEIS model
`get_Xinits(<SEIS>)`	Return initial values as a vector
`set_Xinits(<SEIS>)`	Return the parameters as a list
`set_Xpars(<SEIS>)`	Return the parameters as a list
`update_Xinits(<SEIS>)`	Update inits for the SEIS xde human model from a vector of states
`HTC(<SEIS>)`	Compute the HTC for the SEIS model
`xds_plot_X(<SEIS>)`	Plot the density of infected individuals for the SEIS model
`add_lines_X_SEIS()`	Add lines for the density of infected individuals for the SEIS model
`xde_steady_state_X(<SEIS>)`	Compute the steady states for the SEIS model as a function of the daily EIR
`dts_steady_state_X(<SEIS>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
SEISd Specialized methods for the SEISd (Susceptible-Infected-Susceptible) model of human dynamics.
`dXdt(<SEISd>)`	$\cal X$ Component Derivatives for the `SEISd` Model
`Update_Xt(<SEISd>)`	DTS updating for the SEISd model for human / vertebrate host infections
`setup_Xpar(<SEISd>)`	Setup Xpar.SEISd
`make_Xpar_SEISd()`	Make parameters for SEISd xde human model, with defaults
`xde_steady_state_X(<SEISd>)`	Compute the steady states for the SEISd model as a function of the daily EIR
`setup_Xinits(<SEISd>)`	Setup Xinits.SEISd
`make_Xinits_SEISd()`	Make initial values for the SEISd xde human model, with defaults
`setup_Xix(<SEISd>)`	Add indices for human population to parameter list
`list_Xvars(<SEISd>)`	Return the variables as a list
`set_Xpars(<SEISd>)`	Return the parameters as a list
`put_Xvars(<SEISd>)`	Return the SEISd model variables as a list, returned from Update_Xt.SISd
`F_X(<SEISd>)`	Size of effective infectious human population
`F_H(<SEISd>)`	Size of effective infectious human population
`F_b(<SEISd>)`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits(<SEISd>)`	Parse the output of deSolve and return variables for the SEISd model
`get_Xinits(<SEISd>)`	Return initial values as a vector
`set_Xinits(<SEISd>)`	Return the parameters as a list
`get_Xpars(<SEISd>)`	Return the parameters as a list
`update_Xinits(<SEISd>)`	Update inits for the SEISd xde human model from a vector of states
`HTC(<SEISd>)`	Compute the HTC for the SEISd model
`F_pr(<SEISd>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<SEISd>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<SEISd>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<SEISd>)`	Compute the prevalence of infection by pcr
`F_ni(<SEISd>)`	Compute the NI
`xds_plot_X(<SEISd>)`	Plot the density of infected individuals for the SEISd model
`add_lines_X_SEISd()`	Add lines for the density of infected individuals for the SEISd model
SIP Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics.
`dXdt(<SIP>)`	Derivatives for the `SIP` Module (X Component)
`Update_Xt(<SIP>)`	Derivatives for human population
`setup_Xpar(<SIP>)`	Setup `Xpar` for an `SIP`
`make_Xpar_SIP()`	Make parameters for SIP human model, with defaults
`xde_steady_state_X(<SIP>)`	Compute the steady states for the SIP model as a function of the daily foi
`dts_steady_state_X(<SIP>)`	Compute the steady states for the dts SIP model as a function of the daily EIR
`setup_Xinits(<SIP>)`	Setup Xinits.SIP
`make_Xinits_SIP()`	Make initial values for the SIP human model, with defaults
`setup_Xix(<SIP>)`	Add indices for human population to parameter list
`list_Xvars(<SIP>)`	Return the variables as a list
`get_Xpars(<SIP>)`	Return the parameters as a list
`set_Xpars(<SIP>)`	Return the parameters as a list
`F_X(<SIP>)`	Size of effective infectious human population
`F_H(<SIP>)`	Size of effective infectious human population
`F_b(<SIP>)`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits(<SIP>)`	Parse the output of deSolve and return variables for the SIP model
`get_Xinits(<SIP>)`	Return initial values as a vector
`set_Xinits(<SIP>)`	Return the parameters as a list
`update_Xinits(<SIP>)`	Update inits for the SIP human model from a vector of states
`HTC(<SIP>)`	Compute the HTC for the SIP model
`F_pr(<SIP>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<SIP>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<SIP>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<SIP>)`	Compute the prevalence of infection by pcr
`F_ni(<SIP>)`	Compute the "true" prevalence of infection / parasite rate
`xds_plot_X(<SIP>)`	Plot the density of infected individuals for the SIP model
`add_lines_X_SIP()`	Add lines for the density of infected individuals for the SIP model
SIPd Specialized methods for the SIPd (Susceptible-Infected-Prophylaxis) model of human dynamics.
`dXdt(<SIPd>)`	$\cal X$ Component Derivatives for the `SIPd` Model
`Update_Xt(<SIPd>)`	Derivatives for human population
`setup_Xpar(<SIPd>)`	Setup `Xpar` for an `SIPd`
`make_Xpar_SIPd()`	Make parameters for SIPd human model, with defaults
`xde_steady_state_X(<SIPd>)`	Compute the steady states for the SIPd model as a function of the daily foi
`dts_steady_state_X(<SIPd>)`	Compute the steady states for the dts SIPd model as a function of the daily EIR
`setup_Xinits(<SIPd>)`	Setup Xinits.SIPd
`make_Xinits_SIPd()`	Make initial values for the SIPd human model, with defaults
`setup_Xix(<SIPd>)`	Add indices for human population to parameter list
`list_Xvars(<SIPd>)`	Return the variables as a list
`get_Xpars(<SIPd>)`	Return the parameters as a list
`set_Xpars(<SIPd>)`	Return the parameters as a list
`F_X(<SIPd>)`	Size of effective infectious human population
`F_H(<SIPd>)`	Size of effective infectious human population
`F_b(<SIPd>)`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits(<SIPd>)`	Parse the output of deSolve and return variables for the SIPd model
`get_Xinits(<SIPd>)`	Return initial values as a vector
`set_Xinits(<SIPd>)`	Return the parameters as a list
`update_Xinits(<SIPd>)`	Update inits for the SIPd human model from a vector of states
`HTC(<SIPd>)`	Compute the HTC for the SIPd model
`F_pr(<SIPd>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<SIPd>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<SIPd>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<SIPd>)`	Compute the prevalence of infection by pcr
`F_ni(<SIPd>)`	Compute the "true" prevalence of infection / parasite rate
`xds_plot_X(<SIPd>)`	Plot the density of infected individuals for the SIPd model
`add_lines_X_SIPd()`	Add lines for the density of infected individuals for the SIPd model

Reference

MYZ - Adult Mosquito

The Adult Mosquito RMG Model

The Adult Mosquito SBRQ Model

ENBRQ_dts

The SEI compartment model

bionomics

L-Aquatic Mosquito

stages_dts

X-Vertebrate Hosts

The Garki model

XH Component

The SIPw model

The workhorse model

The SIR model

The SIRS Model

The SEIR model

The SEIRV model

SEIS

SEISd

SIP

SIPd