Package index • ramp.library

MY - 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
`dMYdt(<RMG>)`	Derivatives for adult mosquitoes
`get_MY_pars(<RMG>)`	Return the parameters as a list
`change_MY_pars(<RMG>)`	Return the parameters as a list
`change_MY_inits(<RMG>)`	Set new MY parameter values
`setup_MY_inits(<RMG>)`	Setup initial values for the RMG model
`setup_MY_obj(<RMG>)`	Setup MY_obj for the RMG model
`make_MY_inits_RMG()`	Make inits for RMG adult mosquito model
`make_MY_obj_RMG()`	Make parameters for RM ODE adult mosquito model
`setup_MY_ix(<RMG>)`	Add indices for adult mosquitoes to parameter list
`parse_MY_orbits(<RMG>)`	parse the output of deSolve and return variables for the RMG 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
`check_MY(<RMG>)`	Run a check before solving
`get_MY_vars(<RMG>)`	Return the variables as a list
`skill_set_MY(<RMG>)`	The RMG Module Skill Set
The SEI compartment model Specialized methods for simple infection dynamics for an adult mosquito population
`Update_MYt(<SEI>)`	Derivatives for adult mosquitoes
`check_MY(<SEI>)`	Run a check before solving
`get_MY_vars(<SEI>)`	Return the variables as a list
`skill_set_MY(<SEI>)`	The SEI Module Skill Set
`dMYdt(<SEI>)`	\(\cal MY\) Component Derivatives for the `SEI` Mosquito Model
`MBaseline(<SEI>)`	Set mosquito bionomics to baseline
`MBionomics(<SEI>)`	Set mosquito bionomics to baseline
`steady_state_MY(<SEI>)`	Steady States: MY-SEI
`setup_MY_obj(<SEI>)`	Setup MY_obj for the SEI model
`make_MY_obj_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
`get_MY_pars(<SEI>)`	Return the parameters as a list
`change_MY_pars(<SEI>)`	Return the parameters as a list
`setup_MY_inits(<SEI>)`	Setup initial values for the SEI model
`make_MY_inits_SEI()`	Make inits for SEI adult mosquito model
`setup_MY_ix(<SEI>)`	Add indices for adult mosquitoes to parameter list
`parse_MY_orbits(<SEI>)`	parse the output of deSolve and return variables for the SEI model
`change_MY_inits(<SEI>)`	Set new MY parameter values
`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
X-Vertebrate Hosts Models for parasites infecting human / vertebrate hosts
The Garki model
`F_ni(<garki>)`	Infection blocking pre-erythrocytic immunity
`skill_set_XH(<garki>)`	The XH Module Skill Set
`check_XH(<garki>)`	Check / update before solving
`get_XH_vars(<garki>)`	Return the variables as a list
`F_X(<garki>)`	Size of effective infectious human population
`F_H(<garki>)`	Size of effective infectious human population
`F_prevalence(<garki>)`	Compute the "true" prevalence of infection / parasite rate
`F_infectivity(<garki>)`	Infection blocking pre-erythrocytic immunity
`dXHdt(<garki>)`	Derivatives for human population
`setup_XH_obj(<garki>)`	make XH_obj for the Garki model
`make_XH_obj_garki()`	Make parameters for garki human model
`setup_XH_inits(<garki>)`	Setup XH_inits.garki
`make_XH_inits_garki()`	Make inits for garki human model.
`setup_XH_ix(<garki>)`	Add indices for human population to parameter list
`parse_XH_orbits(<garki>)`	parse the output of deSolve and return variables for the garki model
`change_XH_inits(<garki>)`	Set XH_inits.garki
`change_XH_pars(<garki>)`	Return the parameters as a list
`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 SIR model
`F_ni(<SIR>)`	Infection blocking pre-erythrocytic immunity
`check_XH(<SIR>)`	Check / update before solving
`skill_set_XH(<SIR>)`	The XH Module Skill Set
`dXHdt(<SIR>)`	Compute the derivatives for parasite infection dynamics in human population strata
`Update_XHt(<SIR>)`	DTS updating for the SIS model for human / vertebrate host infections
`setup_XH_obj(<SIR>)`	Setup XH_obj.SIR
`make_XH_obj_SIR()`	Make parameters for SIR human model, with defaults
`get_XH_vars(<SIR>)`	Return the variables as a list
`F_X(<SIR>)`	Size of effective infectious human population
`F_H(<SIR>)`	Size of effective infectious human population
`F_prevalence(<SIR>)`	Compute the "true" prevalence of infection / parasite rate
`F_infectivity(<SIR>)`	Infection blocking pre-erythrocytic immunity
`setup_XH_inits(<SIR>)`	Setup XH_obj.SIR
`make_XH_inits_SIR()`	Make initial values for the SIR human model, with defaults
`setup_XH_ix(<SIR>)`	Add indices for human population to parameter list
`parse_XH_orbits(<SIR>)`	parse the output of deSolve and return variables for the SIR model
`change_XH_inits(<SIR>)`	Return the parameters as a list
`change_XH_pars(<SIR>)`	Return the parameters as a list
`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
`steady_state_X(<SIR_ode>)`	Compute the steady states for the SIR model as a function of the daily EIR
`steady_state_X(<SIR_dts>)`	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_ni(<SIRS>)`	Infection blocking pre-erythrocytic immunity
`check_XH(<SIRS>)`	Check / update before solving
`skill_set_XH(<SIRS>)`	The XH Module Skill Set
`get_XH_vars(<SIRS>)`	Return the variables as a list
`F_H(<SIRS>)`	Size of effective infectious human population
`F_prevalence(<SIRS>)`	Compute the "true" prevalence of infection / parasite rate
`F_infectivity(<SIRS>)`	Infection blocking pre-erythrocytic immunity
`dXHdt(<SIRS>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_XH_obj(<SIRS>)`	Setup XH_obj.SIRS
`setup_XH_inits(<SIRS>)`	Setup XH_obj.SIRS
`make_XH_obj_SIRS()`	Make parameters for SIRS human model, with defaults
`make_XH_inits_SIRS()`	Make initial values for the SIRS human model, with defaults
`setup_XH_ix(<SIRS>)`	Add indices for human population to parameter list
`parse_XH_orbits(<SIRS>)`	parse the output of deSolve and return variables for the SIRS model
`change_XH_inits(<SIRS>)`	Return the parameters as a list
`change_XH_pars(<SIRS>)`	Return the parameters as a list
`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
`Update_XHt(<SIRS>)`	DTS updating for the SIS model for human / vertebrate host infections
`steady_state_X(<SIRS_ode>)`	Compute the steady states for the SIRS model as a function of the daily EIR
`steady_state_X(<SIRS_dts>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
The SEIR model
`F_ni(<SEIR>)`	Infection blocking pre-erythrocytic immunity
`check_XH(<SEIR>)`	Check / update before solving
`get_XH_vars(<SEIR>)`	Return the variables as a list
`skill_set_XH(<SEIR>)`	The XH Module Skill Set
`F_X(<SEIR>)`	Size of effective infectious human population
`F_H(<SEIR>)`	Size of effective infectious human population
`F_prevalence(<SEIR>)`	Compute the "true" prevalence of infection / parasite rate
`F_infectivity(<SEIR>)`	Infection blocking pre-erythrocytic immunity
`dXHdt(<SEIR>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_XH_obj(<SEIR>)`	Setup XH_obj.SEIR
`setup_XH_inits(<SEIR>)`	Setup XH_obj.SEIR
`make_XH_obj_SEIR()`	Make parameters for SEIR human model, with defaults
`make_XH_inits_SEIR()`	Make initial values for the SEIR human model, with defaults
`setup_XH_ix(<SEIR>)`	Add indices for human population to parameter list
`parse_XH_orbits(<SEIR>)`	parse the output of deSolve and return variables for the SEIR model
`change_XH_inits(<SEIR>)`	Return the parameters as a list
`change_XH_pars(<SEIR>)`	Return the parameters as a list
`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
`Update_XHt(<SEIR>)`	DTS updating for the SIS model for human / vertebrate host infections
`steady_state_X(<SEIR_ode>)`	Compute the steady states for the SIRS model as a function of the daily EIR
`steady_state_X(<SEIR_dts>)`	Compute the steady states for the dts SEIS model as a function of the daily EIR
The SEIRV model
`F_ni(<SEIRV>)`	Compute the NI
`check_XH(<SEIRV>)`	Check / update before solving
`get_XH_vars(<SEIRV>)`	Return the variables as a list
`skill_set_XH(<SEIRV>)`	The XH Module Skill Set
`F_X(<SEIRV>)`	Size of effective infectious human population
`F_H(<SEIRV>)`	Size of effective infectious human population
`F_prevalence(<SEIRV>)`	Compute the "true" prevalence of infection / parasite rate
`F_infectivity(<SEIRV>)`	Infection blocking pre-erythrocytic immunity
`dXHdt(<SEIRV>)`	Compute the derivatives for parasite infection dynamics in human population strata
`setup_XH_obj(<SEIRV>)`	Setup XH_obj.SEIRV
`setup_XH_inits(<SEIRV>)`	Setup XH_obj.SEIRV
`make_XH_obj_SEIRV()`	Make parameters for SEIRV human model, with defaults
`make_XH_inits_SEIRV()`	Make initial values for the SEIRV human model, with defaults
`setup_XH_ix(<SEIRV>)`	Add indices for human population to parameter list
`parse_XH_orbits(<SEIRV>)`	parse the output of deSolve and return variables for the SEIRV model
`change_XH_inits(<SEIRV>)`	Return the parameters as a list
`change_XH_pars(<SEIRV>)`	Return the parameters as a list
`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
`Update_XHt(<SEIRV>)`	DTS updating for the SIS model for human / vertebrate host infections
`steady_state_X(<SEIRV_ode>)`	Compute the steady states for the SEIRV model as a function of the daily EIR
`steady_state_X(<SEIRV_dts>)`	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.
`check_XH(<SEIS>)`	Check / update before solving
`get_XH_vars(<SEIS>)`	Return the variables as a list
`skill_set_XH(<SEIS>)`	The XH Module Skill Set
`dXHdt(<SEIS>)`	\(\cal X\) Component Derivatives for the `SEIS` Model
`Update_XHt(<SEIS>)`	DTS updating for the SEIS model for human / vertebrate host infections
`setup_XH_obj(<SEIS>)`	Setup XH_obj.SEIS
`make_XH_obj_SEIS()`	Make parameters for SEIS xde human model, with defaults
`setup_XH_inits(<SEIS>)`	Setup Xinits.SEIS
`make_XH_inits_SEIS()`	Make initial values for the SEIS xde human model, with defaults
`setup_XH_ix(<SEIS>)`	Add indices for human population to parameter list
`get_XH_pars(<SEIS>)`	Return the parameters as a list
`F_X(<SEIS>)`	Size of effective infectious human population
`F_H(<SEIS>)`	Size of effective infectious human population
`F_prevalence(<SEIS>)`	Compute the "true" prevalence of infection / parasite rate
`F_pfpr_by_lm(<SEIS>)`	Compute the prevalence of infection by light microscopy
`F_pfpr_by_pcr(<SEIS>)`	Compute the prevalence of infection by pcr
`F_pfpr_by_rdt(<SEIS>)`	Compute the prevalence of infection by RDT
`F_ni(<SEIS>)`	Compute the NI
`F_infectivity(<SEIS>)`	Infection blocking pre-erythrocytic immunity
`parse_XH_orbits(<SEIS>)`	parse the output of deSolve and return variables for the SEIS model
`change_XH_inits(<SEIS>)`	Return the parameters as a list
`change_XH_pars(<SEIS>)`	Return the parameters as a list
`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
`steady_state_X(<SEIS_ode>)`	Compute the steady states for the SEIS model as a function of the daily EIR
`steady_state_X(<SEIS_dts>)`	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.
`check_XH(<SEISd>)`	Check / update before solving
`get_XH_vars(<SEISd>)`	Return the variables as a list
`skill_set_XH(<SEISd>)`	The XH Module Skill Set
`dXHdt(<SEISd>)`	Compute derivatives for the XH module `SEISd`
`setup_XH_obj(<SEISd>)`	Setup XH_obj.SEISd
`make_XH_obj_SEISd()`	Make parameters for SEISd Update_XHt human model, with defaults
`setup_XH_inits(<SEISd>)`	Setup initial values for `SEISd`
`make_XH_inits_SEISd()`	Make initial values for the SEISd Update_XHt human model, with defaults
`setup_XH_ix(<SEISd>)`	Add indices for human population to parameter list
`change_XH_pars(<SEISd>)`	Return the parameters as a list
`F_X(<SEISd>)`	Size of effective infectious human population
`F_H(<SEISd>)`	Size of effective infectious human population
`F_infectivity(<SEISd>)`	Infection blocking pre-erythrocytic immunity
`parse_XH_orbits(<SEISd>)`	parse the output of deSolve and return variables for the SEISd model
`change_XH_inits(<SEISd>)`	Return the parameters as a list
`get_XH_pars(<SEISd>)`	Return the parameters as a list
`HTC(<SEISd>)`	Compute the HTC for the SEISd model
`F_prevalence(<SEISd>)`	Compute the "true" prevalence of infection / parasite rate
`F_pfpr_by_lm(<SEISd>)`	Compute the prevalence of infection by light microscopy
`F_pfpr_by_pcr(<SEISd>)`	Compute the prevalence of infection by pcr
`F_pfpr_by_rdt(<SEISd>)`	Compute the prevalence of infection by RDT
`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
`steady_state_X(<SEISd>)`	Compute the steady states for the SEISd model as a function of the daily EIR
SIP Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics.
`check_XH(<SIP>)`	Check / update before solving
`skill_set_XH(<SIP>)`	The XH Module Skill Set
`dXHdt(<SIP>)`	Derivatives for the `SIP` Module (X Component)
`Update_XHt(<SIP>)`	Derivatives for human population
`setup_XH_obj(<SIP>)`	Setup `XH_obj` for an `SIP`
`make_XH_obj_SIP()`	Make parameters for SIP human model, with defaults
`get_XH_vars(<SIP>)`	Return the variables as a list
`steady_state_X(<SIP_ode>)`	Compute the steady states for the SIP model as a function of the daily foi
`steady_state_X(<SIP_dts>)`	Compute the steady states for the dts SIP model as a function of the daily EIR
`setup_XH_inits(<SIP>)`	Setup Xinits.SIP
`make_XH_inits_SIP()`	Make initial values for the SIP human model, with defaults
`setup_XH_ix(<SIP>)`	Add indices for human population to parameter list
`get_XH_pars(<SIP>)`	Return the parameters as a list
`change_XH_pars(<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_infectivity(<SIP>)`	Infection blocking pre-erythrocytic immunity
`parse_XH_orbits(<SIP>)`	Parse Solutions Matrix for the SIP model
`change_XH_inits(<SIP>)`	Return the parameters as a list
`HTC(<SIP>)`	Compute the HTC for the SIP model
`F_prevalence(<SIP>)`	Compute the "true" prevalence of infection / parasite rate
`F_pfpr_by_lm(<SIP>)`	Compute the prevalence of infection by light microscopy
`F_pfpr_by_rdt(<SIP>)`	Compute the prevalence of infection by RDT
`F_pfpr_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.
`check_XH(<SIPd>)`	Check / update before solving
`skill_set_XH(<SIPd>)`	The XH Module Skill Set
`dXHdt(<SIPd>)`	Compute derivatives for the XH module `SIPd`
`setup_XH_obj(<SIPd>)`	Setup `XH_obj` for an `SIPd`
`make_XH_obj_SIPd()`	Make parameters for SIPd human model, with defaults
`get_XH_vars(<SIPd>)`	Return the variables as a list
`setup_XH_inits(<SIPd>)`	Setup Initial Values
`make_XH_inits_SIPd()`	Make initial values for the SIPd human model, with defaults
`setup_XH_ix(<SIPd>)`	Add indices for human population to parameter list
`get_XH_pars(<SIPd>)`	Return the parameters as a list
`change_XH_pars(<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_infectivity(<SIPd>)`	Infection blocking pre-erythrocytic immunity
`parse_XH_orbits(<SIPd>)`	Parse Solutions Matrix for the SIPd model
`change_XH_inits(<SIPd>)`	Return the parameters as a list
`HTC(<SIPd>)`	Compute the HTC for the SIPd model
`F_prevalence(<SIPd>)`	Compute the "true" prevalence of infection / parasite rate
`F_pfpr_by_lm(<SIPd>)`	Compute the prevalence of infection by light microscopy
`F_pfpr_by_rdt(<SIPd>)`	Compute the prevalence of infection by RDT
`F_pfpr_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
`steady_state_X(<SIPd>)`	Compute the steady states for the dts SIPd model as a function of the daily EIR
`Update_XHt(<SIPd>)`	Derivatives for human population

Reference

MY - Adult Mosquito

The Adult Mosquito RMG Model

The SEI compartment model

X-Vertebrate Hosts

The Garki model

XH Component

The SIR model

The SIRS Model

The SEIR model

The SEIRV model

SEIS

SEISd

SIP

SIPd