Package index • ramp.xds

Model Building & Analysis Methods to support nimble model building and analysis
Build / Setup Methods to set up an `xds` object with basic features
`xds_setup()`	Basic Setup: Make a Fully Defined `xds` Object
`xds_setup_mosy()`	Make an `xds` Object to Study Mosquito Ecology
`xds_setup_aquatic()`	Make an `xds` Object to Study Aquatic Mosquito Ecology
`xds_setup_human()`	Make an `xds` Object to Study Human / Host Epidemiology
`xds_setup_cohort()`	Make an `xds` Object to Study Human / Host Cohort Dynamics
`make_xds_template()`	Make an `xds` Object Template
Solve and Analyze Methods to solve or analyze equations
`xds_solve()`	Solve a system of differential equations
`xde_stable_orbit()`	Compute the stable orbit for a system of differential equations
`xds_solve_cohort()`	Cohort dynamics for a human / host model
`xde_steady()`	Solve for the steady state of a system of equations using rootSolve::steady
`dts_steady()`	Solve for the steady state of a system of equations
`xde_steady_state_X()`	Steady States for \(\cal X\)-Models
`xde_steady_state_MYZ()`	Compute steady states for \(\cal MYZ\) models
`xde_steady_state_L()`	Compute steady states for L Component Modules
Models – Human / Host Models available in `ramp.xds` for human/host infection and immunity
`dXdt(<trivial>)`	X Component Derivatives for the `trivial` model
`dXdt(<SIS>)`	X Component Derivatives for the `SIS` Model
Models – Adult Mosquito Models available in `ramp.xds` for adult mosquito ecology and infection dynamics
`dMYZdt(<trivial>)`	MYZ Component Derivatives for the `trivial` model
`dMYZdt(<SI>)`	MYZ Component Derivatives for the `SI` Mosquito Module
`dMYZdt(<macdonald>)`	MYZ Component for the `macdonald` Adult Mosquito Module
`dMYZdt(<GeRM>)`	MYZ Component Derivatives for the `GeRM` model
`dMYZdt(<basicM>)`	MYZ Component Derivatives for `basicM`
Models – Aquatic Mosquito Models available in `ramp.xds` for the ecology of immature mosquitoes in aquatic habitats
`dLdt(<trivial>)`	Derivatives for `trivial` (L Component)
`dLdt(<basicL>)`	Derivatives for `basicL` (L Component)
Interface Functions that compute dynamical terms and exogenous variables
`Forcing()`	Set the values of exogenous variables
`Health()`	Set the values variables for health interventions
`VectorControl()`	Implement Vector Control
`Resources()`	Set the values of exogenous variables describing available mosquito resources
`BloodFeeding()`	Blood feeding
`EggLaying()`	Compute eggs laid
`BaselineBionomics()`	Set bionomic parameter rates relative to baseline
`Bionomics()`	Set bionomic parameter rates relative to baseline
`Transmission()`	Compute the mixing matrix and transmission terms
`Exposure()`	Compute Infection Rates
Change Parameters & Initial Values Methods to set up basic models
`set_H()`	Change human population density
`set_eir()`	Reset the mean daily EIR
`set_eir(<cohort>)`	Reset the mean daily EIR
`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
`parse_orbits()`	Parse the outputs of an object created by xde_solve or dts_solve
`parse_y()`	Parse the output of an object returned by deSolve
`get_inits()`	Get the stored initial values, \(y_0\)
`get_H()`	Get the initial values as a vector
`get_XH()`	Get XH outputs
`get_MYZ()`	Get MYZ outputs
`make_indices()`	Make indices for all the model variables
`trigger_setup()`	Trigger `setup`
Examine Methods to
`get_inits()`	Get the stored initial values, \(y_0\)
`get_last()`	Get the last state
`parse_orbits()`	Parse the outputs of an object created by xde_solve or dts_solve
`parse_y()`	Parse the output of an object returned by deSolve
Blood Feeding and Transmission Methods to compute terms describing blood feeding and transmission
`create_residence_matrix()`	Create the residence matrix, \(\cal J\)
`view_residence_matrix()`	View residence membership
Blood Feeding Methods to compute vertebrate host availibility and time at risk
`setup_BLOOD_FEEDING()`	Set up Blood Feeding
`BloodFeeding()`	Blood feeding
`BloodFeeding(<static>)`	Compute blood feeding objects: static models
`BloodFeeding(<dynamic>)`	Compute blood feeding objects dynamically
`BloodFeeding(<setup>)`	Compute blood feeding objects: setup for static models
`change_blood_weights()`	Set static blood feeding search weights
`compute_W()`	Compute Host Availability for Blood Feeding
`compute_B()`	Compute Vertebrate Host Availability for Blood Feeding
`make_WB()`	Compute availability blood hosts of the i^th species
`compute_RBR()`	Compute relative biting rates
`make_RBR()`	Compute and attach the relative biting rates
`compute_TaR()`	Compute blood feeding availability of all vertebrate hosts
`make_TaR()`	Make TaR
Transmision Specialized methods to compute the transmission terms
`setup_TRANSMISSION()`	Setup the interface for parasite / pathogen transmission
`Transmission()`	Compute the mixing matrix and transmission terms
`Transmission(<static>)`	Compute transmission terms with a static mixing matrix
`Transmission(<dynamic>)`	Compute transmission, the dynamic case
`Transmission(<setup>)`	Compute transmission, the static case
`compute_beta()`	Compute beta, the biting distribution matrix
`make_beta()`	Compute beta
`compute_EIR()`	Compute the daily Entomological Inoculation Rate (EIR)
`make_EIR_full()`	Compute EIR for each vector-host pair
`make_EIR()`	Compute EIR
`compute_kappa()`	Net infectiousness of human population to mosquitoes
`make_kappa()`	Compute kappa
`compute_local_frac()`	Compute the local fraction
`make_local_frac()`	Compute the local fraction
Time Spent Method to set up Time Spent Matrices
`change_TimeSpent()`	Change the time spent matrix
`make_TimeSpent()`	Make a time spent matrix, called TimeSpent
`make_TimeSpent(<athome>)`	Make a mosquito dispersal matrix, called TimeSpent with a here / away
`create_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
`create_TimeSpent_xy()`	Make a mosquito dispersal matrix, called TimeSpent
Egg Laying & Emergence Generic methods for the aquatic (immature) mosquito component.
`create_habitat_matrix()`	Create the habitat membership matrix, \(\cal N\)
`setup_EGG_LAYING()`	Setup Egg Laying
`Emergence()`	Compute emerging adults
`EggLaying()`	Compute eggs laid
`EggLaying(<setup>)`	Compute eggs laid, the first time
`EggLaying(<static>)`	Compute eggs laid
`EggLaying(<dynamic>)`	Compute eggs laid
`change_habitat_weights()`	Change the habitat search weights
`compute_Q()`	Compute the total availability of egg-laying habitats, \(Q\)
`compute_Qtot()`	Compute the total availability of egg-laying habitats, \(Q\)
`make_Q()`	Compute and store availability of egg-laying habitats
`compute_calU()`	Compute the egg distribution matrix - \(\cal U\)
`make_calU()`	Compute and store \(\cal U\)
`compute_eggs_laid()`	Compute eggs laid
`make_eggs_laid()`	Compute eggs laid
`view_habitat_matrix()`	View habitat membership, \(\cal N\)
Exposure Methods for environmental heterogeneity
`Exposure()`	Compute Infection Rates
`Exposure(<xde>)`	Compute the FoI
`Exposure(<dts>)`	Compute Attack Rates
`Exposure(<multiday>)`	Exposure and Infection
`setup_exposure_multiday()`	Make parameters for the null model of exposure
`F_foi()`	Compute the Local FoI
`foi2eir()`	Convert FoI to EIR
`F_ar()`	Compute Local Attack Rates
`ar2eir()`	Convert AR to EIR
Poisson Exposure Specialized methods the Poisson exposure model
`F_foi(<pois>)`	Poisson Force of Infection
`F_ar(<pois>)`	Poisson Attack Rates
`foi2eir(<pois>)`	Convert FoI to EIR under a Poisson model for Exposure
`ar2eir(<pois>)`	Convert AR to EIR under a Poisson model for Exposure
`setup_exposure_pois()`	Set up a Poisson model for Exposure and Infection
`setup_exposure_pois(<xde>)`	Set up Poisson Exposure and Infection for `xde`
`setup_exposure_pois(<dts>)`	Set up Poisson Exposure and Infection for `dts`
Negative Binomial Exposure Specialized methods the Negative Binomial exposure model
`F_foi(<nb>)`	Negative Binomial Force of Infection
`F_ar(<nb>)`	Negative Binomial Attack Rates
`foi2eir(<nb>)`	A negative binomial model for the daily FoI as a function of the daily EIR.
`ar2eir(<nb>)`	A negative binomial model for the daily EIR. as a function of the daily attack rate
`setup_exposure_nb()`	Set up the negative binomial model of exposure
`setup_exposure_nb(<xde>)`	Set up the negative binomial model of exposure for continuous time models
`setup_exposure_nb(<dts>)`	Set up the negative binomial model for exposure for discrete time models
Adult Mosquito Dynamics Generic methods for the adult mosquito dynamics component.
`dMYZdt()`	\(\cal MYZ\) Component Derivatives for the `GeRM` model
`MBaseline()`	Adult Mosquito - Baseline Bionomics
`MBionomics()`	Adult Mosquito - Bionomics
`xde_steady_state_MYZ()`	Compute steady states for \(\cal MYZ\) models
`xde_steady_state_M()`	Compute the steady states as a function of the daily EIR
`setup_MYZpar()`	A function to set up adult mosquito models
`Update_MYZt()`	Derivatives for adult mosquitoes
`MYZ_rates2probs()`	Compute probabilities from rates
`dts_steady_state_MYZ()`	Compute the steady states as a function of the daily EIR
`F_fqZ()`	Blood feeding rate of the infective mosquito population
`F_fqM()`	Blood feeding rate of the mosquito population
`F_eggs()`	Number of eggs laid by adult mosquitoes
`list_MYZvars()`	Return the variables as a list
`get_MYZpars()`	Return the parameters as a list
`set_MYZpars()`	Set new MYZ parameter values
`put_MYZvars()`	Put MYZvars in place of the MYZ variables in y
`setup_MYZinits()`	A function to set up adult mosquito models
`get_MYZinits()`	Return initial values as a vector
`set_MYZinits()`	Set new MYZ parameter values
`update_MYZinits()`	Set the initial values as a vector
`setup_MYZix()`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits()`	Parse the outputs and return the variables by name in a list
Visualization for Adult Mosquito Basic Plotting
`xds_plot_M()`	Plot adult mosquito population density
`xds_lines_M()`	Add lines for adult mosquito population density
`xds_plot_Y()`	Plot the density of infected and infective mosquitoes
`xds_lines_Y()`	Add lines for the density of infected and infective mosquitoes
`xds_plot_Z()`	Plot the density of infected and infective mosquitoes
`xds_lines_Z()`	Add lines for the density of infected and infective mosquitoes
`xds_plot_Y_fracs()`	Plot the fraction of infected and infective mosquitoes
`xds_lines_Y_fracs()`	Add lines for the fraction of infected and infective mosquitoes
`xds_plot_Z_fracs()`	Plot the fraction infective
`xds_lines_Z_fracs()`	Add lines for the fraction of infected and infective mosquitoes
Mosquito Demography Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics
`compute_Omega_xde()`	Make the mosquito demography matrix for spatial RM model in continuous time
`compute_Omega_dts()`	Make the mosquito demography matrix for spatial RM model in discrete time
`compute_Omega()`	Make the mosquito demography matrix for spatial RM model in continuous time
`compute_Omega(<xde>)`	Make the mosquito demography matrix for spatial RM model in continuous time
`compute_Omega(<dts>)`	Make the mosquito demography matrix for spatial RM model in continuous time
`compute_Upsilon()`	Make the mosquito demography matrix for spatial RM model in continuous time
`compute_Upsilon(<xde>)`	Make the mosquito demography matrix for spatial RM model in continuous time
`make_Omega()`	Make the mosquito demography matrix
`make_Omega(<xde>)`	Make the mosquito demography matrix
`make_Omega(<dts>)`	Make the mosquito demography matrix
`get_Omega()`	Make the mosquito demography matrix
`get_Upsilon()`	Make the mosquito demography matrix
EIP Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics
`F_eip()`	Compute the EIP
`d_F_eip_dt()`	Compute the derivative of the EIP as a function of time
`setup_EIP()`	Set up the fixed model for control forcing (do nothing)
`F_eip(<static>)`	Modify parameters due to exogenous forcing by all kinds of control
`d_F_eip_dt(<static>)`	This function computes the negative derivative of the EIP as a function of time
`F_eip(<fixedlag_dts>)`	Modify parameters due to exogenous forcing by all kinds of control
`setup_EIP(<fixedlag_dts>)`	Set up a fixedlag_dts model for the EIP
`setup_eip_fixedlag_dts()`	Set up a fixedlag_dts model for the EIP
trivial Specialized methods for NULL dynamics: a funtion generates values for F_eggs or F_fqZ or F_fqM
`F_fqZ(<trivial>)`	Blood feeding rate of the infective mosquito population
`F_fqM(<trivial>)`	Blood feeding rate of the infective mosquito population
`F_eggs(<trivial>)`	Number of eggs laid by adult mosquitoes
`dMYZdt(<trivial>)`	MYZ Component Derivatives for the `trivial` model
`MBaseline(<trivial>)`	Macdonald-style adult mosquito bionomics
`MBionomics(<trivial>)`	Macdonald-style adult mosquito bionomics
`Update_MYZt(<trivial>)`	Derivatives for aquatic stage mosquitoes
`setup_MYZpar(<trivial>)`	Setup the trivial
`get_MYZpars(<trivial>)`	Return the parameters as a list
`set_MYZpars(<trivial>)`	Return the parameters as a list
`set_MYZinits(<trivial>)`	Set new MYZ parameter values
`make_MYZpar_trivial()`	Make parameters for trivial aquatic mosquito model
`xde_steady_state_MYZ(<trivial>)`	Steady States: MYZ-trivial
`setup_MYZinits(<trivial>)`	Setup the trivial model
`setup_MYZix(<trivial>)`	Add indices for aquatic stage mosquitoes to parameter list
`parse_MYZorbits(<trivial>)`	Parse the output of deSolve and return variables for the trivial model
`get_MYZinits(<trivial>)`	Return initial values as a vector
`update_MYZinits(<trivial>)`	Update inits for trivial
basicM Specialized methods for basicM, a model of adult mosquito dynamics with no parasite infection dynamics.
`dMYZdt(<basicM>)`	MYZ Component Derivatives for `basicM`
`MBaseline(<basicM>)`	Set mosquito bionomics to baseline
`MBionomics(<basicM>)`	Set mosquito bionomics to baseline
`xde_steady_state_M(<basicM>)`	Compute the steady states as a function of the daily EIR
`Update_MYZt(<basicM>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<basicM>)`	Setup MYZpar for the basicM xde model
`F_fqZ(<basicM>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<basicM>)`	The net blood feeding rate of the mosquito population in a patch
`F_eggs(<basicM>)`	Number of eggs laid by adult mosquitoes
`setup_MYZinits(<basicM>)`	Setup the basicM model
`make_MYZinits_basicM()`	Make inits for basicM adult mosquito model
`setup_MYZix(<basicM>)`	Add indices for adult mosquitoes to parameter list
`list_MYZvars(<basicM>)`	Return the variables as a list
`get_MYZpars(<basicM>)`	Return the parameters as a list
`set_MYZpars(<basicM>)`	Return the parameters as a list
`set_MYZinits(<basicM>)`	Set new MYZ parameter values
`parse_MYZorbits(<basicM>)`	Parse outputs for basicM
`get_MYZinits(<basicM>)`	Return initial values as a vector
`update_MYZinits(<basicM>)`	Make inits for RM adult mosquito model
The “SI” model for infection Specialized methods for simple infection dynamics for an adult mosquito population
`dMYZdt(<SI>)`	MYZ Component Derivatives for the `SI` Mosquito Module
`MBaseline(<SI>)`	Macdonald-style adult mosquito bionomics
`MBionomics(<SI>)`	Macdonald-style adult mosquito bionomics
`xde_steady_state_MYZ(<SI>)`	Steady States: MYZ-SI
`Update_MYZt(<SI>)`	Derivatives for adult mosquitoes
`setup_MYZpar(<SI>)`	Setup MYZpar for the SI model
`make_MYZpar_SI()`	Make parameters for si ODE adult mosquito model
`F_fqZ(<SI>)`	Net Blood Feeding by Infectious Mosquitoes - `SI` Mosquito Model
`F_fqM(<SI>)`	\(\cal MYZ\) Component Net Blood Feeding by Mosquitoes for the `SI` Mosquito Model
`F_eggs(<SI>)`	\(\cal MYZ\) Component Egg Laying for the `SI` Mosquito Model
`list_MYZvars(<SI>)`	Return the variables as a list
`get_MYZpars(<SI>)`	Return the parameters as a list
`set_MYZpars(<SI>)`	Return the parameters as a list
`set_MYZinits(<SI>)`	Set new MYZ parameter values
`put_MYZvars(<SI>)`	Return the variables as a list
`setup_MYZinits(<SI>)`	Setup initial values for the `SI` model
`make_MYZinits_SI()`	Make inits for `SI` adult mosquito model
`setup_MYZix(<SI>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<SI>)`	Parse the output of deSolve and return variables for the `SI` model
`get_MYZinits(<SI>)`	Return initial values as a vector
`update_MYZinits(<SI>)`	Make inits for `SI` adult mosquito model
`get_f(<SI>)`	Get the feeding rate
`get_q(<SI>)`	Get the feeding rate
`get_g(<SI>)`	Get the feeding rate
`get_sigma(<SI>)`	Get the feeding rate
macdonald Specialized methods for a Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982).
`dMYZdt(<macdonald>)`	MYZ Component for the `macdonald` Adult Mosquito Module
`MBaseline(<macdonald>)`	macdonald-style adult mosquito bionomics
`MBionomics(<macdonald>)`	macdonald-style adult mosquito bionomics
`xde_steady_state_MYZ(<macdonald>)`	Compute the steady states as a function of the daily EIR
`setup_MYZpar(<macdonald>)`	Setup MYZpar for the macdonald model
`make_MYZpar_macdonald()`	Make parameters for macdonald ODE adult mosquito model
`list_MYZvars(<macdonald>)`	Return the variables as a list
`get_MYZpars(<macdonald>)`	Return the parameters as a list
`set_MYZpars(<macdonald>)`	Return the parameters as a list
`set_MYZinits(<macdonald>)`	Set new MYZ parameter values
`F_fqZ(<macdonald>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<macdonald>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<macdonald>)`	Number of eggs laid by adult mosquitoes
`setup_MYZinits(<macdonald>)`	Setup initial values for the macdonald model
`make_MYZinits_macdonald()`	Make inits for macdonald adult mosquito model
`get_MYZinits(<macdonald>)`	Return initial values as a list
`update_MYZinits(<macdonald>)`	Update inits for macdonald adult mosquito model
`setup_MYZix(<macdonald>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<macdonald>)`	Parse the output of deSolve and return variables for the macdonald model
`get_f(<macdonald>)`	Get the feeding rate
`get_q(<macdonald>)`	Get the feeding rate
`get_g(<macdonald>)`	Get the feeding rate
`get_sigma(<macdonald>)`	Get the feeding rate
GeRM Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982).
`dMYZdt(<GeRM>)`	MYZ Component Derivatives for the `GeRM` model
`MBaseline(<GeRM>)`	Set mosquito bionomics to baseline
`MBionomics(<GeRM>)`	Set mosquito bionomics to baseline
`Update_MYZt(<GeRM>)`	Derivatives for adult mosquitoes
`xde_steady_state_MYZ(<GeRM>)`	Compute the steady states as a function of the daily EIR
`setup_MYZpar(<GeRM>)`	Setup MYZpar for the GeRM model
`make_MYZpar_GeRM()`	Make parameters for GeRM ODE adult mosquito model
`list_MYZvars(<GeRM>)`	Return the variables as a list
`get_MYZpars(<GeRM>)`	Return the parameters as a list
`set_MYZpars(<GeRM>)`	Return the parameters as a list
`set_MYZinits(<GeRM>)`	Set new MYZ parameter values
`F_fqZ(<GeRM>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_fqM(<GeRM>)`	The net blood feeding rate of the infective mosquito population in a patch
`F_eggs(<GeRM>)`	Number of eggs laid by adult mosquitoes
`setup_MYZinits(<GeRM>)`	Setup initial values for the GeRM model
`make_MYZinits_GeRM()`	Make inits for GeRM adult mosquito model
`get_MYZinits(<GeRM>)`	Return initial values as a list
`update_MYZinits(<GeRM>)`	Update inits for GeRM adult mosquito model
`setup_MYZix(<GeRM>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<GeRM>)`	Parse the output of deSolve and return variables for the GeRM model
`get_f(<GeRM>)`	Get the feeding rate
`get_q(<GeRM>)`	Get the feeding rate
`get_g(<GeRM>)`	Get the feeding rate
`get_sigma(<GeRM>)`	Get the feeding rate
RM-Mosquito in discrete-time Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, in discrete time.
`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
`Update_MYZt(<RM_dts>)`	Derivatives for adult mosquitoes
`setup_MYZinits(<RM_dts>)`	Setup initial values for the RM_dts model
`list_MYZvars(<RM_dts>)`	Return the variables as a list
`put_MYZvars(<RM_dts>)`	Return the variables as a list
`make_MYZinits_RM_dts()`	Make inits for RM_dts adult mosquito model
`setup_MYZix(<RM_dts>)`	Add indices for adult mosquitoes to parameter list
`parse_MYZorbits(<RM_dts>)`	Parse the output of deSolve and return variables for the RM_dts model
`get_MYZinits(<RM_dts>)`	Return initial values as a vector
`update_MYZinits(<RM_dts>)`	Make inits for RM_dts adult mosquito model
Aquatic Mosquito Dynamics Generic methods for the aquatic (immature) mosquito component.
`dLdt()`	Derivatives for an L Component Module
`Update_Lt()`	Update State Variables for an L Component Module
`F_emerge()`	Compute Emergent Adults
`LBionomics()`	Bionomics for an L Component Module
`LBaseline()`	Baseline Bionomics for an L Component Module
`setup_Lpar()`	Set up `Lpar` for L Component modules
`get_Lpars()`	Get parameters for the L Component module
`set_Lpars()`	Set L Component Parameters
`setup_Linits()`	Setup Initial Values for the L Component
`list_Lvars()`	List L Component Variables
`update_Linits()`	Update L Component Initial Values
`set_Linits()`	Set L Component Initial Values
`get_Linits()`	Get Initial Values for the L Component
`setup_Lix()`	Set the Values of the Indices for L Component Modules
`parse_Lorbits()`	Parse L Component Outputs
`xde_steady_state_L()`	Compute steady states for L Component Modules
`dts_steady_state_L()`	Compute steady States for L Component Modules
trivial Specialized methods for the exogeneously forced trivial model of aquatic mosquito dynamics.
`dLdt(<trivial>)`	Derivatives for `trivial` (L Component)
`Update_Lt(<trivial>)`	Update State Variables for `trivial` (L Component)
`F_emerge(<trivial>)`	Compute Emergent Adults for `trivial` (L Component)
`LBionomics(<trivial>)`	Bionomics for `trivial` (L Component)
`LBaseline(<trivial>)`	Baseline Bionomics for `trivial` (L Component)
`setup_Lpar(<trivial>)`	Setup `Lpar` for the `trivial` module
`make_Lpar_trivial()`	Make `Lpar` for `trivial` (L Component)
`get_Lpars(<trivial>)`	Get L Component Parameters for `trivial`
`set_Lpars(<trivial>)`	Set L Component parameters for `trivial`
`setup_Linits(<trivial>)`	Setup Initial Values for the L Component `trivial` Module
`list_Lvars(<trivial>)`	List L Component Variables for `trivial`
`set_Linits(<trivial>)`	Set the Initial Values for `trivial` (L Component)
`update_Linits(<trivial>)`	Update Initial Values for `basicL` from a state vector `y`
`setup_Lix(<trivial>)`	Setup Variable Indices for `trivial` (L Component)
`parse_Lorbits(<trivial>)`	Parse L Component Variables for `basicL`
`xde_steady_state_L(<trivial>)`	Compute the Steady State of `dLdt.trivial` (L Component)
basicL Specialized methods for a basicL competition model of aquatic mosquito dynamics.
`dLdt(<basicL>)`	Derivatives for `basicL` (L Component)
`Update_Lt(<basicL>)`	Update State Variables for `basicL` (L Component)
`setup_Lpar(<basicL>)`	Setup `Lpar` for `basicL` (L Component)
`make_Lpar_basicL()`	Make `Lpar` for `basicL` (L Component)
`LBionomics(<basicL>)`	Bionomics for `basicL` (L Component)
`LBaseline(<basicL>)`	Baseline Bionomics for `basicL` (L Component)
`F_emerge(<basicL>)`	Compute Emergent Adults for `basicL` (L Component)
`setup_Linits(<basicL>)`	Setup Initial Values for `basicL` (L Component)
`make_Linits_basicL()`	Make Initial Values for `basicL` (L Component)
`list_Lvars(<basicL>)`	List L Component Variables for `basicL`
`get_Lpars(<basicL>)`	Get L Component Parameters for `basicL`
`set_Lpars(<basicL>)`	Set L Component parameters for `basicL`
`set_Linits(<basicL>)`	Set the Initial Values for `basicL` (L Component)
`setup_Lix(<basicL>)`	Setup Variable Indices for `basicL` (L Component)
`parse_Lorbits(<basicL>)`	Parse L Component Variables for `basicL`
`update_Linits(<basicL>)`	Update Initial Values for `basicL` from a state vector `y`
`xde_steady_state_L(<basicL>)`	Compute the Steady State of `dLdt.basicL` (L Component)
Mosquito Bionomics Methods to compute or update mosquito bionomic parameters
`Bionomics()`	Set bionomic parameter rates relative to baseline
Functional Responses Compute bionomic parameters as functional responses to resource availability
`F_f()`	Compute the blood feeding rate, f
`F_q()`	Compute the human blood fraction
`F_g()`	Compute mosguito survival
`F_p()`	Compute the human blood fraction
`F_sigma()`	Compute mosquito emigration rates
`F_mu()`	Compute the emigration loss
`F_nu()`	Compute the egg laying rate
`F_calK()`	Compute the egg laying rate
`F_f(<static>)`	Static model for the blood feeding rate
`F_q(<static>)`	Static model for human blood fraction
`F_g(<static>)`	Static model for mosquito survival
`F_sigma(<static>)`	Static model for mosquito emigration
`F_mu(<static>)`	Static model for mosquito survival
`F_nu(<static>)`	Static model for the egg laying rate
`F_calK(<static>)`	Static model for mosquito emigration
`F_sigma(<BQS>)`	Model for mosquito emigration based on resource availability
`F_nu(<type2>)`	Type 2 functional response for the blood feeding rate
`F_f(<type2>)`	Type 2 functional response for the blood feeding rate
`F_q(<dynamic>)`	Static model for human blood fraction
Mosquito Dispersal Specialized methods to set up mosquito dispersal matrices
`change_calK()`	Change the time spent matrix
`make_calK()`	Make a mosquito dispersal matrix, called calK
`make_calK(<herethere>)`	Dispersal to every other patch, with equal probability
`create_calK_herethere()`	Develop a mosquito dispersal matrix from a kernel and xy-coordinates
`make_calK(<as_matrix>)`	Pass a pre-configured calK
`make_calK(<xy>)`	Develop a mosquito dispersal matrix from a kernel and xy-coordinates
`create_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()`	Compute Derivatives for an \(\cal X\) - Component Model
`Update_Xt()`	Update X states for a discrete time system
`setup_Xinits()`	A function to set up Xpar
`setup_Xix()`	Add indices for human population to parameter list
`list_Xvars()`	Return the variables as a list
`get_Xpars()`	Return the parameters as a list
`set_Xpars()`	Set new X parameter values
`put_Xvars()`	Put Xvars in place of the X variables in y
`setup_Xpar()`	Make Parameters for a \(cal X\) - Component Model
`F_X()`	Size of effective infectious human population
`F_H()`	Size of human population denominators
`F_b()`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits()`	Parse the output of deSolve and return the variables by name in a list
`get_Xinits()`	Return initial values as a vector
`set_Xinits()`	Set new X parameter values
`update_Xinits()`	Set the initial values from a vector of states
`HTC()`	Compute the human transmitting capacity
`F_pr()`	Compute the true prevalence of infection / parasite rate
`F_pr_by_lm()`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt()`	Compute the prevalence of infection by RDT
`F_pr_by_pcr()`	Compute infection prevalence by PCR
`xds_plot_X()`	Basic plotting for epidemiological models
`xde_steady_state_X()`	Steady States for \(\cal X\)-Models
`xde_steady_state_XH()`	Steady States for \(\cal XH\)-Models
`dts_steady_state_X()`	Compute the steady states as a function of the daily EIR
trivial Specialized methods for a human trivial model to pass kappa as a parameter
`F_X(<trivial>)`	Size of effective infectious human population
`F_H(<trivial>)`	Size of the human population
`F_pr(<trivial>)`	Compute the "true" prevalence of infection / parasite rate
`xde_steady_state_X(<trivial>)`	Compute the steady states for the trivial model as a function of the daily EIR
`F_pr_by_lm(<trivial>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<trivial>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<trivial>)`	Compute the prevalence of infection by PCR
`F_b(<trivial>)`	Infection blocking pre-erythrocytic immunity
`dXdt(<trivial>)`	X Component Derivatives for the `trivial` model
`Update_Xt(<trivial>)`	Update States for the `trivial` \(\cal X\) Model
`setup_Xpar(<trivial>)`	xde_setup Xpar.trivial
`make_Xpar_trivial()`	Make parameters for trivial human model
`setup_Xinits(<trivial>)`	Setup Xinits.trivial
`setup_Xix(<trivial>)`	Add indices for human population to parameter list
`parse_Xorbits(<trivial>)`	Parse the output of deSolve and return variables for the trivial model
`get_Xinits(<trivial>)`	Return initial values as a vector
`set_Xinits(<trivial>)`	Return the parameters as a list
`get_Xpars(<trivial>)`	Return the parameters as a list
`set_Xpars(<trivial>)`	Return the parameters as a list
`update_Xinits(<trivial>)`	Update inits for the trivial human model from a vector of states
hMoI Specialized methods for a hybrid model of MoI (Multiplicity of Infection) for human infection dynamics.
`dXdt(<hMoI>)`	X Component Derivatives for the `hMoI` module
`setup_Xpar(<hMoI>)`	Setup Xpar.hMoI
`make_Xpar_hMoI()`	Make parameters for hybrid MoI human model
`xde_steady_state_X(<hMoI>)`	Steady States: hMoI
`setup_Xinits(<hMoI>)`	Setup Xinits.hMoI
`make_Xinits_hMoI()`	Make inits for hybrid MoI human model
`setup_Xix(<hMoI>)`	Add indices for human population to parameter list
`F_X(<hMoI>)`	Size of effective infectious human population
`F_H(<hMoI>)`	Size of the human population
`F_b(<hMoI>)`	Infection blocking pre-erythrocytic immunity
`F_pr(<hMoI>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<hMoI>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<hMoI>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<hMoI>)`	Compute the prevalence of infection by PCR
`parse_Xorbits(<hMoI>)`	Parse the output of deSolve and return variables for the hMoI model
`get_Xinits(<hMoI>)`	Return initial values as a vector
`set_Xinits(<hMoI>)`	Return the parameters as a list
`get_Xpars(<hMoI>)`	Return the parameters as a list
`set_Xpars(<hMoI>)`	Return the parameters as a list
`update_Xinits(<hMoI>)`	Update inits for hybrid MoI human model from a vector of states
`HTC(<hMoI>)`	Compute the HTC for the hMoI model
SIS Specialized methods for the SIS (Susceptible-Infected-Susceptible) model of human dynamics.
`dXdt(<SIS>)`	X Component Derivatives for the `SIS` Model
`Update_Xt(<SIS>)`	DTS updating for the SIS model for human / vertebrate host infections
`setup_Xpar(<SIS>)`	Setup Xpar.SIS
`make_Xpar_SIS()`	Make parameters for SIS xde human model, with defaults
`setup_Xinits(<SIS>)`	Setup Xinits.SIS
`make_Xinits_SIS()`	Make initial values for the SIS xde human model, with defaults
`setup_Xix(<SIS>)`	Add indices for human population to parameter list
`list_Xvars(<SIS>)`	Return the variables as a list
`get_Xpars(<SIS>)`	Return the parameters as a list
`set_Xpars(<SIS>)`	Return the parameters as a list
`put_Xvars(<SIS>)`	Return the SIS model variables as a list, returned from Update_Xt.SIS
`F_X(<SIS>)`	Size of effective infectious human population
`F_H(<SIS>)`	Size of effective infectious human population
`F_b(<SIS>)`	Infection blocking pre-erythrocytic immunity
`parse_Xorbits(<SIS>)`	Parse the output of deSolve and return variables for the SIS model
`get_Xinits(<SIS>)`	Return initial values as a vector
`set_Xinits(<SIS>)`	Return the parameters as a list
`update_Xinits(<SIS>)`	Update inits for the SIS xde human model from a vector of states
`HTC(<SIS>)`	Compute the HTC for the SIS model
`F_pr(<SIS>)`	Compute the "true" prevalence of infection / parasite rate
`F_pr_by_lm(<SIS>)`	Compute the prevalence of infection by light microscopy
`F_pr_by_rdt(<SIS>)`	Compute the prevalence of infection by RDT
`F_pr_by_pcr(<SIS>)`	Compute the prevalence of infection by PCR
`xds_plot_X(<SIS>)`	Plot the density of infected individuals for the SIS model
`add_lines_X_SIS()`	Add lines for the density of infected individuals for the SIS model
`xde_steady_state_X(<SIS>)`	Compute the steady states for the SIS model as a function of the daily EIR
`dts_steady_state_X(<SIS>)`	Compute the steady states for the dts SIS model as a function of the daily EIR
Human Population Dynamics 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
`Births(<zero>)`	Derivatives of demographic changes in human populations
`dHdt(<zero>)`	Compute Demographic Changes
`Births(<static>)`	Derivatives of demographic changes in human populations
`setup_births_static()`	Setup a static birth_rate
`dHdt(<matrix>)`	Derivatives of demographic changes in human populations
`setup_Hmatrix()`	Setup a matrix for `dHdt`
Care Seeking Methods to implement care seeking
`CareSeeking()`	Set the values of exogenous variables describing care seeking
`CareSeeking(<no_behavior>)`	Set the values of exogenous variables describing care seeking
`setup_care_seeking_no_behavior()`	Make parameters for the no_behavior model for care seeking (do nothing)
Imported Malaria Methods to implement time spent traveling
`traveling()`	Time Spent Traveling
`traveling(<static>)`	Time Spent Traveling
`traveling(<setup>)`	Time Spent Traveling
`traveling(<dynamic>)`	Time Spent Traveling
`setup_no_travel()`	Set up no travel
`setup_static_travel()`	Set up static travel
`setup_dynamic_travel()`	Set up a dynamic model for travel
`Visiting()`	Visiting
Travel Malaria Model the EIR while traveling
`travel_eir()`	Travel EIR
`setup_travel_eir()`	Setup Travel EIR
Visiting Methods for the availability and infectiousness of a visitor population
`Visiting(<static>)`	Visiting, a static model
`setup_visitors_static()`	Make parameters for the static model visitors (no visitors)
`Visiting(<basic>)`	Visiting, the basic model
`setup_visitors_basic()`	Make parameters and functions for the basic model for visitors
Exogeneous Forcing Methods to implement exogeneous forcing.
`Exogenous()`	Compute Derivatives
`Forcing()`	Set the values of exogenous variables
`Weather()`	Set the values of exogenous variables describing weather
`Rainfall()`	Set the rainfall
`Shock()`	System Shocks
`Health()`	Set the values variables for health interventions
`VectorControl()`	Implement Vector Control
`Clinic()`	Methods for distributing interventions during clinical visits
`Development()`	Set the development
`MassHealth()`	Methods for mass distributing health interventions
Forcing Specialized methods the null model (no exogenous forcing)
`Forcing()`	Set the values of exogenous variables
`Forcing(<none>)`	Set the values of exogenous variables
`setup_no_forcing()`	none set up for exogenous forcing
`Forcing(<dynamic>)`	Set the values of exogenous variables
`Forcing(<setup>)`	The `setup` case for exogenous forcing
`dynamic_forcing()`	Set up dynamic forcing
`dynamic_forcing(<none>)`	Set up dynamic forcing
`dynamic_forcing(<setup>)`	Set up dynamic forcing
`dynamic_forcing(<dynamic>)`	Set up dynamic forcing
Models Specialized methods the null model (no exogenous forcing)
`Shock(<none>)`	Set no shock
`setup_no_shock()`	Set up "no shock"
`Development(<none>)`	Set no development
`Development(<func>)`	Set no development
`setup_no_development()`	Set up "no development"
`Health(<none>)`	Set no exogenous health variables
`setup_no_health()`	none set up for exogenous health
Weather Specialized methods for weather
`Weather()`	Set the values of exogenous variables describing weather
`Weather(<none>)`	Methods for exogenous variables describing weather
`Weather(<dynamic>)`	Methods for exogenous variables describing weather
`setup_no_weather()`	Set up the no_forcing model for weather
`dynamic_weather()`	Set up dynamic weather
`dynamic_weather(<none>)`	Set up dynamic weather
`dynamic_weather(<setup>)`	Set up dynamic weather
`dynamic_weather(<dynamic>)`	Set up dynamic weather
Temperature Specialized methods for temperature
`Temperature()`	Set the temperature
`Temperature(<none>)`	Set no temperature
`setup_no_temperature()`	Set up "no temperature"
`setup_temperature()`	Set up dynamic forcing
`Temperature(<func>)`	Set no temperature
`setup_temperature(<func>)`	Set up dynamic forcing
`setup_temperature_func()`	Set up dynamic forcing
Rainfall Specialized methods for rainfall
`Rainfall()`	Set the rainfall
`Rainfall(<none>)`	Set no rainfall
`setup_no_rainfall()`	Set up "no rainfall"
`setup_rainfall()`	Set up dynamic forcing
`Rainfall(<func>)`	Set no rainfall
`setup_rainfall(<func>)`	Set up dynamic forcing
`setup_rainfall_func()`	Set up dynamic forcing
Humidity Specialized methods for humidity
`Humidity()`	Set the humidity
`Humidity(<none>)`	Set no humidity
`setup_no_humidity()`	Set up "no humidity"
`setup_humidity()`	Set up dynamic forcing
`Humidity(<func>)`	Set no humidity
`setup_humidity(<func>)`	Set up dynamic forcing
`setup_humidity_func()`	Set up dynamic forcing
Hydrology Specialized methods for hydrology
`Hydrology()`	Set the hydrology
`Hydrology(<none>)`	Set no hydrology
`setup_no_hydrology()`	Set up "no hydrology"
`Hydrology(<func>)`	Set no hydrology
`setup_hydrology()`	Set up dynamic forcing
`setup_hydrology(<func>)`	Set up dynamic forcing
`setup_hydrology_func()`	Set up dynamic forcing
Shock Specialized methods for hydrology
`Shock()`	System Shocks
`Shock(<none>)`	Set no shock
`setup_no_shock()`	Set up "no shock"
`setup_shock()`	Set up dynamic forcing
`Shock(<func>)`	Set no shock
`setup_shock(<func>)`	Set up dynamic forcing
`setup_shock_func()`	Set up dynamic forcing
Development Specialized methods for hydrology
`Development()`	Set the development
`Development(<none>)`	Set no development
`setup_no_development()`	Set up "no development"
`setup_development()`	Set up dynamic forcing
`Development(<func>)`	Set no development
`setup_development(<func>)`	Set up dynamic forcing
`setup_development_func()`	Set up dynamic forcing
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_static()`	Set up parameters for the static 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
`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()`	Implement Vector Control
`VectorControl(<none>)`	Implement No Vector Control
`VectorControl(<dynamic>)`	Implement Some Vector Control
`VectorControl(<setup>)`	Vector Control for Static Vector Control
`VectorControlEffectSizes()`	Vector control effect sizes
`VectorControlEffectSizes(<none>)`	Set the values of exogenous variables
`VectorControlEffectSizes(<dynamic>)`	Distribute vector control, the null model
`setup_no_vector_control()`	Setup Function for No Vector Control (default)
`dynamic_vector_control()`	Turn On Vector Control
`dynamic_vector_control(<none>)`	Turn On Vector Control
`dynamic_vector_control(<setup>)`	Vector Control is Turned On
`dynamic_vector_control(<dynamic>)`	Vector Control is Turned On
Bed Nets Specialized methods to implement Bed Nets
`BedNet()`	Set the bednet
`BedNet(<none>)`	Set no bednet
`BedNetEffectSizes()`	Set the bednet_effectsizes
`BedNetEffectSizes(<none>)`	Set no bednet_effectsizes
`setup_no_bednets()`	Set up "no bednet"
Indoor Residual Spraying Methods to implement IRS
`IRS()`	Implement IRS
`IRS(<none>)`	Set no irs
`IRSEffectSizes()`	Set the irs_effectsizes
`IRSEffectSizes(<none>)`	Set no irs_effectsizes
`setup_no_irs()`	Set up "no irs"
Larval Source Management (LSM) Methods to implement LSM
`LSM()`	Set the LSM
`LSM(<none>)`	Set no LSM
`setup_no_lsm()`	Set up "no LSM"
Area Spraying Methods to implement area spraying
`AreaSpray()`	Set the AreaSpray
`AreaSpray(<none>)`	Set no AreaSpray
`setup_no_area_spray()`	Set up "no AreaSpray"
Sugar Baits Methods to implement sugar baits
`SugarBaits()`	Set the SugarBaits
`SugarBaits(<none>)`	No sugar baits
`setup_no_sugar_baits()`	Set up no sugar baits
Ovitraps Specialized methods for ovitraps
`OviTraps()`	Methods for oviposition traps
`OviTraps(<none>)`	Methods for oviposition traps
`setup_no_ovitraps()`	Set up the none model for oviposition traps (do nothing)
Health Methods to implement health-based Interventions
`Health()`	Set the values variables for health interventions
`Health(<none>)`	Set no exogenous health variables
`setup_no_health()`	none set up for exogenous health
`Health(<dynamic>)`	Set the values of exogenous variables
`Health(<setup>)`	The `setup` case for health variables
`dynamic_health()`	Set up dynamic health
`dynamic_health(<none>)`	Set up dynamic health
`dynamic_health(<setup>)`	Set up dynamic health
`dynamic_health(<dynamic>)`	Set up dynamic health
Clinic Methods to implement clinic-based interventions
`Clinic()`	Methods for distributing interventions during clinical visits
`Clinic(<none>)`	Methods for distributing interventions during clinical visits
`setup_no_clinic()`	Set up the none model for clinical distribution (do nothing)
School Methods to implement school-based interventions
`School()`	Methods for distributing interventions during schoolal visits
`School(<none>)`	Methods for distributing interventions during schoolal visits
`setup_no_school()`	Set up the none model for schoolal distribution (do nothing)
MassHealth Methods to implement clinic-based interventions
`MassHealth()`	Methods for mass distributing health interventions
`MassHealth(<none>)`	Methods for distributing interventions during mass_healthal visits
`setup_no_mass_health()`	Set up the none model for mass_healthal distribution (do nothing)
ActiveCaseDetection Methods to implement clinic-based interventions
`ActiveCaseDetection()`	Methods for mass distributing health interventions
`ActiveCaseDetection(<none>)`	Methods for distributing interventions during active_case_detectional visits
`setup_no_active_case_detection()`	Set up the none model for active_case_detectional distribution (do nothing)
Solving Methods to compute the derivatives and solve the equat
Derivatives
`xde_derivatives()`	Compute Derivatives
`xde_derivatives(<full>)`	Generalized spatial differential equation model
`xde_derivatives(<aquatic>)`	Differential equation models for aquatic mosquito populations
`xde_derivatives(<mosy>)`	Generalized spatial differential equation model (mosquito only)
`xde_derivatives(<human>)`	Differential equations isolating the humans, forced with Ztrace
Cohort Dynamics
`xds_solve_cohort()`	Cohort dynamics for a human / host model
`xde_cohort_derivatives()`	Differential equation models for human cohorts
`xde_cohort_desolve()`	Solve a system of equations as an ode
`xde_cohort_desolve(<dde>)`	Solve a system of equations as a dde
`xde_cohort_desolve(<ode>)`	Solve a system of equations as a ode
Update
`dts_update()`	dts_update_ States for Discrete-Time Systems
`dts_update(<full>)`	Generalized spatial differential equation model
`dts_update(<aquatic>)`	Difference equation models for aquatic mosquito populations
`dts_update(<mosy>)`	Generalized spatial differential equation model (mosquito only)
`dts_update(<human>)`	Difference equations isolating the humans, forced with Ztrace
`dts_update(<cohort>)`	Difference equation models for human cohorts
`dts_update_Lt()`	Difference equations isolating the humans, forced with Ztrace
`dts_update_MYZt()`	Difference equations isolating the humans, forced with Ztrace
`dts_update_Xt()`	Difference equations isolating the humans, forced with Ztrace
`Update_Xt()`	Update X states for a discrete time system
`Update_MYZt()`	Derivatives for adult mosquitoes
`Update_Lt()`	Update State Variables for an L Component Module
Exogenous Forcing
`Exogenous()`	Compute Derivatives
`Exogenous(<full>)`	Generalized spatial differential equation model
`Exogenous(<aquatic>)`	Differential equation models for aquatic mosquito populations
`Exogenous(<mosy>)`	Generalized spatial differential equation model (mosquito only)
`Exogenous(<human>)`	Differential equations isolating the humans, forced with Ztrace
Solving Wrappers around the derivatives functions that handle time and parse outputs
`xds_solve()`	Solve a system of differential equations
`xds_solve(<dde>)`	Solve a system of equations using deSolve::dede
`xds_solve(<ode>)`	Solve a system of equations using deSolve::ode
`xds_solve(<dts>)`	Solve a discrete-time system
`xde_stable_orbit()`	Compute the stable orbit for a system of differential equations
`xde_steady()`	Solve for the steady state of a system of equations using rootSolve::steady
`xde_steady(<ode>)`	Solve for the steady state of a system of equations using rootSolve::steady
`xde_steady(<dde>)`	Solve for the steady state of a system of equations using rootSolve::steady
`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)
Metric Conversions
`fqZ2eir()`	Convert a vector describing infective biting density into the EIR, \(E\)
`eir2fqZ()`	Convert the EIR into a vector describing infective biting density
Compute terms Methods to compute and transmission terms
`parse_orbits()`	Parse the outputs of an object created by xde_solve or dts_solve
`parse_y()`	Parse the output of an object returned by deSolve
`reset_state_i()`	Compute other variables at time t
`reset_state()`	Compute other variables at time t
`reset_state(<full>)`	Compute other variables at time t
`reset_state(<aquatic>)`	Compute other variables at time t
`reset_state(<mosy>)`	Compute other variables at time t
`reset_state(<cohort>)`	Compute other variables at time t
`reset_state(<human>)`	Compute other variables at time t
Plot terms Basic visualization of the transmission terms
`xds_plot_EIR()`	Plot the EIR vs. time
`xds_plot_aEIR()`	Plot the annualized EIR vs. time
`xds_lines_EIR()`	Add lines for the EIR vs. time
`xds_plot_PR()`	Plot the prevalence / parasite rate (PR) from a model of human infection and immunity
`xds_lines_PR()`	Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity
Functions and Utilities stuff that is generally useful
Runtime Basic visualization of the transmission terms
`runt()`	A run-time switch function for mismatched dynamical component run-times
`set_Dday()`	Set up a model for dts_diffeqn
`make_runtime()`	Set up run-time time step support for `dts` models
`make_runtime(<dts>)`	Set up run-time time step support for `dts` models
`make_runtime(<xde>)`	Set up run-time time step support for `xde` models
Utilities Utilities
`trigger_setup()`	Trigger `setup`
`trigger_setup(<static>)`	Trigger `setup`
`trigger_setup(<setup>)`	Trigger `setup`
`trigger_setup(<dynamic>)`	Trigger `setup`
`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
`list_vars()`	Set the initial values to the last values of the last simulation
`xds_flatten()`	Set the initial values to the last values of the last simulation
`xds_dde()`	Set `xds` to `dde`
`xds_dde(<ode>)`	Set `xds` to `dde`
`xds_dde(<dde>)`	Set `xds` for `dde`
`xds_dde(<dts>)`	Set `xds` for `dts`
Functions Basic visualization of the transmission terms
`F_zero()`	The trivial function
`F_one()`	The trivial function
`F_flat()`	The trivial function
`make_function()`	Make a Function
`make_function(<sin>)`	Make a Sine-based Seasonality Function
`makepar_F_sin()`	parameters for make_function
`make_function(<sum>)`	Make a Function that is the sum of Two other Functions
`makepar_F_sum()`	parameters for make_function
`make_function(<product>)`	Make a Sinusoidal Function
`makepar_F_product()`	parameters for make_function
`make_function(<sigmoid>)`	Make a Sigmoidal Function
`makepar_F_sigmoid()`	Make Parameters for a Sigmoidal Function
`make_function(<sharkfin>)`	Make a Sharkfin Function
`makepar_F_sharkfin()`	Make Parameters for a Sharkfin Function
New Basic visualization of the transmission terms
`F_ni()`	Compute Net Infectiousness (NI)
`F_ni(<SIS>)`	Compute the net infectiousness
`F_ni(<hMoI>)`	Compute the "true" nievalence of infection / parasite rate
`get_bionomics()`	Compute dynamical terms
`get_bionomics_s()`	Compute dynamical terms
`get_bionomics_s_t()`	Compute dynamical terms
`get_ft()`	Get the feeding rate
`get_qt()`	Get the human fraction
`get_gt()`	Get the mosquito mortality rate
`get_sigmat()`	Get the mosquito emigration rate
`get_f()`	Get the feeding rate
`get_f(<GeRM>)`	Get the feeding rate
`get_f(<trivial>)`	Get the feeding rate
`get_q()`	Get the feeding rate
`get_q(<GeRM>)`	Get the feeding rate
`get_q(<trivial>)`	Get the feeding rate
`get_g()`	Get the feeding rate
`get_g(<GeRM>)`	Get the feeding rate
`get_g(<trivial>)`	Get the feeding rate
`get_sigma()`	Get the feeding rate
`get_sigma(<GeRM>)`	Get the feeding rate
`get_sigma(<trivial>)`	Get the feeding rate
`make_outputs()`	Make Outputs
`make_outputs(<full>)`	Make Outputs
`make_outputs(<mosy>)`	Make Outputs
`make_outputs(<aquatic>)`	Make Outputs
`make_outputs(<human>)`	Make Outputs
`get_terms()`	Compute dynamical terms
`get_EIR()`	Get the feeding rate

Reference

Model Building & Analysis

Build / Setup

Solve and Analyze

Models – Human / Host

Models – Adult Mosquito

Models – Aquatic Mosquito

Interface

Change Parameters & Initial Values

Examine

Blood Feeding and Transmission

Blood Feeding

Transmision

Time Spent

Egg Laying & Emergence

Exposure

Poisson Exposure

Negative Binomial Exposure

Adult Mosquito Dynamics

Visualization for Adult Mosquito

Mosquito Demography

EIP

trivial

basicM

The “SI” model for infection

macdonald

GeRM

RM-Mosquito in discrete-time

Aquatic Mosquito Dynamics

trivial

basicL

Mosquito Bionomics

Functional Responses

Mosquito Dispersal

Human Infection Dynamics

trivial

hMoI

SIS

Human Population Dynamics

Care Seeking

Imported Malaria

Travel Malaria

Visiting

Exogeneous Forcing

Forcing

Models

Weather

Temperature

Rainfall

Humidity

Hydrology

Shock

Development

Resource Dynamics

Other Blood Hosts

Habitat Dynamics and Availability

Sugar

Vector Control

Bed Nets

Indoor Residual Spraying

Larval Source Management (LSM)

Area Spraying

Sugar Baits

Ovitraps

Health

Clinic

School

MassHealth

ActiveCaseDetection

Solving

Derivatives

Cohort Dynamics

Update

Exogenous Forcing

Solving

Analysis and Visualization

Spatial metrics

Metric Conversions

Compute terms

Plot terms