Package index • ramp.xds

Model Building

Set up & Modify Models

Basic Setup

Build and store xds model objects

xds_setup(): Build a Model and Configure All Components
xds_setup_mosy(): Build a Model of Mosquito Ecology
xds_setup_aquatic(): Build a Model of Immature Mosquito Ecology
xds_setup_human(): Build a Model of Human / Host Epidemiology
xds_setup_eir(): Build a Model for a single Human / Host Epidemiology forced by the EIR
saveXDS(): saveRDS for xds Objects
readXDS(): readRDS for xds Objects

Advanced Setup

Modules for aquatic mosquito ecology

setup_exposure(): Set Up Exposure
setup_travel_object(): Setup the Travel Object
change_K_matrix(): Change Mosquito Dispersal Matrix
change_TimeSpent_matrix(): Set up (or change) a Time Spent matrix
add_variable(): Add Variable

Solve - Analyze - Visualize

Methods to solve or equations

Solving

xds_solve(): Solve a Dynamical System
burnin(): Burn In
get_XH_out(): Get XH outputs
get_MY_out(): Get MY outputs
get_L_out(): Get L outputs

Analysis

Compute Steady States & Stable Orbits

xds_steady(): Solve for the steady state of a system of equations using rootSolve::steady
xds_stable_orbit(): Compute stable orbits
steady_state_X(): Steady States for X
steady_state_XH(): Steady States for XH
steady_state_M(): Compute steady states for M
steady_state_MY(): Compute steady states for MY
steady_state_Y(): Compute steady states for Y
steady_state_L(): Compute steady states for L Component Modules

Visualization

Visualize Outputs

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
xds_plot_EIR(): Plot the EIR vs. time
xds_lines_EIR(): Add lines for the EIR vs. time
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

Working with Models

Get Parameters

Get model parameters

get_XH_pars(): Return the parameters as a list
get_MY_pars(): Return the parameters as a list
get_mean_forcing(): Get mean forcing
get_season(): Get the Seasonal Pattern
get_trend(): Get the trend parameters
get_TimeSpent_matrix(): Get the Time Spent Matrix
get_K_matrix(): Get the Mosquito Dispersal Matrix

Change Parameters

Change parameters

change_XH_pars(): Set new X parameter values
change_MY_pars(): Set new MY parameter values
change_L_pars(): Set L Component Parameters
change_H(): Change human population density
change_mean_forcing(): Set mean forcing
change_season(): Get seasonal pattern
change_trend(): Set the interpolating points
change_TimeSpent_matrix(): Set up (or change) a Time Spent matrix
change_K_matrix(): Change Mosquito Dispersal Matrix

Show

Show patterns for forced systems

show_season(): Plot the seasonal pattern
show_trend(): Plot the Temporal Trend

Blood Feeding & Transmission

Methods to compute terms describing blood feeding and transmission

check_XY_interface(): Check the XY Interface
make_residency_matrix(): Create the Residency Matrix
view_residency_matrix(): View residence membership

Time Spent

Set up Time Spent Matrices

change_TimeSpent_matrix(): Set up (or change) a Time Spent matrix
get_TimeSpent_matrix(): Get the Time Spent Matrix
setup_TimeSpent(): Make a time spent matrix, called TimeSpent
make_TimeSpent_athome(): Make a mosquito dispersal matrix, called TimeSpent
make_TimeSpent_xy(): Make a mosquito dispersal matrix, called TimeSpent

Exposure

Environmental Heterogeneity

setup_exposure(): Set Up Exposure
foi2eir(): Convert FoI to EIR
ar2eir(): Convert AR to EIR
make_exposure_pois(): Make a Poisson Exposure Model Object
make_exposure_nb(): Make a nbson Exposure Model Object

Habitats & Egg Laying

Mosquito Population Dynamic Interface

view_habitat_matrix(): View habitat membership, \(N\)
change_habitat_weights(): Change Habitat Search Weights
change_bad_habitat(): Change Habitat Search Weights

XH Component

Models of human / host infection dynamics - immunity - disease - infectiousness - diagnostics and detection

skill_set_XH(): XH Skill Set
check_XH(): Check / update before solving
get_XH_vars(): Get Variables by Name
get_XH_pars(): Return the parameters as a list
change_XH_pars(): Set new X parameter values
get_XH_inits(): A function to set up XH_obj
change_XH_inits(): Set new X parameter values
get_HTC(): Compute the human transmitting capacity
F_prevalence(): Compute the true prevalence of infection / parasite rate
F_pfpr_by_pcr(): Compute infection prevalence by PCR
xds_plot_X(): Basic plotting for epidemiological models
xds_plot_XH(): Basic plotting for epidemiological models
steady_state_X(): Steady States for X
steady_state_XH(): Steady States for XH

trivial

Specialized methods the trivial human model

skill_set_XH(<trivial>): The XH Module Skill Set
check_XH(<trivial>): Check / update before solving
F_prevalence(<trivial>): Compute the "true" prevalence of infection / parasite rate
F_pfpr_by_pcr(<trivial>): Compute the prevalence of infection by PCR
make_XH_obj_trivial(): Make parameters for trivial human model
get_XH_pars(<trivial>): Return the parameters as a list
change_XH_pars(<trivial>): Return the parameters as a list

hMoI

A hybrid model of MoI (Multiplicity of Infection) for human infection dynamics.

skill_set_XH(<hMoI>): The XH Module Skill Set
make_XH_obj_hMoI(): Make parameters for hybrid MoI human model
steady_state_X(<hMoI>): Compute Steady States for hMoI (X-Model)
make_XH_inits_hMoI(): Make inits for hybrid MoI human model
F_prevalence(<hMoI>): Compute the "true" prevalence of infection / parasite rate
F_pfpr_by_pcr(<hMoI>): Compute the prevalence of infection by PCR
change_XH_inits(<hMoI>): Return the parameters as a list
get_XH_pars(<hMoI>): Return the parameters as a list
change_XH_pars(<hMoI>): Return the parameters as a list
check_XH(<hMoI>): Check / update before solving
get_XH_vars(<hMoI>): Get Variables by Name

SIS

“The SIS (Susceptible-Infected-Susceptible) model of human dynamics”

change_XH_inits(<SIS>): SIS - Change Initial Values
change_XH_pars(<SIS>): Set new values for the SIS model
get_XH_pars(<SIS>): Get SIS module parameters

Human Population Dynamics

Methods for the human demography and aging

Births(): Human (or Host) Population Birth Rate
Births(<zero>): Human (or Host) Population Birth Rate

MY Component

Adult mosquito ecology and infection dynamics

skill_set_MY(): The MY Module Skill Set
check_MY(): Run a check before solving
F_fqM(): Blood feeding rate of the mosquito population
get_MY_vars(): Return the variables as a list
get_MY_pars(): Return the parameters as a list
change_MY_pars(): Set new MY parameter values
get_MY_inits(): Return initial values as a vector
change_MY_inits(): Set new MY parameter values
get_MY_ix(): Get MY Variable Indices
steady_state_MY(): Compute steady states for MY
steady_state_Y(): Compute steady states for Y
steady_state_M(): Compute steady states for M
get_M(): Get mosquito population density
get_Z(): Get the density of infectious, blood feeding mosquitoes

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

setup_Omega(): Make the mosquito demography matrix
setup_Omega(<xde>): Make the mosquito demography matrix
setup_Omega(<dts>): Make the mosquito demography matrix
make_Omega(): Make the mosquito demography matrix for spatial RM model in continuous time
make_Omega(<xde>): Make the mosquito demography matrix for spatial RM model in continuous time
make_Omega_xde(): Make the mosquito demography matrix for spatial RM model in continuous time
make_Omega(<dts>): Make the mosquito demography matrix for spatial RM model in continuous time
make_Omega_dts(): Make the mosquito demography matrix for spatial RM model in discrete time
make_Upsilon(): Make the mosquito demography matrix for spatial RM model in continuous time
make_Upsilon(<xde>): Make the mosquito demography matrix for spatial RM model in continuous time
get_Omega(): Make the mosquito demography matrix
get_Upsilon(): Make the mosquito demography matrix

EIP

Methods for the extrinsic incubation period (EIP)

setup_eip_obj(): Setup an EIP Bionomic Object
F_eip(): Compute the EIP
F_eip(<static>): Static model patch emigration

trivial

The trivial model for adult mosquitoes

skill_set_MY(<trivial>): The trivial Module Skill Set
check_MY(<trivial>): Run a check before solving
F_fqM(<trivial>): Blood feeding rate of the infective mosquito population
get_MY_pars(<trivial>): Return the parameters as a list
change_MY_pars(<trivial>): Return the parameters as a list
make_MY_obj_trivial(): Make parameters for trivial aquatic mosquito model

basicM

Methods for basicM - adult mosquito ecology without infection dynamics.

skill_set_MY(<basicM>): The MY Module Skill Set
check_MY(<basicM>): Run a check before solving
make_M_obj_basicM(): Make parameters for GeRM ODE adult mosquito model
F_fqM(<basicM>): The net blood feeding rate of the mosquito population in a patch
make_MY_inits_basicM(): Make inits for basicM adult mosquito model
get_MY_pars(<basicM>): Return the parameters as a list
change_MY_pars(<basicM>): Return the parameters as a list
steady_state_M(<basicM_ode>): Compute the steady states as a function of the daily EIR
steady_state_M(<basicM_dts>): Compute the steady states as a function of the daily EIR

The “SI” model for infection

Specialized methods for simple infection dynamics for an adult mosquito population

skill_set_MY(<SI>): The SI Module Skill Set
check_MY(<SI>): Run a check before solving
make_MY_obj_SI(): Make parameters for SI ODE adult mosquito model
F_fqM(<SI>): Compute Net Blood Feeding by Mosquitoes for SI
get_MY_pars(<SI>): Return the parameters as a list
change_MY_pars(<SI>): Return the parameters as a list
make_MY_inits_SI(): Make inits for SI adult mosquito model
steady_state_MY(<SI_ode>): Steady States: MY-SI

macdonald

Specialized methods for a Macdonald-style model of adult mosquito dynamics - modified slightly from a model published by Joan Aron & Robert May (1982).

skill_set_MY(<macdonald>): The macdonald Module Skill Set
check_MY(<macdonald>): Run a check before solving
steady_state_MY(<macdonald>): Compute the steady states as a function of the daily EIR
make_MY_obj_macdonald(): Make parameters for macdonald ODE adult mosquito model
get_MY_pars(<macdonald>): Return the parameters as a list
change_MY_pars(<macdonald>): Return the parameters as a list
F_fqM(<macdonald>): The net blood feeding rate of the infective mosquito population in a patch
make_MY_inits_macdonald(): Make inits for macdonald adult mosquito model

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).

skill_set_MY(<GeRM>): The GeRM Module Skill Set
check_MY(<GeRM>): Run a check before solving
steady_state_MY(<GeRM>): Compute the steady states as a function of the daily EIR
make_MY_obj_GeRM(): Make parameters for GeRM ODE adult mosquito model
get_MY_pars(<GeRM>): Return the parameters as a list
change_MY_pars(<GeRM>): Return the parameters as a list
F_fqM(<GeRM>): The net blood feeding rate of the infective mosquito population in a patch
make_MY_inits_GeRM(): Make inits for GeRM adult mosquito model

RM-Mosquito in discrete-time

Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics - in discrete time.

skill_set_MY(<RMdts>): The RMdts Module Skill Set
check_MY(<RMdts>): Run a check before solving
F_fqM(<RMdts>): The net blood feeding rate of the infective mosquito population in a patch
make_MY_inits_RMdts(): Make inits for RMdts adult mosquito model

L Component (Immature Mosquitoes)

Generic methods for the aquatic (immature) mosquito component.

skill_set_L(): The skill set (L module)
check_L(): Run a check before solving
F_emerge(): Compute Emergent Adults
LBionomics(): Bionomics for an L Component Module
LBaseline(): Baseline Bionomics for an L Component Module
get_L_pars(): Get parameters for the L Component module
change_L_pars(): Set L Component Parameters
get_L_vars(): List L Component Variables
change_L_inits(): Set L Component Initial Values
get_L_inits(): Get Initial Values for the L Component
steady_state_L(): Compute steady states for L Component Modules

trivial

The trivial model for aquatic dynamics

skill_set_L(<trivial>): The L Module Skill Set
F_emerge(<trivial>): Compute Emergent Adults for trivial (L Component)
check_L(<trivial>): Run a check before solving
make_L_obj_trivial(): Make L_obj for trivial (L Component)
change_L_pars(<trivial>): Set L Component parameters for trivial

basicL

A basic model for aquatic mosquito dynamics

skill_set_L(<basicL>): The L Module Skill Set
check_L(<basicL>): Run a check before solving
make_L_obj_basicL(): Make L_obj 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)
make_L_inits_basicL(): Make Initial Values for basicL (L Component)
get_L_vars(<basicL>): List L Component Variables for basicL
get_L_pars(<basicL>): Get L Component Parameters for basicL
change_L_pars(<basicL>): Set L Component parameters for basicL
change_L_inits(<basicL>): Set the Initial Values for basicL (L Component)
steady_state_L(<basicL_ode>): Compute the Steady State of dLdt.basicL (L Component)

Mosquito Bionomics

Methods to compute or update mosquito bionomic parameters

Functional Responses

Compute bionomic parameters as functional responses to resource availability

setup_f_obj(): Setup Blood Feeding Bionomic Object
F_feeding_rate(): Compute the blood feeding rate, f
F_feeding_rate(<static>): Constant baseline blood feeding rate
setup_f_obj_B2(): Setup Blood Feeding Bionomic Object
F_feeding_rate(<B2>): Type 2 functional response for the blood feeding rate
setup_q_obj(): Setup a Human Fraction Bionomic Object
F_human_frac(): Compute the blood qeeding rate, q
F_human_frac(<static>): Static model for the blood feeding rate
setup_g_obj(): Setup a Mosquito Mortality Bionomic Object
F_mozy_mort(): Compute the blood geeding rate, g
F_mozy_mort(<static>): Static model for the blood feeding rate
setup_sigma_obj(): Setup a Patch Emigration Bionomic Object
F_emigrate(): Compute the Mosquito Patch Emigration Rate
F_emigrate(<static>): Static model patch emigration
setup_sigma_obj_BQS(): Setup Blood Feeding Bionomic Object
F_emigrate(<BQS>): Model for mosquito emigration based on resource availability
setup_mu_obj(): Setup a Dispersal Loss Bionomic Object
F_dispersal_loss(): Compute the emigration loss fraction
F_dispersal_loss(<static>): Static model for the blood feeding rate
setup_nu_obj(): Setup Laying Rate Bionomic Object
F_batch_rate(): Compute the Mosquito Patch Emigration Rate
F_batch_rate(<static>): Static model patch emigration
setup_nu_obj_Q2(): Setup Blood Feeding Bionomic Object
F_batch_rate(<Q2>): Type 2 Functional Response for Egg Laying
setup_psi_obj(): Setup a Human Fraction Bionomic Object
F_maturation(): Compute the blood psieeding rate, psi
F_maturation(<static>): Static model for the blood feeding rate
setup_phi_obj(): Setup a Human Fraction Bionomic Object
F_larval_mort(): Compute the blood phieeding rate, phi
F_larval_mort(<static>): Static model for the blood feeding rate
setup_xi_obj(): Setup a Human Fraction Bionomic Object
F_dlay_maturation(): Compute the blood xieeding rate, xi
F_dlay_maturation(<static>): Static model for the blood feeding rate
setup_theta_obj(): Setup a Human Fraction Bionomic Object
F_larval_dd_mort(): Compute the blood thetaeeding rate, theta
F_larval_dd_mort(<static>): Static model for the blood feeding rate

Mosquito Dispersal

Specialized methods to set up mosquito dispersal matrices

setup_K_obj(): Setup a Human Fraction Bionomic Object
change_K_matrix(): Change Mosquito Dispersal Matrix
get_K_matrix(): Get the Mosquito Dispersal Matrix
setup_K_matrix(): Setup Mosquito Dispersal Matrix
make_K_matrix_herethere(): Make a Here-There Dispersal Matrix
make_K_matrix_xy(): make a Kernel-Based Mosquito Dispersal Matrix
F_K_matrix(): Compute the blood feeding rate, f
F_K_matrix(<static>): Constant baseline blood feeding rate

Other Dynamic Variables

Compute the derivatives for other variables

Other Dynamic Variables

Compute the derivatives for other variables

add_variable(): Add Variable
setup_other_variables(): Set Up the first (null) other variable
setup_V_ix(<setup>): Compute Other Variables
setup_V_obj(): Setup an V Module (Human / Host Epidemiology & Demography)
get_V_vars(): Get Variables by Name
setup_V_ix(): Add indices for human population to parameter list
get_V_pars(): Return the parameters as a list
get_V_ix(): Add indices for human population to parameter list
change_V_pars(): Set new X parameter values
setup_V_inits(): Setup Initial Values for V Modules
get_V_inits(): A function to set up V_obj
change_V_inits(): Set new X parameter values

Ports & Junctions

Forcing

Exogenous forcing (see ramp.control)

setup_forcing_object(): Setup the Junction for Exogenous Forcing

Vector Control

The ports for vector control

setup_vector_control_object(): Setup the Vector Control Junction

Health

The ports for malaria control

setup_health_object(): none set up for exogenous health

Resources

The ports for resources

setup_resources_object(): Setup Resources Object

Travel

Time spent traveling & the travel EIR

setup_travel_object(): Setup the Travel Object
change_time_at_home(): Change the travel EIR
change_travel_EIR(): Change the travel EIR
setup_F_travel(): Set up no travel
setup_F_travel(<static>): Set up no travel
setup_F_travel(<ts_func>): Set up no travel
setup_F_travel_eir(): Setup the Travel EIR
setup_F_travel_eir(<static>): Set up no travel
setup_F_travel_eir(<ts_func>): Setup the Travel EIR
travel_dynamics(): Time Spent Here

Visitors

Blood Feeding on non-Residents

setup_F_vis_kappa(): Set up no visitors
setup_F_vis_kappa(<ts_func>): Set
setup_F_visitors(): Set up no visitors
setup_F_visitors(<ts_func>): Set up no visitors
setup_visitor_object(): Setup the Visitors Object
visitor_dynamics(): Availabilit of Visitors

Solving

Methods to compute the derivatives and dynamical systems

Solve

make_times_dts(): Times Utility for Discrete Time Systems
make_times_xde(): Times Utility for Differential Equations

Solving

Wrappers around the derivatives functions that handle time and parse outputs

xds_solve(): Solve a Dynamical System
xds_stable_orbit(): Compute stable orbits
xds_steady(): 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

Compute terms

Methods to compute and transmission terms

average_PR_true(): Compute the average True PR
average_EIR(): Compute the average EIR

Get and plot terms

Basic visualization of the transmission terms

get_H(): Get the initial values as a vector
get_PR(): Get the PfPR from a Malaria Model
get_XH_out(): Get XH outputs
get_MY_out(): Get MY outputs
get_L_out(): Get L outputs
xds_plot_EIR(): Plot the 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

Utilities

print(<xds_obj>): Print the xds model object
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 model 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
ode_to_dde(): Compute as DDE
ode_to_dde(<ode>): Compute as DDE
ode_to_dde(<dde>): Compute as DDE
ode_to_dde(<dts>): Compute as DDE

Change Parameters & Initial Values

Methods to set up basic models

change_H(): Change human population density
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
get_inits(): Get the stored initial values, \(y_0\)
get_last(): Get the last state
make_indices(): Make indices for all the model variables

Functions

Basic visualization of the transmission terms

F_zero(): The trivial function
make_function(<zero>): Make a Function that is the sum of Two other Functions
makepar_F_zero(): parameters for make_function
F_one(): The trivial function
make_function(<one>): Make a Function
makepar_F_one(): parameters for make_function
make_function(<val>): Make a Function that is the sum of Two other Functions
makepar_F_val(): parameters for make_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(<nproduct>): Make a Sinusoidal Function
makepar_F_nproduct(): 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
make_function(<sharkbite>): Make a sharkbite Function
makepar_F_sharkbite(): Make Parameters for a sharkbite Function
make_function(<type2>): Make a type2 function for age
makepar_F_type2(): parameters for make_function
make_function(<splinef>): Make a spline function
make_function(<splineX>): Make a spline function
make_function(<spline2>): Make a spline function
makepar_F_spline(): Make Parameters for a Spline

Update Forcing

Methods to get - set - and update forcing functions

show_season(): Plot the seasonal pattern
F_season(): Plot the seasonal pattern
show_trend(): Plot the Temporal Trend
F_trend(): Plot the Temporal Trend
show_shock(): Plot the Temporal shock
F_shock(): Plot the Temporal Trend

Get and Set for Mean Forcing

Functions to change Forcing

get_mean_forcing(): Get mean forcing
change_mean_forcing(): Set mean forcing

Get and Set for Seasonality

Utilities to change

get_season(): Get the Seasonal Pattern
get_season_phase(): Get phase
get_season_bottom(): Get phase
get_season_pw(): Get pw for seasonality
change_season(): Get seasonal pattern

Get and Set for Spline Trend Functions

Utilities to change the interpolation points

get_trend(): Get the trend parameters
get_spline(): Get spline interpolation points
get_spline_s(): Get spline interpolation points
change_spline(): Set the interpolating points
change_spline_y(): Set yy
change_shock(): Set the interpolating points
change_shock(<none>): Set yy
change_shock(<Lambda>): Set the \(y\) value for interpolating points
change_shock(<eir>): Set yy

New

Move

F_exp(): Exponential Function
check_models(): Run Checks
get_EIR(): Get the EIR
get_XH_ix(): Add indices for human population to parameter list
get_XH_vars(<trivial>): Get Variables by Name
get_f(): Get the feeding rate(s)
get_g(): Get the adult mosquito mortality rate(s)
get_q(): Get the human fraction(s)
get_sigma(): Get the patch emigration rates
get_variables(): Get Variables
make_ts_function(): Make a Time Series Function
One_tV(): The trivial function
Zero_tV(): The trivial function
setup_traps_object(): Setup the Junction for Exogenous traps
setup_blood_host_object(): Setup the Blood Hosts Object
setup_blood_hosts(): Set up no blood_hosts
setup_blood_hosts(<ts_func>): Set up no blood_hosts
change_blood_hosts(): Set static blood feeding search weights
blood_hosts_dynamics(): blood_hosts Dynamics
setup_sugar_object(): Setup the Junction for Exogenous sugar