Package index • ramp.xds

Help

How to get help for ramp.xds

xds_help_guide: ramp.xds: Getting Help
xds_help_info: ramp.xds: Info Pages

Model Building

Basic Setup

Build an xds model object

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
xds_info_basic_setup: ramp.xds: Basic Setup
xds_object: The xds Model Object
xds_info_setup_options: ramp.xds: All Setup Options

Dynamical Modules

Setting the value of structural parameters

XH_module_list: XH modules
MY_module_list: MY Modules
L_module_list: L modules
xds_info_dynamical_components: Dynamical Components

Model Structure

Setting the value of structural parameters

xds_info_patch_dynamics: Patch Dynamics
xds_info_strata: Population Strata
xds_info_human_populations: The human population
xds_info_aquatic_habitats: Aquatic Habitats

Basic Setup Options

Search Weights, Mosquito Dispersal, Time Spent

xds_info_search_weights: Search Weights
xds_info_heterogeneous_biting_rates: Heterogeneous Biting Rates
xds_info_mosquito_dispersal: Mosquito Dispersal
xds_info_time_spent: Time Spent

Adding Features

Forcing, Malaria Control

xds_info_trivial_forcing: Forcing with Trivial Modules
xds_info_forcing: ramp.xds: Forcing
xds_info_port: Ports
xds_info_junction: Junctions
xds_info_heterogeneity: Heterogeneity
xds_info_environmental_heterogeneity: Environmental Heterogeneity

The xds model object

xds_object: The xds Model Object
xds_info_dynamical_components: Dynamical Components
xds_info_interfaces: Dynamical Interfaces

Solve

Methods to numerically solve differential equations and get the outputs

xds_solve(): Solve a Dynamical System
xds_stable_orbit(): Compute stable orbits
dts_stable_orbit(): Compute the stable orbit for a discrete time system
burnin(): Burn In
xds_info_parsing: Parsing

Variable

Inspect initial values. Get the final state. Copy final state to initial values.

get_inits(): Get the stored initial values, \(y_0\)
get_last(): Get the last state
last_to_inits(): Set the initial values to the last values of the last simulation

Get Outputs

get_XH_orbits(): Get orbits (XH)
get_MY_orbits(): Get orbits (MY)
get_L_orbits(): Get orbits (L)
get_EIR(): Get the EIR
get_PR(): Get the PfPR from a malaria model

Compute Steady States

xds_steady(): Solve for the steady state
dts_steady(): Compute the steady state of a discrete time system
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

Plot

PR & EIR

Plot the prevalence and the entomological inoculation rate

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

Adult Mosquito

Plot common variables and terms

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 infective mosquitoes
xds_lines_Z(): Add lines for the density of 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

Aquatic Mosquito

Plot common variables and terms

xds_plot_L(): Plot aquatic mosquito population density
xds_lines_L(): Add lines for aquatic mosquito population density

Show Forcing

Show patterns for forced systems

show_season(): Plot the seasonal pattern
show_trend(): Plot the Temporal Trend
show_shock(): Plot the temporal shock

Get

Inspect elements of the xds object

Get Orbits

Get orbits

get_XH_orbits(): Get orbits (XH)
get_L_orbits(): Get orbits (L)
get_PR(): Get the PfPR from a malaria model
get_EIR(): Get the EIR
get_H(): Get human population density
get_M(): Get mosquito population density

Get Parameters

Get model parameters

get_XH_pars(): Get parameters (XH)
get_TimeSpent_matrix(): Get the Time Spent Matrix
get_MY_pars(): Get parameters (MY)
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_K_matrix(): Get the Mosquito Dispersal Matrix
get_Omega(): Get Omega
get_Upsilon(): Get Upsilon
get_L_pars(): Get parameters (L)
get_phi(): Get phi, density independent mortality
get_psi(): Get psi, the maturation rate
get_xi(): Get xi, delayed maturation
get_theta(): Get theta, density dependent mortality
get_V_pars(): Return the parameters as a list

Get Variables

Get initial values and indices

get_XH_vars(): List variables (XH)
get_XH_inits(): A function to set up XH_obj
get_MY_vars(): List variables (MY)
get_MY_inits(): Return initial values as a vector
get_L_vars(): List variables (L)
get_L_inits(): Get initial values (L)
get_variables(): Get Variables

Get Forcing

Get the parameters from trace functions

get_mean_forcing(): Get mean forcing
get_season(): Get seasonality parameters
get_season_phase(): Get seasonality parameter phase
get_season_bottom(): Get seasonality parameter bottom
get_season_pw(): Get seasonality parameter pw
get_trend(): Get the trend parameters
get_shock(): Get the shock parameters
get_spline(): Get spline interpolation points
get_spline_s(): Get spline interpolation points

Change

Change parameters

Change for XH

Change parameters

change_XH_pars(): Change parameters (XH)
change_H(): Change human population density
change_TimeSpent_matrix(): Set up (or change) a Time Spent matrix

Change for MY

Change parameters

change_MY_pars(): Change parameters (MY)
change_K_matrix(): Change Mosquito Dispersal Matrix
change_f(): Change the blood feeding rate
change_g(): Change the mosquito mortality rate
change_q(): Change the human fraction
change_sigma(): Change the mosquito patch emigration rate
change_mu(): Change the emigration loss fraction
change_nu(): Change the egg laying rate
change_eip(): Change the EIP

Change for L

Change parameters

change_L_pars(): Change parameters (L)
change_phi(): Change phi
change_psi(): Change psi
change_xi(): Change xi, the maturation delay parameter
change_theta(): Change theta, density dependent mortality

Change for trivial forcing

Change parameters

change_mean_forcing(): Change mean forcing
change_season(): Change season parameters
change_trend(): Set the interpolating points
change_shock(): Change shock parameters

Save & Read

Build and store xds model objects

saveXDS(): saveRDS for xds Objects
readXDS(): readRDS for xds Objects

XH Component

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

XH_module_list: XH modules
XH_functions: Generic methods for the XH component
XH_get: Get functions for XH
XH_change: A list of functions to change the XH component
XH_setup: Setup functions for the XH component

Modules

XH component module implementations

trivial_XH: trivial — XH module
SIS: The SIS module for the XH component
hMoI: The hMoI module for the XH component

Time Spent

Utilities for Time Spent Matrices

xds_info_time_spent: Time Spent
xds_info_time_at_risk: Time at Risk
setup_TimeSpent(): Make a time spent matrix, called TimeSpent
change_TimeSpent_matrix(): Set up (or change) a Time Spent matrix
make_TimeSpent_athome(): Make a mosquito dispersal matrix, called TimeSpent
make_TimeSpent_xy(): Make a mosquito dispersal matrix, called TimeSpent

Utilities for Time Spent Matrices

change_XH_inits(): Change initial values (XH)
get_XH_pars(): Get parameters (XH)
change_XH_pars(): Change parameters (XH)
get_HTC(): Compute the human transmitting capacity
xds_plot_X(): Default plotting for epidemiology (X)
steady_state_X(): Steady states for X
steady_state_XH(): Steady states for XH

MY Component

Adult mosquito ecology and infection dynamics

MY_module_list: MY Modules
MY_functions: Generic Methods for the MY Component
MY_get: Get Functions for the MY Component
MY_change: Change Functions for the MY Component
MY_setup: Setup Functions for the MY Component

Modules

trivial_MY: trivial — MY module
basicM: The basicM Module for the MY Component
SI: The SI module for the MY component
macdonald: The macdonald module (MY component)
GeM: The GeM module for the MY component
RMdts: The RMdts module for the MY component

L Component

Immagure mosquito ecology in aquatic habitats

L_functions: Generic methods for the L component
L_module_list: L modules
L_get: Get functions (L)
L_change: Change functions (L)
L_setup: Setup functions (L)

L Modules

Models for aquatic mosquito development and maturation in aquatic habitats

trivial_L: trivial — L module
basicL: The basicL module for the L component

Other State Variables

Compute the derivatives for other variables

variables: Variables
Other_State_Variables: Other State 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_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
change_spline(): Change spline interpolation points
change_spline_y(): Change y values for spline interpolation points
change_shock(): Change shock parameters

Blood Feeding & Transmission

xds_info_blood_feeding: Blood Feeding
xds_info_local_fraction: The Local Fraction
xds_info_available_blood_hosts: Available Blood
xds_info_search_weights: Search Weights
xds_info_relative_biting_rates: Relative Biting Rate
xds_info_transmission: Transmission
check_XY_interface(): Check the XY Interface
make_residency_matrix(): Create the Residency Matrix
view_residency_matrix(): View residence membership

Exposure

Compute the FoI from local EIR and travel

xds_info_exposure: Exposure
xds_info_environmental_heterogeneity: 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

Malaria Importation

Functions to model travel & visitors

xds_info_importation: Malaria Importation
xds_info_malaria_importation: Malaria Importation

Travel

Time spent traveling & the travel EIR

xds_info_travel_malaria: Travel Malaria
xds_port_travel_eir: Travel EIR
xds_port_time_away: Time Away
change_time_away(): Change the time at home
change_travel_EIR(): Change the travel EIR

Visitors

Blood Feeding on non-Residents

xds_info_visitors: Visitors
change_visitors(): Change Availability of Visitors
xds_port_visitors: Visitors
change_visitor_kappa(): Change Visitor's NI
xds_port_visitor_kappa: Visitors Infectiousness

Mosquito Bionomics

Methods to compute or update mosquito bionomic parameters

xds_info_mosquito_bionomics: Mosquito Bionomics
xds_info_blood_feeding: Blood Feeding
xds_info_mosquito_dispersal: Mosquito Dispersal
xds_info_mosquito_demography: Mosquito Demography

Mosquito Dispersal

Specialized methods to set up mosquito dispersal matrices

xds_info_mosquito_dispersal: Mosquito Dispersal
xds_info_mosquito_demography: Mosquito Demography
setup_K_matrix(): Setup Mosquito Dispersal Matrix
change_K_matrix(): Change Mosquito Dispersal Matrix
get_K_matrix(): Get the Mosquito Dispersal Matrix
make_K_matrix_herethere(): Make a Here-There Dispersal Matrix
make_K_matrix_xy(): make a Kernel-Based Mosquito Dispersal Matrix

Forcing

xds_info_forcing: ramp.xds: Forcing
xds_info_trivial_forcing: Forcing with Trivial Modules
xds_info_vector_control: Vector Control
xds_info_health: Health

Resources

The ports for resources

xds_info_resources: Resources
xds_info_availability: Resource Availability
xds_info_available_blood_hosts: Available Blood
xds_info_search_weights_blood: Blood Search Weights
xds_port_other_blood_hosts: Other Blood Hosts
xds_port_blood_traps: Blood Traps
xds_info_available_habitats: Habitat Availability
xds_info_search_weights_habitat: Habitat Search Weights
xds_info_available_sugar: Sugar Availability
xds_info_mosquito_traps: Available Blood
change_other_blood_hosts(): Set static blood feeding search weights

Habitats & Egg Laying

Mosquito Population Dynamical Interface

xds_info_aquatic_habitats: Aquatic Habitats
xds_info_search_weights_habitat: Habitat Search Weights
xds_info_available_habitats: Habitat Availability
xds_info_egg_laying: Egg Laying
xds_port_bad_habitats: Unproductive Aquatic Habitats
xds_port_ovitraps: Ovitraps
view_habitat_matrix(): View habitat membership, \(N\)
change_habitat_search_weights(): Change Habitat Search Weights
change_bad_habitat(): Change Bad Habitat Availability

Functions

A function maker

make_function(): Make a Function
make_ts_function(): Make a Time Series Function
makepar_F_zero(): parameters for make_function
makepar_F_one(): parameters for make_function
makepar_F_val(): parameters for make_function
makepar_F_sin(): parameters for make_function
makepar_F_sum(): parameters for make_function
makepar_F_product(): parameters for make_function
makepar_F_nproduct(): parameters for make_function
makepar_F_sigmoid(): Make Parameters for a Sigmoidal Function
makepar_F_sharkfin(): Make Parameters for a Sharkfin Function
makepar_F_sharkbite(): Make Parameters for a sharkbite Function
makepar_F_type2(): parameters for make_function
makepar_F_spline(): Make Parameters for a Spline