Package index • ramp.xds

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

dMYdt(<macdonald>): Compute derivatives for the MY module macdonald

MBaseline(<macdonald>): macdonald-style adult mosquito bionomics

MBionomics(<macdonald>): macdonald-style adult mosquito bionomics

steady_state_MY(<macdonald>): Compute the steady states as a function of the daily EIR

setup_MY_obj(<macdonald>): Setup MY_obj for the macdonald model

make_MY_obj_macdonald(): Make parameters for macdonald ODE adult mosquito model

get_MY_vars(<macdonald>): Return the variables as a list

get_MY_pars(<macdonald>): Return the parameters as a list

change_MY_pars(<macdonald>): Return the parameters as a list

change_MY_inits(<macdonald>): change initial values for the macdonald model

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_MY_inits(<macdonald>): Setup initial values for the macdonald model

make_MY_inits_macdonald(): Make inits for macdonald adult mosquito model

setup_MY_ix(<macdonald>): Add indices for adult mosquitoes to parameter list

parse_MY_orbits(<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).

skill_set_MY(<GeRM>): The GeRM Module Skill Set

check_MY(<GeRM>): Run a check before solving

dMYdt(<GeRM>): Compute Derivatives for MY module GeRM

MBaseline(<GeRM>): Set mosquito bionomics to baseline

MBionomics(<GeRM>): Set mosquito bionomics to baseline

Update_MYt(<GeRM>): Derivatives for adult mosquitoes

steady_state_MY(<GeRM>): Compute the steady states as a function of the daily EIR

setup_MY_obj(<GeRM>): Setup MY_obj for the GeRM model

make_MY_obj_GeRM(): Make parameters for GeRM ODE adult mosquito model

get_MY_vars(<GeRM>): Return the variables as a list

get_MY_pars(<GeRM>): Return the parameters as a list

change_MY_pars(<GeRM>): Return the parameters as a list

change_MY_inits(<GeRM>): Set new MY 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_MY_inits(<GeRM>): Setup initial values for the GeRM model

make_MY_inits_GeRM(): Make inits for GeRM adult mosquito model

setup_MY_ix(<GeRM>): Add indices for adult mosquitoes to parameter list

parse_MY_orbits(<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.

skill_set_MY(<RMdts>): The RMdts Module Skill Set

check_MY(<RMdts>): Run a check before solving

F_fqZ(<RMdts>): The net blood feeding rate of the infective mosquito population in a patch

F_fqM(<RMdts>): The net blood feeding rate of the infective mosquito population in a patch

F_eggs(<RMdts>): Number of eggs laid by adult mosquitoes

Update_MYt(<RMdts>): Derivatives for adult mosquitoes

setup_MY_inits(<RMdts>): Setup initial values for the RMdts model

get_MY_vars(<RMdts>): Return the variables as a list

make_MY_inits_RMdts(): Make inits for RMdts adult mosquito model

setup_MY_ix(<RMdts>): Add indices for adult mosquitoes to parameter list

parse_MY_orbits(<RMdts>): parse the output of deSolve and return variables for the RMdts model

Aquatic Mosquito Component

Generic methods for the aquatic (immature) mosquito component.

skill_set_L(): The L Module Skill Set

check_L(): Run a check before solving

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_L_obj(): Set up L_obj for L Component modules

get_L_pars(): Get parameters for the L Component module

change_L_pars(): Set L Component Parameters

setup_L_inits(): Setup Initial Values for the L Component

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

setup_L_ix(): Set the Values of the Indices for L Component Modules

parse_L_orbits(): parse L Component Outputs

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

check_L(<trivial>): Run a check before solving

dLdt(<trivial>): Derivatives for the trivial L module

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_L_obj(<trivial>): Setup L_obj for the trivial module

make_L_obj_trivial(): Make L_obj for trivial (L Component)

get_L_pars(<trivial>): Get L Component Parameters for trivial

change_L_pars(<trivial>): Set L Component parameters for trivial

setup_L_inits(<trivial>): Setup Initial Values for the L Component trivial Module

get_L_vars(<trivial>): List L Component Variables for trivial

change_L_inits(<trivial>): Set the Initial Values for trivial (L Component)

setup_L_ix(<trivial>): Setup Variable Indices for trivial (L Component)

parse_L_orbits(<trivial>): parse L Component Variables for basicL

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

dLdt(<basicL>): Compute Derivatives for L module basicL

Update_Lt(<basicL>): Update State Variables for basicL (L Component)

setup_L_obj(<basicL>): Setup L_obj for basicL (L Component)

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)

setup_L_inits(<basicL>): Setup Initial Values 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)

setup_L_ix(<basicL>): Setup Variable Indices for basicL (L Component)

parse_L_orbits(<basicL>): parse L Component Variables for basicL

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

setup_K_matrix(<as_matrix>): Setup a Here-There Dispersal Matrix

setup_K_matrix(<herethere>): Setup a Here-There Dispersal Matrix

make_K_matrix_herethere(): Make a Here-There Dispersal Matrix

setup_K_matrix(<xy>): Setup a Kernel-Based Mosquito 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

dVdt(): Compute Other Variables

dVdt(<setup>): Compute Other Variables

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

parse_V_orbits(): Parse V Outputs

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

Junctions

Functions that compute dynamical terms and exogenous variables

Forcing(): Exogenous Forcing

Health(): Set the values variables for health-based malaria control

VectorControl(): Vector Control

Resources(): Resources

BloodFeeding(): Blood feeding

EggLaying(): Compute eggs laid

Traps(): Set up Mosquito traps

BaselineBionomics(): Set bionomic parameter rates relative to baseline

ModifiedBionomics(): Set bionomic parameter rates relative to baseline

Transmission(): Compute the mixing matrix and transmission terms

Exposure(): Compute Infection Rates

Ports & Junctions

Junctions

Set up junction boxes to add features

Forcing

Exogenous forcing (see ramp.control)

setup_forcing_object(): Setup the Junction for Exogenous Forcing

Forcing(): Exogenous Forcing

Forcing(<none>): Exogenous Forcing

Vector Control

The ports for vector control

setup_vector_control_object(): Setup a Junction for Vector Control

VectorControl(): Vector Control

VectorControl(<none>): Compute Vector Control Effect Sizes

VectorControlEffectSizes(): Vector control effect sizes

VectorControlEffectSizes(<none>): Set the values of exogenous variables

Health

The ports for malaria control

setup_health_object(): none set up for exogenous health

Health(): Set the values variables for health-based malaria control

Health(<none>): Set no exogenous health variables

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(): Time Spent F_travel

Travel(<static>): Time Spent F_travel

Travel(<setup>): Time Spent F_travel

Travel(<dynamic>): Time Spent F_travel

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

Visitors(): Visitors

Visitors(<dynamic>): Visitor Dynamics

Visitors(<setup>): Visitors

Visitors(<static>): 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

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

xde_derivatives(<eir>): Differential equation models for aquatic mosquito populations

Compute Terms

xds_compute_terms(): Compute Derivatives

xds_compute_terms(<aquatic>): Differential equation models for aquatic mosquito populations

xds_compute_terms(<eir>): Differential equation models for aquatic mosquito populations

xds_compute_terms(<full>): Generalized spatial differential equation model

xds_compute_terms(<human>): Differential equations isolating the humans, forced with Ztrace

xds_compute_terms(<mosy>): Generalized spatial differential equation model (mosquito only)

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

DTS 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(<eir>): Difference equation models for aquatic mosquito populations

dts_update_Lt(): Difference equations isolating the humans, forced with Ztrace

dts_update_MYt(): Difference equations isolating the humans, forced with Ztrace

dts_update_XHt(): Difference equations isolating the humans, forced with Ztrace

Update_XHt(): Update X states for a discrete time system

Update_MYt(): Update States for a Adult Mosquito Model

Update_Lt(): Update State Variables for an L Component Module

Solving

Wrappers around the derivatives functions that handle time and parse outputs

xds_solve(): Solve a Dynamical System

xds_solve(<dde>): Solve a System of Delay Differential Equations

xds_solve(<ode>): Solve a System of Ordinary Differential Equations

xds_solve(<dts>): Solve a Discrete-Time System

xds_stable_orbit(): Solve for the steady state of a system of equations using rootSolve::steady

xds_stable_orbit(<dts>): Compute the stable orbit for a system of differential equations

xds_stable_orbit(<xde>): Compute the stable orbit for a system of differential equations

xds_steady(): Solve for the steady state of a system of equations using rootSolve::steady

xds_steady(<ode>): Solve for the steady state of a system of equations using rootSolve::steady

xds_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

Compute terms

Methods to compute and transmission terms

average_PR_true(): Compute the average True PR

average_EIR(): Compute the average EIR

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

parse_L_terms(): Pull L Terms

parse_MY_terms(): Pull MY Terms

parse_XH_terms(): Pull XH Terms

parse_bionomics(): Pull bionomic parameters

parse_outputs(): Make Outputs

parse_outputs(<aquatic>): Make Outputs

parse_outputs(<eir>): Make Outputs

parse_outputs(<full>): Make Outputs

parse_outputs(<human>): Make Outputs

parse_outputs(<mosy>): Make Outputs

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

Utilities

print(<xds_obj>): Print the xds model object

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 model object

xds_shrink(): Shrink an xds xds_obj object

xds_shrink(<cohort>): Shrink an xds xds_obj 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

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_last(): Get the last state

get_H(): Get the initial values as a vector

get_XH(): Get XH outputs

get_PR(): Get the PfPR from a Malaria Model

get_PR(<true>): Get the PfPR from a Malaria Model

get_PR(<lm>): Get the PfPR from a Malaria Model

get_PR(<rdt>): Get the PfPR from a Malaria Model

get_PR(<pcr>): Get the PfPR from a MalariasModel

make_indices(): Make indices for all the model variables

trigger_setup(): Trigger setup

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 that is the sum of Two other Functions

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(<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

update_F_season(<Lambda>): Update the seasonality function

update_F_season(): Update the seasonality function

update_F_season(<cohort>): Update the seasonality function

update_F_season(<eir>): Update the seasonality function

update_F_trend(<Lambda>): Update the trend function

update_F_trend(): Update the trend function

update_F_trend(<cohort>): Update the trend function

update_F_trend(<eir>): Update the trend function

show_season(): Plot the seasonal pattern

show_season(<Lambda>): Plot the seasonal pattern

show_season(<none>): Plot the seasonal pattern

show_season(<eir>): Plot the seasonal pattern

show_trend(): Plot the temporal trend

show_trend(<Lambda>): Plot the temporal trend

show_trend(<eir>): Plot the temporal trend

show_trend(<none>): Plot the temporal trend

Get and Set for Mean Forcing

Functions to change Forcing

get_mean_forcing(): Get mean forcing

get_mean_forcing(<none>): Get mean forcing

get_mean_forcing(<Lambda>): Get mean forcing

get_mean_forcing(<eir>): Get mean forcing

get_mean_forcing(<cohort>): Get mean forcing

set_mean_forcing(): Set mean forcing

set_mean_forcing(<none>): Set mean forcing

set_mean_forcing(<Lambda>): Set mean forcing

set_mean_forcing(<eir>): Set mean forcing

set_mean_forcing(<cohort>): set mean forcing

Get and Set for Seasonality

Utilities to change

get_season(): Get the Seasonal Pattern

get_season(<none>): Get seasonal pattern

get_season(<Lambda>): Get seasonal pattern

get_season(<eir>): Get seasonal pattern

get_season(<cohort>): Get seasonal pattern

get_season_phase(): Get phase

get_season_bottom(): Get phase

get_season_pw(): Get pw for seasonality

set_season(): Get seasonal pattern

set_season_phase(): Set phase

set_season_phase(<none>): Set phase

set_season_phase(<Lambda>): Set phase

set_season_phase(<eir>): Set phase

set_season_phase(<cohort>): set phase

set_season_bottom(): Set bottom

set_season_bottom(<none>): Set bottom

set_season_bottom(<Lambda>): Set bottom

set_season_bottom(<eir>): Set bottom

set_season_bottom(<cohort>): set bottom

set_season_pw(): Set pw, a seasonality shape parameter

set_season_pw(<none>): Set pw, a seasonality shape parameter

set_season_pw(<Lambda>): Set pw, a seasonality shape parameter

set_season_pw(<eir>): Set pw, a seasonality shape parameter

set_season_pw(<cohort>): Set pw, a seasonality shape parameter

Get and Set for Spline Trend Functions

Utilities to change the interpolation points

get_trend(): Get the trend parameters

get_trend(<none>): Get the trend parameters

get_trend(<Lambda>): Get the trend parameters

get_trend(<eir>): Get the trend parameters

get_trend(<cohort>): Get the trend parameters

get_spline(): Get spline interpolation points

get_spline_s(): Get spline interpolation points

get_spline_s(<none>): Get spline interpolation points

get_spline_s(<Lambda>): Get spline interpolation points

get_spline_s(<eir>): Get spline interpolation points

get_spline_s(<cohort>): Get spline interpolation points

set_spline(): Set the interpolating points

set_spline(<none>): Set yy

set_spline(<Lambda>): Set the \(y\) value for interpolating points

set_spline(<eir>): Set yy

set_spline(<cohort>): set yy

set_spline_y(): Set yy

set_spline_y(<none>): Set yy

set_spline_y(<Lambda>): Set the \(y\) value for interpolating points

set_spline_y(<eir>): Set yy

set_spline_y(<cohort>): set yy

New

Move

F_exp(): Exponential Function

change_MY_inits(<RMdts>): Make inits for RMdts adult mosquito model

check_models(): Run Checks

get_EIR(): Get the

get_MY_inits.trivial(): Return initial values as a vector

get_MY_vars(<trivial>): Return the variables as a list

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_f(<basicM>): Get the feeding rate

get_f(<trivial>): Get the feeding rate

get_g(): Get the adult mosquito mortality rate(s)

get_g(<basicM>): Get the feeding rate

get_g(<trivial>): Get the feeding rate

get_q(): Get the human fraction(s)

get_q(<basicM>): Get the feeding rate

get_q(<trivial>): Get the feeding rate

get_sigma(): Get the patch emigration rates

get_sigma(<basicM>): Get the feeding rate

get_sigma(<trivial>): Get the feeding rate

get_variables(): Get Variables

get_variables(<na>): 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

Traps(<none>): Set the values of exogenous variables

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

BloodHosts(): Other Blood Hosts

BloodHosts(<dynamic>): Time Spent F_blood_hosts

BloodHosts(<setup>): Time Spent F_blood_hosts

BloodHosts(<static>): Time Spent F_blood_hosts

blood_hosts_dynamics(): blood_hosts Dynamics

setup_sugar_object(): Setup the Junction for Exogenous sugar

Sugar(): Set up Mosquito sugar

Sugar(<none>): Set the values of exogenous variables