ramp.xds: Basic Setup

Basic Setup for ramp.xds uses xds_setup or one of its variants.

Basic Setup uses one of the following functions to build an xds model:

• xds_setup sets up a full model with:

  • an XH Component

  • an MY Component

  • an L Component

• xds_setup_human sets up models to study human epidemiology, given exposure:

  • an XH component

  • a trivial MY component is configured for infectious biting in patches

  • the time spent matrix is used

  • the L component is not used

• xds_setup_eir sets up models to study human epidemiology, given exposure:

  • an XH component with one population stratum

  • a trace function to output the daily EIR

  • a function configures relative biting rates by age for cohort dynamics

  • the MY component is not used

  • the L component is not used

• xds_setup_mosy sets up models for mosquito ecology:

  • the L component

  • the M component (eg basicM)

  • a trivial H module (for blood feeding)

  • the X and Y components are not used

• xds_setup_aquatic sets up models for aquatic mosquito ecology:

  • the L component

  • a trivial MY component is configured for egg laying

  • the XH component is not used

Modularity

ramp.xds is designed for modular computation. The mathematical framework has five core biological processes organized into three chunks called dynamical components (see xds_info_dynamical_components). The modular design makes it possible to build models that fully define all components (using xds_setup), or to develop systems of equations to isolate and study some part of a system.

To implement plug-and-play modularity, a trivial module was developed for each component: a trace function in the trivial upstream component is configured to pass known inputs (see xds_info_trivial_forcing).

The Frame

xds_setup sets up a model that has all three components. Functions were developed to setup and solve systems that making another component completely unnecessary.

All xds_setup_* functions define xds_obj$frame and the functions used to solve and parse differential equations use the S3 system, with methods that dispatch on class(xds_obj$frame).

• xds_setup (frame="full") sets up all three components.

• xds_setup_mosy (frame="mosy") sets up models for mosquito ecology:

  • the model includes an L component

  • the model has an M component but no Y component (eg basicM)

  • a trivial H module can be configured

  • the X component is not used

• xds_setup_aquatic (frame="aquatic") sets up models aquatic mosquito ecology:

  • a trivial MY component is configured for egg laying

  • the XH component is not used

• xds_setup_human (frame="human") sets up models to study epidemiology

  • a trivial MY component is configured for infectious biting in patches

  • the L component is not used

• xds_setup_eir (frame="eir") sets up models to study epidemiology

  • a trace function computes the EIR, denoted \(F_E(t)\)

  • the MY component is not used

  • the XH component is not used

Each one of the basic setup functions assigns a different value to class(xds_obj$frame), which dispatches the S3 methods that solve and parse differential equations:

• xds_setup sets class(frame) = "full"

• xds_setup_human sets class(frame) = "human"

• xds_setup_eir sets class(frame) = "eir"

• xds_setup_mosy sets class(frame) = "mosy"

• xds_setup_aquatic sets class(frame) = "aquatic"

See also

xds_info_dynamical_components, xds_info_trivial_forcing and xds_object

xds_info_dynamical_components, xds_info_trivial_forcing and xds_object