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Make an xds model object template

Source: R/xds_object_template.R
make_xds_object_template.Rd

This function is called by xds_setup to create a structured object, called an xds model object template. The template has configured interfaces, created stubs for the model objects, created junctions, and set up empty ports. A template has set up all the basic structural elements, but it has not configured any of the component model objects.

Usage

make_xds_object_template(
  xds = "ode",
  frame = "full",
  nPatches = 1,
  membership = 1,
  residency = 1
)

Arguments

xds

is used to dispatch various functions to set up and solve systems of differential equations. 'xde' for ordinary or delay differential equations; 'dts' for "discrete time systems"

frame

model component subset

nPatches

is the number of patches

membership

is the habitat membership vector

residency

is the strata residency vector

Value

an xds model object

Details

This function sets up the interfaces and the core objects used by ramp.xds.

First, the function sets up some short text strings (assigned to the same S3 class) to dispatch various cases of of various S3 functions:

  • xds is either "xde" for differential equations, or "dts" for discrete time systems

  • xde is either "ode" for ordinary differential equations; "dde" for delay differential equations; or "dts" for discrete time systems

  • frame is one of several cases:

    • "full" includes all three dynamical components: a human/host dynamical component, \(\cal XH\); and adult mosquito dynamical component, \(\cal MYZ\); and an aquatic mosquito dynamical component, \(\cal L\). in some form (possibly the trivial case) (see xds_setup())

    • "mozy" is for mosquito ecology models (see xds_setup_mosy()), including models without pathogen infection dynamics in mosquitoes

    • "aquatic" is for aquatic mosquito ecology models (see xds_setup_aquatic()), forced by a function describing egg laying

    • "human" is for human/host infection dynamics(see xds_setup_human()), forced by the infective density of adult mosquitoes, \(fqZ\)

    • "eir" is for human/host cohort infection dynamics (see xds_setup_eir()), forced by a function F_eir

    • "cohort" is for human/host cohort infection dynamics (see xds_setup_cohort()), forced by a function F_eir

  • forcing is set to "static"

Second, the function sets the values of the structural parameters:

  • nPatches or \(N_p\) is the number of patches

  • nHabitats or \(N_q\), the number of aquatic habitats, is set to length(membership)

  • nStrata or \(N_h\), the number of human/ host population strata, is set to length(HPop)

  • nVectorSpecies or \(N_s\), the number of vector species is set to 1;

  • nHostSpecies or \(N_i\), the number of host species is set to 1;

Next, the function sets up empty lists to hold the model objects that define components:

model for the availability of visitors; by default, there are no visitors Next, the function sets up egg laying, blood feeding, and transmission:

Finally, the function sets up a few other miscellaneous options:

  • Exposure is called after Transmission to compute environmentally heterogeneous exposure and malaria importation through travel:

Note

xds stands for extensible differential equation

See also

Related: xds_setup and setup_forcing_object. Illustrated in a vignette: 5-3-4 Example