Make an xds Object Template

Creates and returns structured template for an xds object. The returned object has set up generic features and placeholders for options that must be configured to fully define an xds object

Usage

make_xds_template(
  xds = "ode",
  frame = "full",
  nPatches = 1,
  membership = 1,
  residence = 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

residence

is the strata residence vector

Value

an xds object

Details

This function sets up the basic structures required to configure and run a basic model. The returned object is a list with various required elements attached and configured, but without specifying the dynamical components or any advanced features.

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 "ode" or "dde" for ordinary / delay differential equations; or "dts" for difference equations;

• 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, \(fqZ\)

  • "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:

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

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

• 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)

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

• Xpar

• Transmission calls setup_TRANSMISSION() and setup_visitors_static() sets up a static

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

• Egg Laying calls create_habitat_matrix(), then setup_EGG_LAYING()

• Blood Feeding calls create_residence_matrix(), then setup_BLOOD_FEEDING()

• Transmission calls setup_TRANSMISSION() and setup_visitors_static() sets up a static model for the availability of visitors; by default, there are no visitors

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:

  • setup_exposure_pois sets up a Poisson model for environmental heterogeneity

  • setup_no_travel sets up a model with no exposure through travel

See also

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