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Build a Model and Configure All Components

Source: R/xds_setup.R
xds_setup.Rd

Make an xds model object:

  • Define the dynamical components:

    • XH - Component modules for human / host infection dynamics of class Xname with trivial demographics

    • MY - Component modules for adult mosquito ecology and infection dynamics of class MYname

    • L Component modules for aquatic mosquito ecology of class Lname

  • Define basic structural parameters for a single host and vector population:

    • \(n_p\) or nPatches - the number of patches

    • \(n_q\) or nHabitats = length(membership) - the numer and locations of aquatic habitats

    • \(n_h\) or nStrata = length(residence) - the number of human / host population strata and basic demographic information

  • Configure some of the basic elements

    • Search weights for human population strata

    • Search weights for aquatic habitats

    • The mosquito dispersal matrix, \(K\)

    • The time spent matrix \(\Theta\)

Advanced options can be configured after basic setup.

Usage

xds_setup(
  xds = "ode",
  Xname = "SIS",
  XHoptions = list(),
  MYname = "macdonald",
  MYoptions = list(),
  Lname = "trivial",
  Loptions = list(),
  nPatches = 1,
  HPop = 1000,
  residence = 1,
  membership = 1,
  searchB = 1,
  TimeSpent = list(),
  K_matrix = list(),
  searchQ = 1,
  BFopts = list(),
  model_name = "unnamed"
)

Arguments

xds

is ode or dde or dts for ordinary OR delay differential OR difference equations

Xname

a character string defining a X Component module

XHoptions

a list to configure the X Component module

MYname

a character string defining an MY module

MYoptions

options to set up the MY component

Lname

a character string defining a L Component module

Loptions

a list to configure the L Component module

nPatches

is the number of patches

HPop

is the number of humans in each patch

residence

is a vector that describes the patch where each human stratum lives

membership

is a vector that describes the patch where each aquatic habitat is found

searchB

is a vector of search weights for blood feeding

TimeSpent

is either a TimeSpent matrix or a string to call a function that sets it up

K_matrix

is either a K_matrix matrix or a string that defines how to set it up

searchQ

is a vector of search weights for egg laying

BFopts

a list to configure the blood feeding model

model_name

is a name for the model (arbitrary)

Value

an xds object

Details

  1. Using the basic structural parameters, a basic template is created by make_xds_object_template with a properly configured interface for blood feeding and egg laying, and xds_obj$frame = class(xds_obj$frame) = 'full' .

    • nPatches is passed as a parameter

    • nHabitats is configured by passing the habitat membership vector, and nHabitats = length(membership)

    • nStrata is configured by passing a vector of human population densities and a residence vector, and nStrata = length(residence) = length(HPop)

    • nHostSpecies=1 (basic setup handles only the first host species)

    • nVectorSpecies=1 (basic setup handles only the first vector species)

. 2. Each one of the dynamical components is configured.

  • xds_obj$XH_obj[[1]] defines a model for human / host infection dynamics of class Xname (the X component). The parameter values passed in a named list, XHoptions.

  • xds_obj$MY_obj[[1]] defines a model for adult mosquito ecology & infection dynamics of class MYname (the MY Component). The parameter values are passed in a named list, MYoptions.

  • xds_obj$L_obj[[1]] defines a model for aquatic mosquito ecology of class Lname (The L Component). The parameter values are passed in a named list, Loptions.

  1. After configuring the dynamical components, several structural parameters can be configured at the command line:

    • Habitat search weights can be set

    • Host population search weights can be set

    • A mosquito dispersal matrix, \(\cal K\), can be set

    • A time spent matrix, \(\Theta\), can be set

Advanced features must be configured later, including:

  • multiple-host species or multiple-vector species

  • exogenous forcing by weather, resources, or other factors

  • vector control, vaccines, or other mass

Note

If the MY Component is the trivial module, consider using xds_setup_aquatic or xds_setup_human or xds_setup_cohort. Models for mosquito ecology need not include states describing infection status (see xds_setup_mosy).

See also

make_xds_object_template