Build a Model and Configure All Components

Make an xds model object:

Define a module for each dynamical component (see xds_info_dynamical_components):
- XH Component – human / host infection dynamics
- MY Component – adult mosquito ecology and infection dynamics
- L Component – aquatic mosquito ecology
Define basic structural parameters for a single host and vector population:
- nPatches - the number of patches (see xds_info_patch_dynamics)
- membership - the habitat membership vector (see xds_info_aquatic_habitats)
- nHabitats = length(membership)
- residence - the human residence vector (see xds_info_human_populations)
- HPop - the human population size (see xds_info_human_populations)
- nStrata = length(residence) = length(HPop)
Configure some of the basic elements:
- Search Weights (see xds_info_search_weights)
- Mosquito Dispersal matrix (if nPatches>1; see xds_info_mosquito_dispersal)
- Time Spent matrix (if nPatches>1; see xds_info_time_spent)

Usage

xds_setup(
  xds = "ode",
  Xname = "SIS",
  XHoptions = list(),
  MYname = "SI",
  MYoptions = list(),
  Lname = "trivial",
  Loptions = list(),
  nPatches = 1,
  HPop = 1000,
  residence = 1,
  TimeSpent = list(),
  searchB = 1,
  membership = 1,
  Koptions = list(Kname = "no_setup"),
  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
TimeSpent: is either a TimeSpent matrix or a string to call a function that sets it up
searchB: is a vector of search weights for blood feeding
membership: is a vector that describes the patch where each aquatic habitat is found
Koptions: a K matrix, or options for setup_K_matrix (see xds_info_mosquito_dispersal)
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

make_xds_object_template returns an object template with a properly configured interface for blood feeding and egg laying (see xds_object):
- nPatches is passed as a parameter
- nHabitats = length(membership)
- 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)
- class(xds_obj$frame) = 'full'
Each one of the dynamical components is configured.
- xds_obj$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.
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, $\cal Koptions$, can be set
- A time spent matrix, $\Theta$, can be set

Note

Other options can be configured after basic setup (see xds_info_setup_options). If the MY Component is the trivial module, consider using xds_setup_aquatic or xds_setup_human or xds_setup_eir. Models for mosquito ecology need not include states describing infection status (see xds_setup_mosy).