Make an xds model object:
Define the dynamical components:
\(\cal XH\) - a model for human / host infection dynamics of class Xname with trivial demographics
\(\cal MYZ\) - a model for adult mosquito ecology and infection dynamics of class MYZname
\(\cal L\) - a model 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 number 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, \(\cal K\)
The time spent matrix \(\Theta\)
Configure runtime parameters for discrete-time systems
Advanced options can be configured after basic setup.
xds_setup(
xds = "ode",
Xname = "SIS",
Xopts = list(),
MYZname = "macdonald",
MYZopts = list(),
Lname = "trivial",
Lopts = list(),
nPatches = 1,
HPop = 1000,
residence = 1,
membership = 1,
searchB = 1,
TimeSpent = list(),
calK = list(),
searchQ = 1,
Xday = 1,
MYZday = 1,
Lday = 1,
BFopts = list(),
model_name = "unnamed"
)is ode or dde or dts for ordinary OR delay differential OR difference equations
a character string defining a \(\cal X\) model
a list to configure the X model
a character string defining a \(\cal MYZ\) model
a list to configure the MYZ model
a character string defining a \(\cal L\) model
a list to configure the L model
is the number of patches
is the number of humans in each patch
is a vector that describes the patch where each human stratum lives
is a vector that describes the patch where each aquatic habitat is found
is a vector of search weights for blood feeding
is either a TimeSpent matrix or a string to call a function that sets it up
is either a calK matrix or a string that defines how to set it up
is a vector of search weights for egg laying
is the run-time time step for X component (in days): integer or 1/integer
is the run-time time step for MYZ component (in days): integer or 1/integer
is the run-time time step for L component (in days): integer or 1/integer
a list to configure the blood feeding model
is a name for the model (arbitrary)
an xds object
Using the basic structural parameters, a basic template is created by make_xds_template with
a properly configured interface for blood feeding and egg laying, and pars$frame = class(pars$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)
nHosts=1 -- basic setup handles the first host species
nVectors=1 -- basic setup handles the first vector species
Each one of the dynamical components is configured.
pars$Xpar[[1]] defines a model for human / host infection dynamics of class Xname (the \(\cal XH\) dynamical component). The parameter values passed in a named list, Xopts.
pars$MYZpar[[1]] defines a model for adult mosquito ecology & infection dynamics of class MYZname (the \(\cal MYZ\) dynamical component). The parameter values are passed in a named list, MYZopts.
pars$Lpar[[1]] defines a model for aquatic mosquito ecology of class Lname (The \(\cal L\) dynamical component). The parameter values are passed in a named list, Lopts.
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
Runtime parameters for dts models can be configured by passing values: Xday, MYZday, and Lday
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
If \(\cal MYZ\) is the trivial model, 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).