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
make_xds_template(
xds = "ode",
frame = "full",
nPatches = 1,
membership = 1,
residence = 1
)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"
model component subset
is the number of patches
is the habitat membership vector
is the strata residence vector
an xds object
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
Related: xds_setup and setup_no_forcing. Illustrated in a vignette: 5-3-4 Example