Set up a part of the xds object that defines the interface for blood feeding
Details
This implements a blood feeding model described by Wu SL, et al., (2023).
Modular computation in ramp.xds requires a rigid interface to
guarantee mathematical consistency for blood feeding and transmission.
The interface is for blood feeding is defined by an object called BFpar that
is attached to the xds object pars as pars$BFpar. The blood feeding interface
the residency matrix \(\cal J\)
a time spent (TiSp) matrix \(\Theta\)
a circadian function
F_circadianfor each vector speciesa time at risk (TaR) matrix \(\Psi\) that is the product the TiSp matrix and the circadian function
blood feeding search weights
a vector describing \(W\), the availability the population strata for blood feeding: the availability of the parasite/pathogen's hosts
a vector describing the availability of visitors
a vector describing the availability of other blood hosts
a vector describing \(B\), the total availability of all vertebrate blood hosts for blood feeding (see
compute_B())
These quantities are used to model transmission (see setup_TRANSMISSION()).
Mosquito bionomic parameters ought to be constrained. If bionomic parameters are assigned, there's no guarantee they are internally mathematically consistent or sensible. To guarantee internal consistency, the the concept of resource availability should be used to compute the blood feeding rates (\(f\)) using functional responses. The human fraction ought to be \(q=W/B\). Availability can also be used to model mosquito movement.
Mulit-Host Models - In models with multiple host species, with availability \(W_i\), the fraction on each host species would be \(W_i/B\). In models with multiple vector species, each species could have different search habits and preferences, so blood feeding availability is indexed for each species: \(B_s\) and \(W_{s}\). In models with multiple host species, \(W_{i,s}\) is the availability of the \(i^{th}\) host species to the \(s^{th}\) vector species. For hosts, availability is based on time spent in each patch, and time at risk, or time spent by time of day weighted by mosquito species-specific search weights reflecting different preferences and a circadian function describing relative mosquito blood feeding rates by time of day.