This function, called by make_xds_object_template, sets up
the blood feeding interface, xds_obj$XY_interface.
Details
This implements a framework to model blood feeding described by Wu SL, et al., (2023).
Modular computation in ramp.xds requires a rigid interface to
guarantee mathematical consistency in computing quantites related to blood feeding and transmission.
The interface for blood feeding is defined by an object called
XY_interface,
attached to the xds model object as xds_obj$XY_interface.
The blood feeding interface sets up several objects:
the residency matrix \(J\) (see make_residency_matrix)
a time spent (TiSp) matrix \(\Theta\) (see setup_TimeSpent)
a circadian function
F_circadianfor each vector speciesa time at risk (TaR) matrix \(\Psi,\) the product of the TiSp matrix and the circadian function
blood feeding search weights \(\omega\)
a vector describing the available of humans (or hosts), \(W\) (see F_W_available)
a vector describing the available of visitors, \(V\)
a vector describing the available of other blood hosts, \(O\)
a vector describing the total available of blood hosts, \(B\) (see F_B_available)
These quantities are used to compute the transmission matrix, \(\beta\), to models 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 available should be used to compute the blood feeding rates (\(f\)) using functional responses. The human fraction ought to be \(q=W/B\). available can also be used to model mosquito movement.
Mulit-Host Models
In models with multiple host species, let \(W_i\) denote the available of the \(i^{th}\) host species. Total availablity of blood hosts is $$B = \sum_i W_i + O + V,$$ so the the fraction of bites on each host species is \(W_i/B\).
In models with multiple vector species and one host species, each vector species could have different search habits and preferences. so blood feeding available is computed for each species, denoted \(B_s\) and \(W_{s}\).
In models with multiple vector and multiple host species, \(W_{i,s}\) is the available of the \(i^{th}\) host species to the \(s^{th}\) vector species.
For hosts, available 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.
References
Wu SL, Henry JM, Citron DT, Ssebuliba DM, Nsumba JN, C HMS, Brady OJ, Guerra CA, García GA, Carter AR, Ferguson HM, Afolabi BE, Hay SI, Jr RCR, Kiware S, Smith DL (2023). “Spatial dynamics of malaria transmission.” PLoS Computational Biology, 19(6), e1010684. doi:10.1371/journal.pcbi.1010684 , 2023-06-27.