This function creates the residency matrix that is used to sum quantities describing human (or host) populations at the level of a patch.
It is created
from the residency vector (residence), an ordered list
of the patch index for each stratum.
The structural
parameter nPatches to handle cases where some patches
have no residents.
Details
The residency matrix, herein denoted \(J\), holds information about residency for each human (or host) population stratum.
Information about residence in a patch location for each stratum is passed as the residence vector, an ordered list of patch locations. If the \(i^{th}\) stratum lives in the \(j^{th}\) patch, then \({J}_{j,i}=1.\) Otherwise, \({J}_{j,i}=0.\)
Let:
\(N_h = \)
nStrata, the number of population strata;\(N_p = \)
nPatches, the number of patches.
\(J\) is an \(N_p \times N_h\) matrix that is used to map information about human (or host) populations onto patches.
If \(w\) is any vector describing a quantity in strata (i.e., \(\left|w\right|=N_h\)), then $$W={J}\cdot w$$ computes a vector that sums \(w\) by residency for the strata, and \(\left|W\right|= N_p\).
It is a template for the time spent and time at risk matrices, making it possible to compute mosquito parameters describing blood feeding, the mixing matrix, and terms describing transmission.