relative biting rates: updated vignettes

R/blood_feeding.R

@@ -68,8 +68,11 @@ setup_BFpar_static <- function(pars){
 #' @export
 setup_BloodFeeding <- function(pars, i, s=1, BFopts = list(), residence=1, searchWts=1, F_circadian=NULL){
   nStrata = pars$Hpar[[i]]$nStrata
-  pars$BFpar$searchWts[[i]][[s]] = checkIt(searchWts, nStrata)
-  pars$BFpar$relativeBitingRate[[i]][[s]] = checkIt(searchWts, nStrata)
+  searchWts = checkIt(searchWts, nStrata)
+  pars$BFpar$searchWts[[i]][[s]] = searchWts
+  H = pars$Hpar[[i]]$H
+  rbr = searchWts*sum(H)/sum(searchWts*H)
+  pars$BFpar$relativeBitingRate[[i]][[s]] = rbr
   pars$BFpar$residence[[i]] = checkIt(residence, nStrata)
   if(is.null(F_circadian)) pars$BFpar$F_circadian[[s]] = function(d){return(1)}
   return(pars)

vignettes/environmental_heterogeneity.Rmd

@@ -14,4 +14,11 @@ knitr::opts_chunk$set(
 )
 ```
 
-Heterogeneous blood feeding is a basic feature of malaria transmission (see [Heterogeneous Transmission](heterogeneous_transmission.html)). In `exDE` the term **environmental heterogeneity** is used to describe the distribution of the mean within a homogenous human population stratum. The approach is motivated by a study of heterogeneous exposure by (Cooper L, *et al.*, 2019)^[Cooper L, Kang SY, *et al.* (2019). Pareto rules for malaria super-spreaders and super-spreading. Nat Commun 10, 3939, https://doi.org/10.1038/s41467-019-11861-y].
+Heterogeneous blood feeding is a basic feature of malaria transmission (see [Heterogeneous Transmission](heterogeneous_transmission.html)). In `exDE` the term **environmental heterogeneity** is used to describe the distribution of the expected number of bites within a homogenous human population stratum: biting is extremely heterogeneous even for individuals who have the same expectation. The approach is motivated by a study of heterogeneous exposure by (Cooper L, *et al.*, 2019)^[Cooper L, Kang SY, *et al.* (2019). Pareto rules for malaria super-spreaders and super-spreading. Nat Commun 10, 3939, https://doi.org/10.1038/s41467-019-11861-y].
+
+## The Force of Infection and Attack Rates
+
+
+
+
+

vignettes/heterogeneous_mixing.Rmd

@@ -14,4 +14,5 @@ knitr::opts_chunk$set(
 )
 ```
 
-Heterogeneous blood feeding is a basic feature of malaria transmission (see [Heterogeneous Transmission](heterogeneous_transmission.html). In `exDE,` the term **heterogeneous biting** is used to describe differences in the expected rate of exposure among population strata. Other departures from being *well-mixed* fall under the category of *heterogeneous mixing.* Computation of the mixing matrix, $\beta$, is described in detail by Wu SL, *et al.*, (2023)^[Wu SL, Henry JM, Citron DT, *et al.* (2023). Spatial dynamics of malaria transmission. PLoS Comput Biol 19: e1010684, https://doi.org/10.1371/journal.pcbi.1010684].
+Heterogeneous blood feeding is a basic feature of malaria transmission (see [Heterogeneous Transmission](heterogeneous_transmission.html). In `exDE,` the term **heterogeneous biting** is used to describe departures from the ideal assumption of *mass-action,* a topic explored by Perkins TA, *et al.* (2013)^[Perkins TA, Scott TW, Le Menach A, Smith DL (2013). Heterogeneity, mixing, and the spatial scales of mosquito-borne pathogen transmission. PLoS Comput Biol 9: e1003327, https://doi.org/10.1371/journal.pcbi.1003540].
+. Other departures from being *well-mixed* fall under the category of *heterogeneous mixing.* Computation of the mixing matrix, $\beta$, is described in detail by Wu SL, *et al.*, (2023)^[Wu SL, Henry JM, Citron DT, *et al.* (2023). Spatial dynamics of malaria transmission. PLoS Comput Biol 19: e1010684, https://doi.org/10.1371/journal.pcbi.1010684].

vignettes/heterogeneous_transmission.Rmd

@@ -26,7 +26,7 @@ Heterogeneous transmission includes several concepts:
 
 + **[Heterogeneous Biting](heterogeneous_biting.html)** describes differences among population strata in the average rate of exposure. In effect, heterogeneous biting is a kind of *frailty.* Heterogeneous biting is implemented through *blood feeding search weights.*
 
-+ **[Environmental Heterogeneity](environmental_heterogeneity.html)** describes the distribution of the expected number of bites in a homogenous populations stratum. For example, if the expected number of bites is *Gamma* distributed, then the number of bites, per person, would have a negative binomial distribution. Environmental heterogeneity is implemented through a function `F_foi` that converts the daily entomological inoculation rate into a daily force of infection (in `Exposure`). 
++ **[Environmental Heterogeneity](environmental_heterogeneity.html)** describes the distribution of the expected number of bites in a homogenous populations stratum. For example, if the expected number of bites is *Gamma* distributed, then the number of bites, per person, would have a negative binomial distribution. Environmental heterogeneity is implemented through a function `F_foi` that converts the daily entomological inoculation rate into a daily force of infection (in `Exposure`) under some probabilistic model for the distribution of the expectation. 
 
 + **[Heterogeneous Mixing](heterogeneous_mixing.html)** describes departures in a model from the idealized *mass-action* assumption for two-species mixing. The algorithms in `exDE` compute the mixing matrix, $\beta$ integrates information about time spent, mosquito daily activity patterns, the sizes of various population strata, search weights, other vertebrate hosts, and visitors.