Parameter and output documentation.

DESCRIPTION

@@ -69,15 +69,13 @@ LazyData: true
 Remotes:
   mrc-ide/malariaEquilibrium,
   mrc-ide/individual
-Additional_repositories:
-  https://mrc-ide.r-universe.dev
 Imports:
     individual (>= 0.1.16),
     malariaEquilibrium (>= 1.0.1),
     Rcpp,
     statmod,
     MASS,
-    dqrng (>= 0.3.2.2),
+    dqrng (>= 0.4),
     sitmo,
     BH,
     R6,

R/biting_process.R

@@ -210,9 +210,7 @@ simulate_bites <- function(
 calculate_eir <- function(species, solvers, variables, parameters, timestep) {
   a <- human_blood_meal_rate(species, variables, parameters, timestep)
   infectious <- calculate_infectious(species, solvers, variables, parameters)
-  age <- get_age(variables$birth$get_values(), timestep)
-  psi <- unique_biting_rate(age, parameters)
-  infectious * a * mean(psi)
+  infectious * a
 }
 
 effective_biting_rates <- function(a, .pi, p_bitten) {

R/model.R

@@ -29,16 +29,13 @@
 #'  * n: number of humans between an inclusive age range at this timestep. This
 #' defaults to n_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * n_detect: number of humans with an infection detectable by microscopy between an inclusive age range at this timestep. This
+#'  * n_detect_lm (or pcr): number of humans with an infection detectable by microscopy (or pcr) between an inclusive age range at this timestep. This
 #' defaults to n_detect_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * p_detect: the sum of probabilities of detection by microscopy between an
+#'  * p_detect_lm (or pcr): the sum of probabilities of detection by microscopy (or pcr) between an
 #' inclusive age range at this timestep. This
 #' defaults to p_detect_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * n_severe: number of humans with a severe infection between an inclusive
-#' age range at this timestep. Age ranges can be set with
-#' severe_prevalence_rendering_min_ages and severe_prevalence_rendering_max_ages parameters.
 #'  * n_inc: number of new infections for humans between an inclusive age range at this timestep.
 #' incidence columns can be set with
 #' incidence_rendering_min_ages and incidence_rendering_max_ages parameters.

R/render.R

@@ -4,8 +4,11 @@ in_age_range <- function(birth, timestep, lower, upper) {
 
 #' @title Render prevalence statistics
 #' 
-#' @description renders prevalence numerators and denominators for indivduals
-#' detected by microscopy and with severe malaria
+#' @description renders prevalence numerators and denominators for individuals
+#' detected by light microscopy and pcr, where those infected asymptomatically by
+#' P. falciparum have reduced probability of infection due to detectability
+#' immunity (reported as an integer sample: n_detect_lm, and summing over
+#' detection probabilities: p_detect_lm)
 #' 
 #' @param state human infection state
 #' @param birth variable for birth of the individual
@@ -32,7 +35,8 @@ create_prevelance_renderer <- function(
 
     clinically_detected <- state$get_index_of(c('Tr', 'D'))
     detected <- clinically_detected$copy()$or(asymptomatic_detected)
-
+    pcr_detected <- state$get_index_of(c('Tr', 'D', 'A', 'U'))
+
     for (i in seq_along(parameters$prevalence_rendering_min_ages)) {
       lower <- parameters$prevalence_rendering_min_ages[[i]]
       upper <- parameters$prevalence_rendering_max_ages[[i]]
@@ -43,17 +47,22 @@ create_prevelance_renderer <- function(
         timestep
       ) 
       renderer$render(
-        paste0('n_detect_', lower, '_', upper),
+        paste0('n_detect_lm_', lower, '_', upper),
         in_age$copy()$and(detected)$size(),
         timestep
       )
       renderer$render(
-        paste0('p_detect_', lower, '_', upper),
+        paste0('p_detect_lm_', lower, '_', upper),
         in_age$copy()$and(clinically_detected)$size() + sum(
           prob[bitset_index(asymptomatic, in_age)]
         ),
         timestep
       )
+      renderer$render(
+        paste0('n_detect_pcr_', lower, '_', upper),
+        pcr_detected$copy()$and(in_age)$size(),
+        timestep
+      )
     }
   }
 }