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

@@ -36,9 +36,6 @@
 #' 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.

src/Random.cpp

@@ -60,7 +60,7 @@ void Random::prop_sample_bucket(
 
     // all probabilities are the same
     if (heavy == n) {
-        for (auto i = 0; i < size; ++i) {
+        for (size_t i = 0; i < size; ++i) {
             *result = (*rng)((uint64_t)n);
             ++result;
         }
@@ -121,9 +121,9 @@ void Random::prop_sample_bucket(
     }
 
     // sample
-    for (auto i = 0; i < size; ++i) {
+    for (size_t i = 0; i < size; ++i) {
         size_t bucket = (*rng)((uint64_t)n);
-        double acceptance = dqrng::uniform01((*rng)());
+        double acceptance = rng->uniform01();
         *result = (acceptance < dividing_probs[bucket]) ? bucket :
             alternative_index[bucket];
         ++result;