Making 12 the new adult age

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mpoxseir
 Title: Stochastic compartmental model of mpox transmission
-Version: 0.2.5
+Version: 0.2.6
 Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
                     email = "l.whittles@imperial.ac.uk"),
              person("Ruth", "McCabe", role = c("aut")),

NEWS.md

@@ -1,4 +1,16 @@
 
+# mpoxseir 0.2.6
+
+* Those aged 12 and above are considered adults (relevant to 12 - 17 & CSWs)
+
+# mpoxseir 0.2.5
+
+* Fixed lag issue affecting some states
+
+# mpoxseir 0.2.4
+
+* Increase population of SWs in Sud Kivu
+
 # mpoxseir 0.2.3
 
 * Export cases by transmission route

R/parameters.R

@@ -263,12 +263,14 @@ get_compartment_indices <- function() {
 get_group_bins <- function() {
 
   age_bins <- get_age_bins()
-  age_bins$children <- proportion_in_age_bins(0, 17)
+  age_bins$children <- proportion_in_age_bins(0, 11)
+  age_bins$fifteen_plus <- 1 - proportion_in_age_bins(0,14)
 
   groups <- data.frame(label = c("CSW", "ASW", "PBS", "HCW"),
                        start = c(12, 18, 20, 20),
                        end = c(17, 49, 49, 69),
-                       children = c(1, 0, 0, 0))
+                       children = c(0, 0, 0, 0),
+                       fifteen_plus = c(0.5,1,1,1))
   ret <- rbind(age_bins, groups)
   ret$adults <- 1 - ret$children
 

inst/dust/model-targeted-vax.cpp

@@ -1086,7 +1086,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_S.dim[0]; ++i) {
       internal.n_vaccination_t_S[i - 1 + shared.dim.n_vaccination_t_S.mult[1]] = internal.n_vaccination_t_S_children[i - 1] + internal.n_vaccination_t_S_adults[i - 1];
     }
-    internal.n_vaccination_t_S[3 + shared.dim.n_vaccination_t_S.mult[1]] = monty::math::min(internal.n_vaccination_t_S[3 + shared.dim.n_vaccination_t_S.mult[1]], S[3 + shared.dim.S.mult[1]]);
+    internal.n_vaccination_t_S[2 + shared.dim.n_vaccination_t_S.mult[1]] = monty::math::min(internal.n_vaccination_t_S[2 + shared.dim.n_vaccination_t_S.mult[1]], S[2 + shared.dim.S.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_S.dim[0]; ++i) {
       internal.n_vaccination_t_S[i - 1 + 2 * shared.dim.n_vaccination_t_S.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * S[i - 1 + 2 * shared.dim.S.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), S[i - 1 + 2 * shared.dim.S.mult[1]]));
     }
@@ -1098,7 +1098,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Ea.dim[0]; ++i) {
       internal.n_vaccination_t_Ea[i - 1 + shared.dim.n_vaccination_t_Ea.mult[1]] = internal.n_vaccination_t_Ea_children[i - 1] + internal.n_vaccination_t_Ea_adults[i - 1];
     }
-    internal.n_vaccination_t_Ea[3 + shared.dim.n_vaccination_t_Ea.mult[1]] = monty::math::min(internal.n_vaccination_t_Ea[3 + shared.dim.n_vaccination_t_Ea.mult[1]], Ea[3 + shared.dim.Ea.mult[1]]);
+    internal.n_vaccination_t_Ea[2 + shared.dim.n_vaccination_t_Ea.mult[1]] = monty::math::min(internal.n_vaccination_t_Ea[2 + shared.dim.n_vaccination_t_Ea.mult[1]], Ea[2 + shared.dim.Ea.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Ea.dim[0]; ++i) {
       internal.n_vaccination_t_Ea[i - 1 + 2 * shared.dim.n_vaccination_t_Ea.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * Ea[i - 1 + 2 * shared.dim.Ea.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), Ea[i - 1 + 2 * shared.dim.Ea.mult[1]]));
     }
@@ -1110,7 +1110,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Eb.dim[0]; ++i) {
       internal.n_vaccination_t_Eb[i - 1 + shared.dim.n_vaccination_t_Eb.mult[1]] = internal.n_vaccination_t_Eb_children[i - 1] + internal.n_vaccination_t_Eb_adults[i - 1];
     }
-    internal.n_vaccination_t_Eb[3 + shared.dim.n_vaccination_t_Eb.mult[1]] = monty::math::min(internal.n_vaccination_t_Eb[3 + shared.dim.n_vaccination_t_Eb.mult[1]], Eb[3 + shared.dim.Eb.mult[1]]);
+    internal.n_vaccination_t_Eb[2 + shared.dim.n_vaccination_t_Eb.mult[1]] = monty::math::min(internal.n_vaccination_t_Eb[2 + shared.dim.n_vaccination_t_Eb.mult[1]], Eb[2 + shared.dim.Eb.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Eb.dim[0]; ++i) {
       internal.n_vaccination_t_Eb[i - 1 + 2 * shared.dim.n_vaccination_t_Eb.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * Eb[i - 1 + 2 * shared.dim.Eb.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), Eb[i - 1 + 2 * shared.dim.Eb.mult[1]]));
     }
@@ -1122,7 +1122,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_R.dim[0]; ++i) {
       internal.n_vaccination_t_R[i - 1 + shared.dim.n_vaccination_t_R.mult[1]] = internal.n_vaccination_t_R_children[i - 1] + internal.n_vaccination_t_R_adults[i - 1];
     }
-    internal.n_vaccination_t_R[3 + shared.dim.n_vaccination_t_R.mult[1]] = monty::math::min(internal.n_vaccination_t_R[3 + shared.dim.n_vaccination_t_R.mult[1]], R[3 + shared.dim.R.mult[1]]);
+    internal.n_vaccination_t_R[2 + shared.dim.n_vaccination_t_R.mult[1]] = monty::math::min(internal.n_vaccination_t_R[2 + shared.dim.n_vaccination_t_R.mult[1]], R[2 + shared.dim.R.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_R.dim[0]; ++i) {
       internal.n_vaccination_t_R[i - 1 + 2 * shared.dim.n_vaccination_t_R.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * R[i - 1 + 2 * shared.dim.R.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), R[i - 1 + 2 * shared.dim.R.mult[1]]));
     }
@@ -1179,14 +1179,14 @@ class model_targeted_vax {
     }
     const real_type new_dose1 = dust2::array::sum<real_type>(internal.n_vaccination_t.data(), shared.dim.n_vaccination_t, {0, shared.dim.n_vaccination_t.dim[0] - 1}, {1, 1});
     const real_type new_dose1_00_04 = internal.n_vaccination_t[shared.dim.n_vaccination_t.mult[1]];
-    const real_type new_dose1_SW_12_14 = monty::random::binomial<real_type>(rng_state, internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]], static_cast<real_type>(0.5));
+    const real_type new_dose1_SW_12_14 = monty::math::round(internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]] * static_cast<real_type>(0.5));
     const real_type new_dose1_CSW = internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_ASW = internal.n_vaccination_t[17 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_PBS = internal.n_vaccination_t[18 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_HCW = internal.n_vaccination_t[19 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2 = dust2::array::sum<real_type>(internal.n_vaccination_t.data(), shared.dim.n_vaccination_t, {0, shared.dim.n_vaccination_t.dim[0] - 1}, {2, 2});
     const real_type new_dose2_00_04 = internal.n_vaccination_t[2 * shared.dim.n_vaccination_t.mult[1]];
-    const real_type new_dose2_SW_12_14 = monty::random::binomial<real_type>(rng_state, internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]], static_cast<real_type>(0.5));
+    const real_type new_dose2_SW_12_14 = monty::math::round(internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]] * static_cast<real_type>(0.5));
     const real_type new_dose2_CSW = internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2_ASW = internal.n_vaccination_t[17 + 2 * shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2_PBS = internal.n_vaccination_t[18 + 2 * shared.dim.n_vaccination_t.mult[1]];

inst/odin/model-targeted-vax.R

@@ -222,7 +222,7 @@ n_vaccination_t_S[, 2] <-
 
 ## for the boundary case do an extra check that we haven't gone over the number
 ## of people in each compartment
-n_vaccination_t_S[4, 2] <- min(n_vaccination_t_S[4, 2], S[4, 2])
+n_vaccination_t_S[3, 2] <- min(n_vaccination_t_S[3, 2], S[3, 2])
 
 ## allocate 2nd doses (adults only for now)
 n_vaccination_t_S[, 3] <- if (sum(n_eligible_for_dose2_adults[]) == 0) 0 else
@@ -262,7 +262,7 @@ n_vaccination_t_Ea[, 2] <-
 
 ## for the boundary case do an extra check that we haven't gone over the number
 ## of people in each compartment
-n_vaccination_t_Ea[4, 2] <- min(n_vaccination_t_Ea[4, 2], Ea[4, 2])
+n_vaccination_t_Ea[3, 2] <- min(n_vaccination_t_Ea[3, 2], Ea[3, 2])
 
 ## adults 2nd doses
 n_vaccination_t_Ea[, 3] <- if (sum(n_eligible_for_dose2_adults[]) == 0) 0 else
@@ -302,7 +302,7 @@ n_vaccination_t_Eb[, 2] <-
 
 ## for the boundary case do an extra check that we haven't gone over the number
 ## of people in each compartment
-n_vaccination_t_Eb[4, 2] <- min(n_vaccination_t_Eb[4, 2], Eb[4, 2])
+n_vaccination_t_Eb[3, 2] <- min(n_vaccination_t_Eb[3, 2], Eb[3, 2])
 
 ## adults 2nd doses
 n_vaccination_t_Eb[, 3] <- if (sum(n_eligible_for_dose2_adults[]) == 0) 0 else
@@ -342,7 +342,7 @@ n_vaccination_t_R[, 2] <-
 
 ## for the boundary case do an extra check that we haven't gone over the number
 ## of people in each compartment
-n_vaccination_t_R[4, 2] <- min(n_vaccination_t_R[4, 2], R[4, 2])
+n_vaccination_t_R[3, 2] <- min(n_vaccination_t_R[3, 2], R[3, 2])
 
 ## adults 2nd doses
 n_vaccination_t_R[, 3] <- if (sum(n_eligible_for_dose2_adults[]) == 0) 0 else
@@ -549,7 +549,7 @@ n_vaccination_t[, ] <- n_vaccination_t_S[i, j] + n_vaccination_t_Ea[i, j] +
 
 new_dose1 <- sum(n_vaccination_t[, 2])
 new_dose1_00_04 <- n_vaccination_t[1, 2]
-new_dose1_SW_12_14 <- Binomial(n_vaccination_t[17, 2], 0.5)
+new_dose1_SW_12_14 <- round(n_vaccination_t[17, 2] * 0.5)
 new_dose1_SW_15_17 <- n_vaccination_t[17, 2] - new_dose1_SW_12_14
 new_dose1_05_14 <- sum(n_vaccination_t[2:3, 2]) + new_dose1_SW_12_14
 new_dose1_15_plus <-
@@ -572,7 +572,7 @@ update(dose1_inc_HCW) <- dose1_inc_HCW + new_dose1_HCW
 
 new_dose2 <- sum(n_vaccination_t[, 3])
 new_dose2_00_04 <- n_vaccination_t[1, 3]
-new_dose2_SW_12_14 <- Binomial(n_vaccination_t[17, 3], 0.5)
+new_dose2_SW_12_14 <- round(n_vaccination_t[17, 3] * 0.5)
 new_dose2_SW_15_17 <- n_vaccination_t[17, 3] - new_dose2_SW_12_14
 new_dose2_05_14 <- sum(n_vaccination_t[2:3, 3]) + new_dose2_SW_12_14
 new_dose2_15_plus <-

src/model-targeted-vax.cpp

@@ -1088,7 +1088,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_S.dim[0]; ++i) {
       internal.n_vaccination_t_S[i - 1 + shared.dim.n_vaccination_t_S.mult[1]] = internal.n_vaccination_t_S_children[i - 1] + internal.n_vaccination_t_S_adults[i - 1];
     }
-    internal.n_vaccination_t_S[3 + shared.dim.n_vaccination_t_S.mult[1]] = monty::math::min(internal.n_vaccination_t_S[3 + shared.dim.n_vaccination_t_S.mult[1]], S[3 + shared.dim.S.mult[1]]);
+    internal.n_vaccination_t_S[2 + shared.dim.n_vaccination_t_S.mult[1]] = monty::math::min(internal.n_vaccination_t_S[2 + shared.dim.n_vaccination_t_S.mult[1]], S[2 + shared.dim.S.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_S.dim[0]; ++i) {
       internal.n_vaccination_t_S[i - 1 + 2 * shared.dim.n_vaccination_t_S.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * S[i - 1 + 2 * shared.dim.S.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), S[i - 1 + 2 * shared.dim.S.mult[1]]));
     }
@@ -1100,7 +1100,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Ea.dim[0]; ++i) {
       internal.n_vaccination_t_Ea[i - 1 + shared.dim.n_vaccination_t_Ea.mult[1]] = internal.n_vaccination_t_Ea_children[i - 1] + internal.n_vaccination_t_Ea_adults[i - 1];
     }
-    internal.n_vaccination_t_Ea[3 + shared.dim.n_vaccination_t_Ea.mult[1]] = monty::math::min(internal.n_vaccination_t_Ea[3 + shared.dim.n_vaccination_t_Ea.mult[1]], Ea[3 + shared.dim.Ea.mult[1]]);
+    internal.n_vaccination_t_Ea[2 + shared.dim.n_vaccination_t_Ea.mult[1]] = monty::math::min(internal.n_vaccination_t_Ea[2 + shared.dim.n_vaccination_t_Ea.mult[1]], Ea[2 + shared.dim.Ea.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Ea.dim[0]; ++i) {
       internal.n_vaccination_t_Ea[i - 1 + 2 * shared.dim.n_vaccination_t_Ea.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * Ea[i - 1 + 2 * shared.dim.Ea.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), Ea[i - 1 + 2 * shared.dim.Ea.mult[1]]));
     }
@@ -1112,7 +1112,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Eb.dim[0]; ++i) {
       internal.n_vaccination_t_Eb[i - 1 + shared.dim.n_vaccination_t_Eb.mult[1]] = internal.n_vaccination_t_Eb_children[i - 1] + internal.n_vaccination_t_Eb_adults[i - 1];
     }
-    internal.n_vaccination_t_Eb[3 + shared.dim.n_vaccination_t_Eb.mult[1]] = monty::math::min(internal.n_vaccination_t_Eb[3 + shared.dim.n_vaccination_t_Eb.mult[1]], Eb[3 + shared.dim.Eb.mult[1]]);
+    internal.n_vaccination_t_Eb[2 + shared.dim.n_vaccination_t_Eb.mult[1]] = monty::math::min(internal.n_vaccination_t_Eb[2 + shared.dim.n_vaccination_t_Eb.mult[1]], Eb[2 + shared.dim.Eb.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_Eb.dim[0]; ++i) {
       internal.n_vaccination_t_Eb[i - 1 + 2 * shared.dim.n_vaccination_t_Eb.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * Eb[i - 1 + 2 * shared.dim.Eb.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), Eb[i - 1 + 2 * shared.dim.Eb.mult[1]]));
     }
@@ -1124,7 +1124,7 @@ class model_targeted_vax {
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_R.dim[0]; ++i) {
       internal.n_vaccination_t_R[i - 1 + shared.dim.n_vaccination_t_R.mult[1]] = internal.n_vaccination_t_R_children[i - 1] + internal.n_vaccination_t_R_adults[i - 1];
     }
-    internal.n_vaccination_t_R[3 + shared.dim.n_vaccination_t_R.mult[1]] = monty::math::min(internal.n_vaccination_t_R[3 + shared.dim.n_vaccination_t_R.mult[1]], R[3 + shared.dim.R.mult[1]]);
+    internal.n_vaccination_t_R[2 + shared.dim.n_vaccination_t_R.mult[1]] = monty::math::min(internal.n_vaccination_t_R[2 + shared.dim.n_vaccination_t_R.mult[1]], R[2 + shared.dim.R.mult[1]]);
     for (size_t i = 1; i <= shared.dim.n_vaccination_t_R.dim[0]; ++i) {
       internal.n_vaccination_t_R[i - 1 + 2 * shared.dim.n_vaccination_t_R.mult[1]] = (dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults) == 0 ? 0 : monty::math::min(monty::math::floor((internal.daily_doses_adults_t[2] * R[i - 1 + 2 * shared.dim.R.mult[1]] * shared.prioritisation_strategy_adults[i - 1 + (prioritisation_step_2nd_dose_adults - 1) * shared.dim.prioritisation_strategy_adults.mult[1]]) / dust2::array::sum<real_type>(internal.n_eligible_for_dose2_adults.data(), shared.dim.n_eligible_for_dose2_adults)), R[i - 1 + 2 * shared.dim.R.mult[1]]));
     }
@@ -1181,14 +1181,14 @@ class model_targeted_vax {
     }
     const real_type new_dose1 = dust2::array::sum<real_type>(internal.n_vaccination_t.data(), shared.dim.n_vaccination_t, {0, shared.dim.n_vaccination_t.dim[0] - 1}, {1, 1});
     const real_type new_dose1_00_04 = internal.n_vaccination_t[shared.dim.n_vaccination_t.mult[1]];
-    const real_type new_dose1_SW_12_14 = monty::random::binomial<real_type>(rng_state, internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]], static_cast<real_type>(0.5));
+    const real_type new_dose1_SW_12_14 = monty::math::round(internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]] * static_cast<real_type>(0.5));
     const real_type new_dose1_CSW = internal.n_vaccination_t[16 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_ASW = internal.n_vaccination_t[17 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_PBS = internal.n_vaccination_t[18 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose1_HCW = internal.n_vaccination_t[19 + shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2 = dust2::array::sum<real_type>(internal.n_vaccination_t.data(), shared.dim.n_vaccination_t, {0, shared.dim.n_vaccination_t.dim[0] - 1}, {2, 2});
     const real_type new_dose2_00_04 = internal.n_vaccination_t[2 * shared.dim.n_vaccination_t.mult[1]];
-    const real_type new_dose2_SW_12_14 = monty::random::binomial<real_type>(rng_state, internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]], static_cast<real_type>(0.5));
+    const real_type new_dose2_SW_12_14 = monty::math::round(internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]] * static_cast<real_type>(0.5));
     const real_type new_dose2_CSW = internal.n_vaccination_t[16 + 2 * shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2_ASW = internal.n_vaccination_t[17 + 2 * shared.dim.n_vaccination_t.mult[1]];
     const real_type new_dose2_PBS = internal.n_vaccination_t[18 + 2 * shared.dim.n_vaccination_t.mult[1]];

tests/testthat/helper-mpoxseir.R

@@ -34,16 +34,16 @@ reference_pars_targeted_vax <- function(region = "equateur") {
                                   times=pars$N_prioritisation_steps_children),
                               ncol=pars$N_prioritisation_steps_children,
                               byrow=FALSE)
-  priority_children[c(3,4,17),1] <- 0
-  priority_children[c(4,17),2] <- 0
+  priority_children[c(2,3),1] <- 0
+  priority_children[3,2] <- 0
 
   pars$prioritisation_strategy_children <- priority_children * 0.5
 
   priority_adults <- matrix(rep(pars$prioritisation_strategy_adults,
                                 times=pars$N_prioritisation_steps_adults),
                             ncol=pars$N_prioritisation_steps_adults,
                             byrow=FALSE)
-  priority_adults[c(4:16,20),1] <- 0
+  priority_adults[c(3:16),1] <- 0
 
   pars$prioritisation_strategy_adults <- priority_adults * 0.5