From bc43c4b7d5b148ecc8a183f984891287d14ce133 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Sat, 14 Dec 2024 18:22:23 +0000
Subject: [PATCH 01/19] changed CSW label to adult in get_group_bins

---
 R/parameters.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/parameters.R b/R/parameters.R
index 54f7f86..f7ee574 100644
--- a/R/parameters.R
+++ b/R/parameters.R
@@ -260,7 +260,7 @@ get_group_bins <- function() {
   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))
   ret <- rbind(age_bins, groups)
   ret$adults <- 1 - ret$children
   

From 5be44b112769ab8bec46790ef789714f936da47c Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Mon, 16 Dec 2024 19:34:24 +0000
Subject: [PATCH 02/19] children defined as those aged under 12 (as per
 vaccination authorisation)

---
 R/parameters.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/parameters.R b/R/parameters.R
index f7ee574..d470c04 100644
--- a/R/parameters.R
+++ b/R/parameters.R
@@ -255,7 +255,7 @@ 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)
   
   groups <- data.frame(label = c("CSW", "ASW", "PBS", "HCW"),
                        start = c(12, 18, 20, 20),

From 51c2a1e579c3e488dcbced8a9ab4498d40f28145 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Tue, 17 Dec 2024 11:57:48 +0000
Subject: [PATCH 03/19] update version number

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d9fa93b..8fa1690 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mpoxseir
 Title: Stochastic compartmental model of mpox transmission
-Version: 0.2.3
+Version: 0.2.4
 Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
                     email = "l.whittles@imperial.ac.uk"),
              person("Ruth", "McCabe", role = c("aut")),

From 16f028f7f02c23cea7eff46e32034083f001b47b Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Tue, 17 Dec 2024 11:58:55 +0000
Subject: [PATCH 04/19] updated model doc

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 53c6b82..a545d7a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
 
+# mpoxseir 0.2.4
+
+* Those aged 12 and above are considered adults (relevant to 12 - 17 & CSWs)
+
 # mpoxseir 0.2.3
 
 * Export cases by transmission route

From d098fd8f5d48d30dee996dbd02df48c1f9ba7835 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Tue, 17 Dec 2024 14:05:56 +0000
Subject: [PATCH 05/19] reupdate version & docs post rebase

---
 DESCRIPTION | 2 +-
 NEWS.md     | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8fa1690..f52022d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mpoxseir
 Title: Stochastic compartmental model of mpox transmission
-Version: 0.2.4
+Version: 0.2.5
 Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
                     email = "l.whittles@imperial.ac.uk"),
              person("Ruth", "McCabe", role = c("aut")),
diff --git a/NEWS.md b/NEWS.md
index a545d7a..4a083b2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,12 @@
 
-# mpoxseir 0.2.4
+# mpoxseir 0.2.5
 
 * Those aged 12 and above are considered adults (relevant to 12 - 17 & CSWs)
 
+# mpoxseir 0.2.4
+
+* Increase population of SWs in Sud Kivu
+
 # mpoxseir 0.2.3
 
 * Export cases by transmission route

From 9841359f078b4be11e791d33e0aa8285a9214426 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Tue, 17 Dec 2024 14:10:00 +0000
Subject: [PATCH 06/19] added test for Sud Kivu for code coverage

---
 tests/testthat/test-parameters.R | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-parameters.R b/tests/testthat/test-parameters.R
index 086b7ef..224c13d 100644
--- a/tests/testthat/test-parameters.R
+++ b/tests/testthat/test-parameters.R
@@ -4,7 +4,7 @@ test_that("assign seeds works", {
   expect_equal(assign_seeds(6, c(3, 2, 1)), c(3, 2, 1))
 })
 
-test_that("Mixing matrices are correct", {
+test_that("Mixing matrices are correct in Equateur", {
   pars <- parameters_demographic(region = "equateur")
   
   expect_equal(sum(pars$N0), sum(pars$N_age))
@@ -22,3 +22,22 @@ test_that("Mixing matrices are correct", {
                sum(upper.tri(M_age, diag = TRUE) * M_age))
   expect_equal(m, pars$m_gen_pop)
 })
+
+test_that("Mixing matrices are correct in Sud Kivu", {
+  pars <- parameters_demographic(region = "sudkivu")
+  
+  expect_equal(sum(pars$N0), sum(pars$N_age))
+  
+  M <- pars$total_contacts_nonsexual
+  M_age <- pars$total_contacts_age
+  
+  m <- M / pars$N0
+  m[is.na(m)] <- 0
+  
+  expect_true(isSymmetric(M))
+  expect_equal(sum(M_age - t(M_age)), 0)
+  
+  expect_equal(sum(upper.tri(M, diag = TRUE) * M), 
+               sum(upper.tri(M_age, diag = TRUE) * M_age))
+  expect_equal(m, pars$m_gen_pop)
+})

From c4e8c1c93ca1ca1399a7128054c0a777d6069b75 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Wed, 18 Dec 2024 11:18:05 +0000
Subject: [PATCH 07/19] updated prioritisation strategies in helper function
 due to age change

---
 tests/testthat/helper-mpoxseir.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/helper-mpoxseir.R b/tests/testthat/helper-mpoxseir.R
index 06eb07a..bd0abbb 100644
--- a/tests/testthat/helper-mpoxseir.R
+++ b/tests/testthat/helper-mpoxseir.R
@@ -34,8 +34,8 @@ 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
   
@@ -43,7 +43,7 @@ reference_pars_targeted_vax <- function(region = "equateur") {
                                 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
 

From 6e0bbaf7d528fcec796ca7a071a0fb8d1cdbec28 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Wed, 18 Dec 2024 12:03:08 +0000
Subject: [PATCH 08/19] lowered number of vaccine doses for children as was
 throwing error otherwise (vaccinating too quickly)

---
 tests/testthat/test-model-targeted-vax.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-model-targeted-vax.R b/tests/testthat/test-model-targeted-vax.R
index 9342e58..302a248 100644
--- a/tests/testthat/test-model-targeted-vax.R
+++ b/tests/testthat/test-model-targeted-vax.R
@@ -436,8 +436,8 @@ test_that("1st/2nd dose and adult/child prioritisation steps can be different de
   pars$prioritisation_strategy_children[,1] <- pars$prioritisation_strategy_children[,1]/4
   pars$prioritisation_strategy_adults[,1] <- pars$prioritisation_strategy_adults[,1]/4
   
-  # give lots of vaccines to push through quickly 
-  pars$daily_doses_children_value <- pars$daily_doses_children_value * 100
+  # give lots of vaccines to push through quickly
+  pars$daily_doses_children_value <- pars$daily_doses_children_value * 10
   pars$daily_doses_adults_value <- pars$daily_doses_adults_value * 100
   
   sys <- dust2::dust_system_create(model_targeted_vax(), pars, time = 1,

From fc4f892460d06629cf4d3c590191d9834e5b523d Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 10:30:52 +0000
Subject: [PATCH 09/19] moved boundary check one age group down to reflect new
 child/adult status

---
 inst/odin/model-targeted-vax.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/odin/model-targeted-vax.R b/inst/odin/model-targeted-vax.R
index a946902..a82c930 100644
--- a/inst/odin/model-targeted-vax.R
+++ b/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

From b2e50f64cc5f39c39da044d906c25847b532df18 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 10:32:21 +0000
Subject: [PATCH 10/19] updated boundaries check for all comps

---
 inst/odin/model-targeted-vax.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/odin/model-targeted-vax.R b/inst/odin/model-targeted-vax.R
index a82c930..b0b5930 100644
--- a/inst/odin/model-targeted-vax.R
+++ b/inst/odin/model-targeted-vax.R
@@ -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

From 677acd5e4a1f295153be4de51c8125f2b531e896 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 11:35:41 +0000
Subject: [PATCH 11/19] failing test expanded with more logic

---
 tests/testthat/test-model-targeted-vax.R | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/testthat/test-model-targeted-vax.R b/tests/testthat/test-model-targeted-vax.R
index 302a248..48117d3 100644
--- a/tests/testthat/test-model-targeted-vax.R
+++ b/tests/testthat/test-model-targeted-vax.R
@@ -733,8 +733,24 @@ test_that("Test vaccine outputs sum correctly", {
   group_bins <- get_group_bins()
   idx_15_plus <- which(group_bins$start >= 15)
   
+  # this is failing
   expect_equal(apply(y$N[idx_15_plus, idx$vax$two_dose, , -1], c(2, 3), sum),
                res["dose2_cumulative_15_plus", , -max(t)])
+  
+  
+  expect_equal(apply(y$N[idx_15_plus, idx$vax$one_dose, , -1], c(2, 3), sum),
+               res["dose1_cumulative_15_plus", , -max(t)])
+  
+  expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`),
+                         idx$vax$one_dose, , -1], c(2, 3), sum),
+               res["dose1_cumulative_05_14", , -max(t)])
+  
+  expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`),
+                         idx$vax$two_dose, , -1], c(2, 3), sum),
+               res["dose2_cumulative_05_14", , -max(t)])
+  
+  
+  # passes from here
   expect_equal(y$N[idx$group$`0-4`, idx$vax$one_dose, , -1],
                res["dose1_cumulative_00_04", , -max(t)])
   

From 2c1620e0f957c8cfe7ec52325f7b61dce3a4673f Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 11:36:05 +0000
Subject: [PATCH 12/19] regenerate model

---
 R/dust.R                         |  2 +-
 inst/dust/model-targeted-vax.cpp |  8 ++++----
 src/model-targeted-vax.cpp       | 10 +++++-----
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/R/dust.R b/R/dust.R
index e063d4a..f678c2d 100644
--- a/R/dust.R
+++ b/R/dust.R
@@ -1,4 +1,4 @@
-## Generated by dust2 (version 0.3.12) - do not edit
+## Generated by dust2 (version 0.3.11) - do not edit
 model_targeted_vax <- structure(
   function() get("model_targeted_vax"),
   class = "dust_system_generator",
diff --git a/inst/dust/model-targeted-vax.cpp b/inst/dust/model-targeted-vax.cpp
index bfd5a97..3f186d4 100644
--- a/inst/dust/model-targeted-vax.cpp
+++ b/inst/dust/model-targeted-vax.cpp
@@ -1074,7 +1074,7 @@ 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]]));
     }
@@ -1086,7 +1086,7 @@ 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]]));
     }
@@ -1098,7 +1098,7 @@ 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]]));
     }
@@ -1110,7 +1110,7 @@ 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]]));
     }
diff --git a/src/model-targeted-vax.cpp b/src/model-targeted-vax.cpp
index 85706a9..74cab42 100644
--- a/src/model-targeted-vax.cpp
+++ b/src/model-targeted-vax.cpp
@@ -1,4 +1,4 @@
-// Generated by dust2 (version 0.3.12) - do not edit
+// Generated by dust2 (version 0.3.11) - do not edit
 
 // Generated by odin2 (version 0.3.14) - do not edit
 #include <dust2/common.hpp>
@@ -1076,7 +1076,7 @@ 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]]));
     }
@@ -1088,7 +1088,7 @@ 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]]));
     }
@@ -1100,7 +1100,7 @@ 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]]));
     }
@@ -1112,7 +1112,7 @@ 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]]));
     }

From 85b1afb067df2f772ae3406231b520df43e77070 Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 12:11:10 +0000
Subject: [PATCH 13/19] added 15+ indicator to get_group_bins to align with
 model outputs

---
 R/parameters.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/parameters.R b/R/parameters.R
index 72c0382..32e787c 100644
--- a/R/parameters.R
+++ b/R/parameters.R
@@ -264,11 +264,13 @@ get_group_bins <- function() {
   
   age_bins <- get_age_bins()
   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(0, 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
   

From 7adfa77fcc009667b49eac929f5a03203a5038cd Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 12:14:12 +0000
Subject: [PATCH 14/19] CSWs vaccine split done by round rather than binomial

---
 inst/odin/model-targeted-vax.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/inst/odin/model-targeted-vax.R b/inst/odin/model-targeted-vax.R
index b0b5930..912dd26 100644
--- a/inst/odin/model-targeted-vax.R
+++ b/inst/odin/model-targeted-vax.R
@@ -534,7 +534,7 @@ 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 <-
@@ -557,7 +557,7 @@ 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 <-

From f1db862e188e8a7b562616b72a7d833ce4a06f4c Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 12:30:11 +0000
Subject: [PATCH 15/19] test updated to resolve 2nd dose issue

---
 inst/dust/model-targeted-vax.cpp         |  4 ++--
 src/model-targeted-vax.cpp               |  4 ++--
 tests/testthat/test-model-targeted-vax.R | 29 +++++++++++-------------
 3 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/inst/dust/model-targeted-vax.cpp b/inst/dust/model-targeted-vax.cpp
index 3f186d4..741bea1 100644
--- a/inst/dust/model-targeted-vax.cpp
+++ b/inst/dust/model-targeted-vax.cpp
@@ -1162,14 +1162,14 @@ 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]];
diff --git a/src/model-targeted-vax.cpp b/src/model-targeted-vax.cpp
index 74cab42..8ef3e0e 100644
--- a/src/model-targeted-vax.cpp
+++ b/src/model-targeted-vax.cpp
@@ -1164,14 +1164,14 @@ 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]];
diff --git a/tests/testthat/test-model-targeted-vax.R b/tests/testthat/test-model-targeted-vax.R
index 48117d3..e71031f 100644
--- a/tests/testthat/test-model-targeted-vax.R
+++ b/tests/testthat/test-model-targeted-vax.R
@@ -731,24 +731,21 @@ test_that("Test vaccine outputs sum correctly", {
   idx <- get_compartment_indices()
   idx_age <- seq_len(nrow(get_age_bins()))
   group_bins <- get_group_bins()
-  idx_15_plus <- which(group_bins$start >= 15)
+  idx_15_plus <- which(group_bins$start >=15)
   
-  # this is failing
-  expect_equal(apply(y$N[idx_15_plus, idx$vax$two_dose, , -1], c(2, 3), sum),
+  ## age based tests
+  ## second doses
+  expect_equal(apply(y$N[idx_15_plus, idx$vax$two_dose, , -1], c(2, 3), sum) + floor(0.5 * (y$N[17, idx$vax$two_dose, , -1])),
                res["dose2_cumulative_15_plus", , -max(t)])
-  
-  
-  expect_equal(apply(y$N[idx_15_plus, idx$vax$one_dose, , -1], c(2, 3), sum),
-               res["dose1_cumulative_15_plus", , -max(t)])
-  
-  expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`),
-                         idx$vax$one_dose, , -1], c(2, 3), sum),
-               res["dose1_cumulative_05_14", , -max(t)])
-  
-  expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`),
-                         idx$vax$two_dose, , -1], c(2, 3), sum),
-               res["dose2_cumulative_05_14", , -max(t)])
-  
+   expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), idx$vax$two_dose, , -1], c(2, 3), sum) + ceiling(0.5 * (y$N[17, idx$vax$two_dose, , -1])),
+               res["dose2_cumulative_05_14", , -max(t)]) 
+  
+   # ## 1st doses 
+   # expect_equal(apply(y$N[idx_15_plus, idx$vax$one_dose, , -1], c(2, 3), sum) + floor(0.5 * (y$N[17, idx$vax$one_dose, , -1])),
+   #              res["dose1_cumulative_15_plus", , -max(t)])
+   # expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), idx$vax$one_dose, , -1], c(2, 3), sum) + ceiling(0.5 * (y$N[17, idx$vax$one_dose, , -1])),
+   #              res["dose1_cumulative_05_14", , -max(t)]) 
+   
   
   # passes from here
   expect_equal(y$N[idx$group$`0-4`, idx$vax$one_dose, , -1],

From 15919dc5f4e19c965ee35bc2920d6fa48d2e4f0d Mon Sep 17 00:00:00 2001
From: ruthmccabe <ruth.mccabe17@imperial.ac.uk>
Date: Fri, 20 Dec 2024 13:44:24 +0000
Subject: [PATCH 16/19] updated 1st dose test & commented out (but not deleted)
 due to rounding issue

---
 tests/testthat/test-model-targeted-vax.R | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-model-targeted-vax.R b/tests/testthat/test-model-targeted-vax.R
index e71031f..fc26f60 100644
--- a/tests/testthat/test-model-targeted-vax.R
+++ b/tests/testthat/test-model-targeted-vax.R
@@ -740,14 +740,17 @@ test_that("Test vaccine outputs sum correctly", {
    expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), idx$vax$two_dose, , -1], c(2, 3), sum) + ceiling(0.5 * (y$N[17, idx$vax$two_dose, , -1])),
                res["dose2_cumulative_05_14", , -max(t)]) 
   
-   # ## 1st doses 
-   # expect_equal(apply(y$N[idx_15_plus, idx$vax$one_dose, , -1], c(2, 3), sum) + floor(0.5 * (y$N[17, idx$vax$one_dose, , -1])),
-   #              res["dose1_cumulative_15_plus", , -max(t)])
-   # expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), idx$vax$one_dose, , -1], c(2, 3), sum) + ceiling(0.5 * (y$N[17, idx$vax$one_dose, , -1])),
-   #              res["dose1_cumulative_05_14", , -max(t)]) 
    
-  
-  # passes from here
+   # # ## 1st doses - slight issues here to do with rounding but very close
+   # expect_equal(apply(y$N[idx_15_plus, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(3, 4), sum)+
+   # floor(0.5 * apply(y$N[17, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(2,3), sum)),
+   # res["dose1_cumulative_15_plus", , -max(t)])
+   # 
+   # expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(3, 4), sum)+
+   #                floor(0.5 * apply(y$N[17, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(2,3), sum)),
+   #              res["dose1_cumulative_05_14", , -max(t)])
+
+   
   expect_equal(y$N[idx$group$`0-4`, idx$vax$one_dose, , -1],
                res["dose1_cumulative_00_04", , -max(t)])
   

From 9607e78c90e0d6b88e8962b8738cd1b049a4860a Mon Sep 17 00:00:00 2001
From: edknock <edwardknock@gmail.com>
Date: Mon, 6 Jan 2025 12:22:08 +0000
Subject: [PATCH 17/19] bump version number

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f52022d..df8e5cc 100644
--- a/DESCRIPTION
+++ b/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")),

From 1755e59b0ae5930314a020f448e89af39ed254bb Mon Sep 17 00:00:00 2001
From: edknock <edwardknock@gmail.com>
Date: Mon, 6 Jan 2025 13:03:12 +0000
Subject: [PATCH 18/19] fix tests

---
 tests/testthat/test-model-targeted-vax.R | 44 +++++++++++++++++-------
 1 file changed, 32 insertions(+), 12 deletions(-)

diff --git a/tests/testthat/test-model-targeted-vax.R b/tests/testthat/test-model-targeted-vax.R
index 9075acd..9a3d67e 100644
--- a/tests/testthat/test-model-targeted-vax.R
+++ b/tests/testthat/test-model-targeted-vax.R
@@ -781,27 +781,47 @@ test_that("Test vaccine outputs sum correctly", {
   group_bins <- get_group_bins()
   idx_15_plus <- which(group_bins$start >=15)
   
-  ## age based tests
+  ## function that does a diff but appends 0 at the beginning
+  diff0 <- function(x) c(0, diff(x))
+  
+  ## age/group based tests
   ## second doses
-  expect_equal(apply(y$N[idx_15_plus, idx$vax$two_dose, , ], c(2, 3), sum) + floor(0.5 * (y$N[17, idx$vax$two_dose, , ])),
+  expect_equal(y$N[idx$group$ASW, idx$vax$two_dose, , ], y$dose2_cumulative_ASW)
+  expect_equal(y$N[idx$group$CSW, idx$vax$two_dose, , ], y$dose2_cumulative_CSW)
+  expect_equal(y$N[idx$group$HCW, idx$vax$two_dose, , ], y$dose2_cumulative_HCW)
+  expect_equal(y$N[idx$group$PBS, idx$vax$two_dose, , ], y$dose2_cumulative_PBS)
+  
+  ## This is a bit fiddly but we calculate daily incidence from cumulative,
+  ## split in half (taking the floor) and then calculate cumulative of that
+  dose2_cumulative_CSW_15_plus <- 
+    t(apply(floor(0.5 * apply(y$dose2_cumulative_CSW, 1, diff0)), 2, cumsum))
+  expect_equal(apply(y$N[idx_15_plus, idx$vax$two_dose, , ], c(2, 3), sum) + 
+                 dose2_cumulative_CSW_15_plus,
                res["dose2_cumulative_15_plus", , ])
-  expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), idx$vax$two_dose, , ], c(2, 3), sum) + ceiling(0.5 * (y$N[17, idx$vax$two_dose, , ])),
+  expect_equal(apply(y$N[c(idx$group$`5-9`, idx$group$`10-14`), idx$vax$two_dose, , ], c(2, 3), sum) +
+                 y$dose2_cumulative_CSW - dose2_cumulative_CSW_15_plus,
                res["dose2_cumulative_05_14", , ])
   
    
-   # # ## 1st doses - slight issues here to do with rounding but very close
-   # expect_equal(apply(y$N[idx_15_plus, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(3, 4), sum)+
-   # floor(0.5 * apply(y$N[17, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(2,3), sum)),
-   # res["dose1_cumulative_15_plus", , -max(t)])
-   # 
-   # expect_equal(apply(y$N[c(idx$group$`5-9`,idx$group$`10-14`), c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(3, 4), sum)+
-   #                floor(0.5 * apply(y$N[17, c(idx$vax$one_dose,idx$vax$two_dose), , -1], c(2,3), sum)),
-   #              res["dose1_cumulative_05_14", , -max(t)])
+  ## first doses - note we have to account also for people who have had two doses!
+  expect_equal(apply(y$N[idx$group$ASW, c(idx$vax$one_dose, idx$vax$two_dose), , ], c(2, 3), sum), y$dose1_cumulative_ASW)
+  expect_equal(apply(y$N[idx$group$CSW, c(idx$vax$one_dose, idx$vax$two_dose), , ], c(2, 3), sum), y$dose1_cumulative_CSW)
+  expect_equal(apply(y$N[idx$group$HCW, c(idx$vax$one_dose, idx$vax$two_dose), , ], c(2, 3), sum), y$dose1_cumulative_HCW)
+  expect_equal(apply(y$N[idx$group$PBS, c(idx$vax$one_dose, idx$vax$two_dose), , ], c(2, 3), sum), y$dose1_cumulative_PBS)
+  
+  dose1_cumulative_CSW_15_plus <- 
+    t(apply(floor(0.5 * apply(y$dose1_cumulative_CSW, 1, diff0)), 2, cumsum)) 
+  expect_equal(apply(y$N[idx_15_plus, c(idx$vax$one_dose,idx$vax$two_dose), , ], c(3, 4), sum) +
+                 dose1_cumulative_CSW_15_plus,
+               res["dose1_cumulative_15_plus", , ])
+  expect_equal(apply(y$N[c(idx$group$`5-9`, idx$group$`10-14`), c(idx$vax$one_dose, idx$vax$two_dose), , ], c(3, 4), sum) +
+                 y$dose1_cumulative_CSW - dose1_cumulative_CSW_15_plus,
+               res["dose1_cumulative_05_14", , ])
 
-   
   expect_equal(y$N[idx$group$`0-4`, idx$vax$one_dose, , ],
                res["dose1_cumulative_00_04", , ])
   
+  
   # check age outputs sum to total doses given
   expect_equal(res["total_vax_1stdose", , ],
                res["dose1_cumulative_00_04", , ] +

From 3a6d9c38fde7a12e5c5204b5353ebf7891caf6c8 Mon Sep 17 00:00:00 2001
From: edknock <edwardknock@gmail.com>
Date: Mon, 6 Jan 2025 14:14:03 +0000
Subject: [PATCH 19/19] correct news

---
 NEWS.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 4a083b2..746dfe2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,12 @@
 
-# mpoxseir 0.2.5
+# 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