update Bujumbura values

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mpoxseir
 Title: Stochastic compartmental model of mpox transmission
-Version: 0.2.13
+Version: 0.2.14
 Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Ruth", "McCabe", role = c("aut")),

R/parameters.R

@@ -26,7 +26,7 @@
   ## Set up population denominators
   if(region %in% c("equateur","sudkivu")){
   country <- "Democratic Republic of Congo"
-  } else if(region %in% c("burundi","bujumbura")){
+  } else if(region %in% c("burundi","bujumbura","bujumbura_mairie")){
     country <- "Burundi"
   }
 
@@ -63,8 +63,11 @@
     p_SW <- 0.007 * 0.5 # 0.7% women (50%) 15-49 Laga et al - assume this holds down to age 12
   } else if (region == "sudkivu"){
     p_SW <- 0.03 * 0.5 # WHO press release
-  } else if (region %in% c("burundi","bujumbura")){
-    p_SW <- 0.028 * 0.5 # Laga et al 
+  } else if (region == "burundi"){
+    p_SW <- 0.028 * 0.5 # Laga et al
+  } else if (region %in% c("bujumbura","bujumbura_mairie")){
+   p_poss_SW  <-  sum(N_ASW + N_CSW)/ sum(N_age)
+   p_SW <- 3852 / (792503 * p_poss_SW)  ## key pops report, taken as median of Bujumbura Mairie in Figure 7 
   }
 
   N_CSW <- round(p_SW * N_CSW)
@@ -91,7 +94,7 @@
   ## HCW
   if(region %in% c("equateur","sudkivu")){
     p_HCW <- 133809 / sum(N_age)
-  } else if(region %in% c("burundi","bujumbura")){
+  } else if(region %in% c("burundi","bujumbura","bujumbura_mairie")){
     p_HCW <- 107721 / sum(N_age)
   }
 
@@ -255,7 +258,8 @@
   province_pop = list("equateur" = 1712000,
                       "sudkivu" = 6565000,
                       "burundi" = 11890781, ## taken from squire (above)
-                      "bujumbura" = 1277050) ## https://worldpopulationreview.com/cities/burundi/bujumbura
+                      "bujumbura" = 1095302,## Annuaire statisitique 2022 (from Olivier, in folder in Teams) - Bujumbura Mairie + Isare
+                      "bujumbura_mairie" = 792503) ## purely for testing purposes
 
   # proportion of susceptibles estimated to be unvaccinated (historically)
   # In Burundi, no-one born after 1970 thought to be historically (smallpox) vaccinated (source: Ruth's email from Jean-Claude)
@@ -265,7 +269,7 @@
     p_unvaccinated[which(age_bins$end < 40)] <- 1
     p_unvaccinated[which(age_bins$start >= 40)] <-
       c(0.54, 0.29, 0.29, 0.23, 0.21, 0.21, 0.21, 0.21)
-  } else if (region %in% c("burundi","bujumbura")) {
+  } else if (region %in% c("burundi","bujumbura","bujumbura_mairie")) {
     p_unvaccinated[which(age_bins$end < 55)] <- 1
     p_unvaccinated[which(age_bins$start >= 55)] <-
       c(0.23, 0.21, 0.21, 0.21, 0.21)
@@ -430,8 +434,9 @@
                              mixing_matrix = "Zimbabwe", overrides = list()) {
 
   ## Checking region
-  if (!(region %in% c("equateur", "sudkivu","burundi","bujumbura"))) {
-    stop("region must be equateur, sudkivu, burundi or bujumbura")
+  if (!(region %in% c("equateur", "sudkivu",
+                      "burundi","bujumbura","bujumbura_mairie"))) {
+    stop("region must be equateur, sudkivu, burundi, bujumbura or bujumbura-mairie")
   }
 
   ## Initialising variable that other parameters depend on
@@ -464,7 +469,7 @@
   Ea0 <- X0
 
 
-  if (region %in% c("sudkivu","burundi","bujumbura")) { # seeding in sex workers in Clade Ib affected areas
+  if (region %in% c("sudkivu","burundi","bujumbura","bujumbura_mairie")) { # seeding in sex workers in Clade Ib affected areas
 
     ## Extract sex-worker index and put initial infections in this group (unvaccinated strata)
     index_asw <- get_compartment_indices()$group$ASW
@@ -479,7 +484,7 @@
     Ea0[index_gen_pop, idx_unvax] <- seeding_infections
 
   } else {
-    stop("something is wrong with the name of the region - change to sudkivu, equateur, burundi or bujumbura")
+    stop("something is wrong with the name of the region - change to sudkivu, equateur, burundi, bujumbura or bujumbura_mairie")
   }
 
   p_unvaccinated <- demographic_params$p_unvaccinated

tests/testthat/test-parameters.R

@@ -85,4 +85,14 @@ test_that("unknown region throws error", {
 })
 
 
+test_that("total sex workers in Bujumbura as we expect", {
+
+  expect_equal(
+    sum(parameters_fixed("bujumbura_mairie",
+                         initial_infections = 10)$N0[c("CSW","ASW")]),
+    3852
+  )
+
+})
+