p.v has a constant asymptomatic infectivity, in contrast to p.f where…

… infectivity is affected by age and immunity. We must therefore change this when asymptomatic infectivity is assigned (when an individual become asymptomatic). This occurs in initial assignments, when someone becomes infected to an asymptomatic status infection and when a clinical diseased individual progresses to asymptomatic. We can use the existing update_infection() function for vivax in human_infection and in disease progression.

We can also now remove the gamma1 parameter from the vivax parameter list, used in the falciparum code.

The P.v vignette has been extended to include modelled infectivity details.

R/data.R

@@ -1,9 +1,29 @@
-#' Parameter draws
+#' Parasite parameters
 #'
-#' 1000 draws from the joint posterior fit from
+#' Parasite-specific parameters for P. falciparum and vivax for use in malariasimulation
+#'
+#' @format ## `parasite_parameters`
+#' A 
+#'
+#' @source <https://www.nature.com/articles/ncomms4136>, <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097992/>
+"parasite_parameters"
+
+#' Parameter draws (P. falciparum)
 #'
-#' @format ## `parameter_draws`
+#' A list of 1000 draws from the joint posterior fit from
+#'
+#' @format ## `parameter_draws_pf`
 #' A list of lists of length 1000, each level contains a list of drawn parameters
 #'
 #' @source <https://www.nature.com/articles/ncomms4136>
-"parameter_draws"
+"parameter_draws_pf"
+
+#' Parameter draws (P. vivax)
+#'
+#' 1000 draws from the joint posterior fit from
+#'
+#' @format ## `parameter_draws_pv`
+#' A list of lists of length 1000, each level contains a list of drawn parameters
+#'
+#' @source <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097992/>
+"parameter_draws_pv"

R/disease_progression.R

@@ -36,12 +36,26 @@ progression_outcome_process <- function(
     renderer
 ){
 
-  update_to_asymptomatic_infection(
-    variables,
-    parameters,
-    timestep,
-    variables$state$get_index_of("D")$and(target)
-  )
+  if(parameters$parasite == "falciparum"){
+    # p.f has immunity-determined asymptomatic infectivity
+    update_to_asymptomatic_infection(
+      variables,
+      parameters,
+      timestep,
+      variables$state$get_index_of("D")$and(target)
+    )
+  } else if (parameters$parasite == "vivax"){
+    # p.v has constant asymptomatic infectivity
+    update_infection(
+      variables$state,
+      "A",
+      variables$infectivity,
+      parameters$ca,
+      variables$progression_rates,
+      1/parameters$da,
+      variables$state$get_index_of("D")$and(target)
+    )
+  }
 
   update_infection(
     variables$state,

R/human_infection.R

@@ -504,12 +504,26 @@ schedule_infections <- function(
   }
 
   if(to_infect_asym$size() > 0) {
-    update_to_asymptomatic_infection(
-      variables,
-      parameters,
-      timestep,
-      to_infect_asym
-    )
+    if(parameters$parasite == "falciparum"){
+      # p.f has immunity-determined asymptomatic infectivity
+      update_to_asymptomatic_infection(
+        variables,
+        parameters,
+        timestep,
+        to_infect_asym
+      )
+    } else if (parameters$parasite == "vivax"){
+      # p.v has constant asymptomatic infectivity
+      update_infection(
+        variables$state,
+        'A',
+        variables$infectivity,
+        parameters$ca,
+        variables$progression_rates,
+        1/parameters$da,
+        to_infect_asym
+      )
+    }
   }
 }