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/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
+      )
+    }
   }
 }
 

R/parameters.R

@@ -631,4 +631,3 @@ set_parameter_draw <- function(parameters, draw){
   }
   return(parameters)
 }
-

R/variables.R

@@ -182,11 +182,17 @@ create_variables <- function(parameters) {
 
   # Set the initial infectivity values for each individual
   infectivity_values[diseased] <- parameters$cd
-  infectivity_values[asymptomatic] <- asymptomatic_infectivity(
-    initial_age[asymptomatic],
-    id$get_values(asymptomatic),
-    parameters
-  )
+  if(parameters$parasite == "falciparum"){
+    # p.f has immunity-determined asymptomatic infectivity
+    infectivity_values[asymptomatic] <- asymptomatic_infectivity(
+      initial_age[asymptomatic],
+      id$get_values(asymptomatic),
+      parameters
+    )
+  } else if (parameters$parasite == "vivax"){
+    # p.v has constant asymptomatic infectivity
+    infectivity_values[asymptomatic] <- parameters$ca
+  }
   infectivity_values[subpatent] <- parameters$cu
 
   # Initialise the infectivity variable

data-raw/parasite_parameters.csv

@@ -110,7 +110,6 @@ vivax,kv,2.00048,to_be_removed
 vivax,fv0,0.141195,to_be_removed
 vivax,av,2493.41,to_be_removed
 vivax,gammav,2.91282,to_be_removed
-vivax,gamma1,1.82425,to_be_removed
 vivax,fd0,0.007055,to_be_removed
 vivax,ad,7993.5,to_be_removed
 vivax,gammad,4.8183,to_be_removed

tests/testthat/test-vivax.R

@@ -24,7 +24,7 @@ test_that('Test difference between falciparum and vivax parameter lists', {
 
   expect_identical(
     in_falciparum_not_vivax,
-    character(0)
+    c("gamma1") # asymptomatic infected infectivity towards mosquitos parameter
   )
 
   expect_identical(

vignettes/Plasmodium_vivax.Rmd

@@ -39,13 +39,23 @@ Then we can run the simulation as normal:
 simulation <- run_simulation(timesteps = 100, parameters = p)
 ```
 
-## Parameters
+## Model details
+
+### Parameters
 
 Our default *P. vivax* parameters are sourced from a version of the analysis in White et al. 2018 (doi: 10.1038/s41467-018-05860-8), where model parameters were fitted to data from Papua New Guinea. The chosen parameter set fixes `b = 0.25` and `sigma_squared = 1.67` (for consistency with the *P. falciparum* model). The default parameters for both parasite species can be found in `data/raw/parasite_parameters.csv`, while parameters common to both models are given in `R/parameters.R` under `get_parameters()`.
 
 Values for the model fitting posterior distribution can be selected using the `set_parameter_draw()` function as found in the [Parameter Variation](https://mrc-ide.github.io/malariasimulation/articles/ParameterVariation.html) vignette.
 
-## Model structure
+### Structure
+
+The *P. falciparum* model has five human disease compartments: susceptible (S), clinical disease (D), asymptomatic infection (A), sub-patent infection (U), and treated (Tr). Asymptomatic infections may or may not be detectable by light-microscopy.
+
+The *P. vivax* model follows a similar structure to the *P. falciparum* model, and also has five human disease compartments. However, the human disease states modeled explicitly focus on parasite density and detectability, such that we have: susceptible (S), clinical disease (D), **light-microscopy detectable infection (A)**, **PCR detectable infection (U)**, and treated (Tr).
+
+### Infectivity of LM-detectable infections
+
+While the *P. falciparum* model calculates the onward infectivity of asymptomatic infections (`ca`) using the age and detectability immunity of each individual, the *P. vivax* model uses a constant infectivity for LM-detectable infections (`ca = 0.1`).
 
 ### Key Model References