Merge pull request #316 from mrc-ide/vivax_competing_hazards_main_con…

…stant_asymptomatic_infectivity

p.v constant asymptomatic infectivity

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