Liver stage drug parameters (the final three on vivax parameter set) …

…are now set explicitly. The vivax drug set must now therefore by a vector of 7, 4 is not allowed. When there is not a liver-stage efficacy or prophylaxis effect, we set the final three parameters to 0.

R/drug_parameters.R

@@ -24,7 +24,8 @@ SP_AQ_params <- c(0.9, 0.32, 4.3, 38.1)
 #' @details Use a vector of preset parameters for the CQ drug (chloroquine) acting on P. vivax
 #' @details Default parameters, from L to R, are: drug_efficacy: 0.899, drug_rel_c: 0.5, drug_prophylaxis_shape: 20, drug_prophylaxis_scale: 5
 #' @export
-CQ_params_vivax <- c(0.899, 0.5, 5, 20)
+CQ_params_vivax <- c(0.899, 0.5, 5, 20, 0, 0, 0)
+
 
 #' @title Preset parameters for the CQ-PQ drug (P. vivax)
 #' @description Efficacy from SI of Nekkab et al., DOI: 10.1371/journal.pmed.1003535 (2021),
@@ -69,24 +70,13 @@ set_drugs <- function(parameters, drugs) {
       if(length(drugs[[drug]]) != 4){
         warning(paste0("Drug ", drug, " has incorrect number of P. falciparum drug parameters. The number of parameters should be 4."),
                 call. = FALSE)
-      } else if (
-        all(drugs[[drug]] == CQ_params_vivax)){
-        warning("P. vivax drug parameters are being applied to P. falciparum",
-                call. = FALSE)
       }
     }
   } else if (parameters$parasite == "vivax"){
     for (drug in seq_along(drugs)) {
-      if(!length(drugs[[drug]]) %in% c(4, 7)){
-        warning(paste0("Drug ", drug, " has incorrect number of P. vivax drug parameters. The number of parameters should be 4, for blood stage treatment only, or 7, for radical cure."),
+      if(length(drugs[[drug]]) != 7){
+        warning(paste0("Drug ", drug, " has incorrect number of P. vivax drug parameters. The number of parameters should be 7 for radical cure. To assign a blood stage drug only, set the liver stage drug parameters to 0: see CQ_params_vivax for an example."),
                 call. = FALSE)
-      } else if(length(drugs[[drug]]) == 4){
-        if(all(drugs[[drug]] == AL_params) |
-           all(drugs[[drug]] == DHA_PQP_params) |
-           all(drugs[[drug]] == SP_AQ_params)){
-          warning("P. falciparum drug parameters are being applied to P. vivax.",
-                  call. = FALSE)
-        }
       }
     }
   }

R/human_infection.R

@@ -488,7 +488,7 @@ relapse_bite_infection_hazard_resolution <- function(
     timestep
 ){
 
-  if(variables$hypnozoites$get_index_of(0)$not(T)$and(infected_humans)$size()>0){
+  if(variables$hypnozoites$get_index_of(0)$not(T)$and(infected_humans)$size() > 0){
 
     hypnozoite_humans <- variables$hypnozoites$get_index_of(0)$not(T)
     potential_relapse_index <- bitset_index(hypnozoite_humans, infected_humans)
@@ -555,7 +555,7 @@ ls_treatment_prophylaxis_efficacy <- function(
 
   ## drug prophylaxis may limit formation of new hypnozoite batches
   ls_prophylaxis <- rep(0, bite_infections$size())
-  if(length(parameters$drug_hypnozoite_efficacy) > 0){
+  if(any(parameters$drug_hypnozoite_efficacy > 0)){
 
     ls_drug <- variables$ls_drug$get_values(bite_infections)
     ls_medicated <- ls_drug > 0
@@ -861,7 +861,7 @@ calculate_successful_treatments <- function(
 
   }
 
-  if(length(parameters$drug_hypnozoite_efficacy) > 0){
+  if(any(parameters$drug_hypnozoite_efficacy > 0)){
     effectively_treated_hypnozoites_index <- bernoulli_multi_p(parameters$drug_hypnozoite_efficacy[drugs])
     successfully_treated_hypnozoites <- bitset_at(target, effectively_treated_hypnozoites_index)
     successfully_treated_list <- c(

R/mda_processes.R

@@ -139,7 +139,7 @@ update_mass_drug_admin <- function(
   }
 
   # Update liver stage drug effects
-  if(length(parameters$drug_hypnozoite_efficacy) > 0){
+  if(any(parameters$drug_hypnozoite_efficacy > 0)){
     if(target$successfully_treated_hypnozoites$size() > 0){
       variables$hypnozoites$queue_update(0, target$successfully_treated_hypnozoites)
       variables$ls_drug$queue_update(drug, target$successfully_treated_hypnozoites)

R/variables.R

@@ -288,7 +288,7 @@ create_variables <- function(parameters) {
   drug <- individual::IntegerVariable$new(rep(0, size))
   drug_time <- individual::IntegerVariable$new(rep(-1, size))
 
-  if(length(parameters$drug_hypnozoite_efficacy) > 0){
+  if(any(parameters$drug_hypnozoite_efficacy > 0)){
     ls_drug <- individual::IntegerVariable$new(rep(0, size))
     ls_drug_time <- individual::IntegerVariable$new(rep(-1, size))
   }

tests/testthat/test-vivax.R

@@ -316,7 +316,6 @@ test_that('relapses are recognised with division between bite infections and rel
 })
 
 test_that('Drug functions provide warnings if applied incorrectly', {
-
   expect_warning(
     get_parameters(parasite = "falciparum") |> 
       set_drugs(drugs = list(c(1,2,3,4,5))),
@@ -326,21 +325,8 @@ test_that('Drug functions provide warnings if applied incorrectly', {
   expect_warning(
     get_parameters(parasite = "vivax") |> 
       set_drugs(drugs = list(c(1,2,3,4,5))),
-    "Drug 1 has incorrect number of P. vivax drug parameters. The number of parameters should be 4, for blood stage treatment only, or 7, for radical cure."
-  )
-
-  expect_warning(
-    get_parameters(parasite = "falciparum") |> 
-      set_drugs(drugs = list(CQ_params_vivax)),
-    regexp = "P. vivax drug parameters are being applied to P. falciparum"
+    "Drug 1 has incorrect number of P. vivax drug parameters. The number of parameters should be 7 for radical cure. To assign a blood stage drug only, set the liver stage drug parameters to 0: see CQ_params_vivax for an example."
   )
-
-  expect_warning(
-    get_parameters(parasite = "vivax") |> 
-      set_drugs(drugs = list(AL_params)),
-    "P. falciparum drug parameters are being applied to P. vivax"
-    )
-
 })
 
 test_that('Liver stage prophylaxis functions correctly', {