Drug names for falciparum are consistent for backwards compatability.…

… Warnings added to set_drugs function for correct parasite drug parameter attribution. Tests to make sure liver stage prophylaxis is correct.

NAMESPACE

@@ -1,13 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export(AL_params)
-export(AL_params_falciparum)
 export(CQ_PQ_params_vivax)
 export(CQ_params_vivax)
 export(DHA_PQP_params)
-export(DHA_PQP_params_falciparum)
 export(SP_AQ_params)
-export(SP_AQ_params_falciparum)
 export(arab_params)
 export(create_pev_profile)
 export(fun_params)

R/drug_parameters.R

@@ -1,52 +1,32 @@
-#' @title Preset parameters for the DHA-PQP drug
-#' @description From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)
-#' @details Use a vector of preset parameters for the DHA-PQP drug (dihydroartemisinin-piperaquine)
-#' @details Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.09434, drug_prophylaxis_shape: 4.4, drug_prophylaxis_scale: 28.1
-#' @export
-DHA_PQP_params_falciparum <- c(.95, 0.09434, 4.4, 28.1)
-
-#' @title Preset parameters for the DHA-PQP drug
+#' @title Preset parameters for the DHA-PQP drug (P. falciparum)
 #' @description From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)
 #' @details Use a vector of preset parameters for the DHA-PQP drug (dihydroartemisinin-piperaquine)
 #' @details Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.09434, drug_prophylaxis_shape: 4.4, drug_prophylaxis_scale: 28.1
 #' @export
 DHA_PQP_params <- c(.95, 0.09434, 4.4, 28.1)
 
-#' @title Preset parameters for the AL drug
-#' @description From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)
-#' @details Use a vector of preset parameters for the AL drug (artemether-lumefantrine)
-#' @details Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.05094, drug_prophylaxis_shape: 11.3, drug_prophylaxis_scale: 10.6
-#' @export
-AL_params_falciparum <- c(.95, 0.05094, 11.3, 10.6)
-
-#' @title Preset parameters for the AL drug
+#' @title Preset parameters for the AL drug (P. falciparum)
 #' @description From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)
 #' @details Use a vector of preset parameters for the AL drug (artemether-lumefantrine)
 #' @details Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.05094, drug_prophylaxis_shape: 11.3, drug_prophylaxis_scale: 10.6
 #' @export
 AL_params <- c(.95, 0.05094, 11.3, 10.6)
 
-#' @title Preset parameters for the SP-AQ drug
-#' @details Use a vector of preset parameters for the SP-AQ drug (sulphadoxine-pyrimethamine and amodiaquine)
-#' @details Default parameters, from L to R, are: drug_efficacy: 0.9, drug_rel_c: 0.32, drug_prophylaxis_shape: 4.3, drug_prophylaxis_scale: 38.1
-#' @export
-SP_AQ_params_falciparum <- c(0.9, 0.32, 4.3, 38.1)
-
-#' @title Preset parameters for the SP-AQ drug
+#' @title Preset parameters for the SP-AQ drug (P. falciparum)
 #' @details Use a vector of preset parameters for the SP-AQ drug (sulphadoxine-pyrimethamine and amodiaquine)
 #' @details Default parameters, from L to R, are: drug_efficacy: 0.9, drug_rel_c: 0.32, drug_prophylaxis_shape: 4.3, drug_prophylaxis_scale: 38.1
 #' @export
 SP_AQ_params <- c(0.9, 0.32, 4.3, 38.1)
 
-#' @title Preset parameters for the CQ drug acting on P. vivax
+#' @title Preset parameters for the CQ drug (P. vivax)
 #' @description Efficacy from SI of Nekkab et al., DOI: 10.1371/journal.pmed.1003535 (2021),
 #' shape and scale consistent with a longer prophylaxis time: 28 days, decreasing gradually
 #' @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)
 
-#' @title Preset parameters for the CQ-PQ drug acting on P. vivax
+#' @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),
 #' BS shape and scale consistent with a longer prophylaxis time: 28 days, decreasing gradually,
 #' LS shape are scale consistent with a 7 day PQ treatment, with rapid decay.
@@ -56,7 +36,7 @@ CQ_params_vivax <- c(0.899, 0.5, 5, 20)
 #' @export
 CQ_PQ_params_vivax <- c(0.948, 0.5, 5, 20, 0.713, 10, 5.5)
 
-#' @title Preset parameters for the CQ-TQ drug acting on P. vivax
+#' @title Preset parameters for the CQ-TQ drug (P. vivax)
 #' @description Efficacy from SI of Nekkab et al., DOI: 10.1371/journal.pmed.1003535 (2021),
 #' BS shape and scale consistent with a longer prophylaxis time: 28 days, decreasing gradually,
 #' LS shape are scale consistent with a single TQ treatment, with longer prophylaxis: 45 days.
@@ -83,6 +63,33 @@ set_drugs <- function(parameters, drugs) {
     'drug_hypnozoite_prophylaxis_scale'
   )
 
+  if(parameters$parasite == "falciparum"){
+    for (drug in seq_along(drugs)) {
+      if(length(drugs[[drug]]) != 4){
+        warning(paste0("Drug ", drug, " has incorrect number of P. falciparum drug parameters. The number of parameters should be 4."),
+                call. = FALSE)
+      } else if (
+        all(drugs[[drug]] == CQ_params_vivax)){
+        warning("P. vivax drug parameters are being applied to P. falciparum",
+                call. = FALSE)
+      }
+    }
+  } else if (parameters$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."),
+                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)
+        }
+      }
+    }
+  }
+
   for (drug in seq_along(drugs)) {
     for (i in seq_along(drugs[[drug]])) {
       parameters[[keys[[i]]]][drug] <- drugs[[drug]][[i]]

R/human_infection.R

@@ -519,24 +519,12 @@ relapse_bite_infection_hazard_resolution <- function(
   ## all bitten humans with an infectious bite (incorporating prophylaxis) get a new batch of hypnozoites
   if(bite_infections$size()>0){
 
-    ## drug prophylaxis may limit formation of new hypnozoite batches
-    ls_prophylaxis <- rep(0, bite_infections$size())
-    if(length(parameters$drug_hypnozoite_efficacy) > 0){
-
-      ls_drug <- variables$ls_drug$get_values(bite_infections)
-      ls_medicated <- (ls_drug > 0)
-      ls_medicated[ls_drug > 0] <- !is.na(parameters$drug_hypnozoite_efficacy[ls_drug])
-
-      if (any(ls_medicated)) {
-        ls_drug <- ls_drug[ls_medicated]
-        ls_drug_time <- variables$ls_drug_time$get_values(bite_infections)[ls_medicated]
-        ls_prophylaxis[ls_medicated] <- weibull_survival(
-          timestep - ls_drug_time,
-          parameters$drug_hypnozoite_prophylaxis_shape[ls_drug],
-          parameters$drug_hypnozoite_prophylaxis_scale[ls_drug]
-        )
-      }
-    }
+    ls_prophylaxis <- ls_treatment_prophylaxis_efficacy(
+      bite_infections,
+      variables,
+      parameters,
+      timestep
+    )
 
     # make sure batches are capped
     new_hypnozoite_batch_formed <- bitset_at(bite_infections, bernoulli_multi_p(1 - ls_prophylaxis))
@@ -550,6 +538,42 @@ relapse_bite_infection_hazard_resolution <- function(
   }
 }
 
+#' @title Calculate protection from formation of new hypnozoite batches due to liver stage drug prophylaxis
+#' @description This function calculates the probability that liver stage drug prophylaxis will 
+#' protect each individual from the formation of new hynozoite batches
+#' @param bite_infections a vector of individuals with prospective formation of new hypnozoite batches
+#' @param variables a list of all of the model variables
+#' @param parameters model parameters
+#' @param timestep current timestep
+#' @noRd
+ls_treatment_prophylaxis_efficacy <- function(
+    bite_infections,
+    variables,
+    parameters,
+    timestep
+){
+
+  ## drug prophylaxis may limit formation of new hypnozoite batches
+  ls_prophylaxis <- rep(0, bite_infections$size())
+  if(length(parameters$drug_hypnozoite_efficacy) > 0){
+
+    ls_drug <- variables$ls_drug$get_values(bite_infections)
+    ls_medicated <- ls_drug > 0
+    ls_medicated[ls_medicated] <- !is.na(parameters$drug_hypnozoite_efficacy[ls_drug])
+
+    if (any(ls_medicated)) {
+      ls_drug <- ls_drug[ls_medicated]
+      ls_drug_time <- variables$ls_drug_time$get_values(bite_infections)[ls_medicated]
+      ls_prophylaxis[ls_medicated] <- weibull_survival(
+        timestep - ls_drug_time,
+        parameters$drug_hypnozoite_prophylaxis_shape[ls_drug],
+        parameters$drug_hypnozoite_prophylaxis_scale[ls_drug]
+      )
+    }
+  }
+
+  ls_prophylaxis
+}
 #' @title Calculate light microscopy detectable infections (p.v only)
 #' @description
 #' Sample light microscopy detectable infections from all infections