Implented the second round of changes requested in the pull request

R/antimalarial_resistance.R

@@ -1,5 +1,7 @@
 #' @title Parameterise antimalarial resistance
-#'
+#' @description
+#' Parameterise antimalarial resistance
+#' 
 #' @param parameters the model parameters
 #' @param drug the index of the drug which resistance is being set, as set by the set_drugs() function, in the parameter list
 #' @param timesteps vector of time steps for each update to resistance proportion and resistance outcome probability
@@ -10,6 +12,7 @@
 #' @param late_clinical_failure_prob vector of updates to the proportion of partner-drug-resistant infections that result in late clinical failure
 #' @param late_parasitological_prob vector of updates to the proportion of partner-drug-resistant infections that result in late parasitological failure
 #' @param reinfection_prob vector of updates to the proportion of partner-drug-resistant infections that result in reinfection during prophylaxis
+#' @param slow_parasite_clearance_time single value representing the mean time individual's experiencing slow parasite clearance reside in the treated state
 #' @export
 set_antimalarial_resistance <- function(parameters,
                                         drug,
@@ -20,9 +23,9 @@ set_antimalarial_resistance <- function(parameters,
                                         early_treatment_failure_prob,
                                         late_clinical_failure_prob,
                                         late_parasitological_prob,
-                                        reinfection_prob) {
+                                        reinfection_prob,
+                                        slow_parasite_clearance_time) {
 
-  # Check that the number of values input is equal for each resistance parameter
   if(any(c(length(artemisinin_resistance),
            length(partner_drug_resistance), 
            length(slow_parasite_clearance_prob), 
@@ -33,59 +36,114 @@ set_antimalarial_resistance <- function(parameters,
     stop("Length of one or more resistance parameter vectors does not match time steps specified for update")
   }
 
-  # Ensure resistance proportions bounded between 0 and 1:
-    if(any(artemisinin_resistance < 0 | artemisinin_resistance > 1 |
+  if(any(artemisinin_resistance < 0 | artemisinin_resistance > 1 |
          partner_drug_resistance < 0 | partner_drug_resistance > 1)) {
     stop("Artemisinin and partner-drug resistance proportions must fall between 0 and 1")
   }
 
-  # Ensure resistance outcome probabilities bounded between 0 and 1:
   if(any(slow_parasite_clearance_prob < 0 | slow_parasite_clearance_prob > 1 |
          early_treatment_failure_prob < 0 | early_treatment_failure_prob > 1 |
          late_clinical_failure_prob < 0 | late_clinical_failure_prob > 1 |
          late_parasitological_prob < 0 | late_parasitological_prob > 1 |
          reinfection_prob < 0 | reinfection_prob > 1)) {
     stop("Resistance outcome probabilities must fall between 0 and 1")
   }
+
+    if(length(slow_parasite_clearance_time) != 1) {
+    stop("Error: length of slow_parasite_clearance_time not equal to 1")
+  }
+
+  if(slow_parasite_clearance_time <= 0) {
+    stop("Error: slow_parasite_clearance_time is non-positive")
+  }
 
-  # Set antimalarial_resistance to TRUE:
   parameters$antimalarial_resistance <- TRUE
 
-  # Store the number of drugs for which parameters are available in the parameter list:
   n_drugs <- length(parameters$drug_efficacy)
 
-  # If the drug index falls outside range 1:n_drugs, terminate the operation:
   if (drug < 1 | drug > n_drugs) {
     stop('Drug index is invalid, please set drugs using set_drugs')
   }
 
-  # Check the drug_index for the drug we're setting parameters for:
   drug_index <- which(parameters$antimalarial_resistance_drug == drug)
 
-  # If drug_index not already assigned, assign the drug the next available index:
   if (length(drug_index) == 0) {
     drug_index <- length(parameters$antimalarial_resistance_drug) + 1
   }
 
-  # Append the drug for which resistance is being assigned to the generated index:
   parameters$antimalarial_resistance_drug[[drug_index]] <- drug
-
-  # Append the timesteps on which the resistance proportions are to be updated:
   parameters$antimalarial_resistance_timesteps[[drug_index]] <- timesteps
-
-  # Append the proportions of all malarial infections that are artemisinin or partner-drug
-  # resistant:
   parameters$prop_artemisinin_resistant[[drug_index]] <- artemisinin_resistance
   parameters$prop_partner_drug_resistant[[drug_index]] <- partner_drug_resistance
-
-  # Append the probabilities that individuals will experience the resistance outcomes:
   parameters$slow_parasite_clearance_prob[[drug_index]] <- slow_parasite_clearance_prob
   parameters$early_treatment_failure_prob[[drug_index]] <- early_treatment_failure_prob
   parameters$late_clinical_failure_prob[[drug_index]] <- late_clinical_failure_prob
   parameters$late_parasitological_failure_prob[[drug_index]] <- late_parasitological_prob
   parameters$reinfection_during_prophylaxis[[drug_index]] <- reinfection_prob
+  parameters$dt_slow_parasite_clearance[[drug_index]] <- slow_parasite_clearance_time
+
+  return(parameters)
+
+}
+
+#' @title Retrieve resistance parameters
+#' @description
+#' Retrieve the resistance parameters associated with the drug each individual receiving clinical 
+#' treatment has been administered in the current time step.
+#' 
+#' @param parameters the model parameters
+#' @param drug vector of integers representing the drugs administered to each individual receiving treatment
+#' @param timestep the current time step
+get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep) {
+
+  if(!parameters$antimalarial_resistance) {
+    stop("Error: Antimalarial resistance has not been parameterised; antimalarial_resistance = FALSE")
+  }
+
+  artemisinin_resistance_proportion <- numeric(length = length(drugs))
+  partner_drug_resistance_proportion <- numeric(length = length(drugs))
+  slow_parasite_clearance_probability <- numeric(length = length(drugs))
+  early_treatment_failure_probability <- numeric(length = length(drugs))
+  late_clinical_failure_probability <- numeric(length = length(drugs))
+  late_parasitological_failure_probability <- numeric(length = length(drugs))
+  reinfection_during_prophylaxis_probability <- numeric(length = length(drugs))
+  dt_slow_parasite_clearance <- rep(parameters$dt, length = length(drugs))
+
+  for(i in seq_along(parameters$antimalarial_resistance_drug)) {
+    drug <- parameters$antimalarial_resistance_drug[[i]]
+    treated_with_drug <- which(drugs == drug)
+    resistance_timestep <- match_timestep(ts = parameters$antimalarial_resistance_timesteps[[i]], t = timestep)
+    artemisinin_resistance_proportion[treated_with_drug] <- parameters$prop_artemisinin_resistant[[i]][resistance_timestep]
+    partner_drug_resistance_proportion[treated_with_drug] <- parameters$prop_partner_drug_resistant[[i]][resistance_timestep]
+    slow_parasite_clearance_probability[treated_with_drug] <- parameters$slow_parasite_clearance_prob[[i]][resistance_timestep]
+    early_treatment_failure_probability[treated_with_drug] <- parameters$early_treatment_failure_prob[[i]][resistance_timestep]
+    late_clinical_failure_probability[treated_with_drug] <- parameters$late_clinical_failure_prob[[i]][resistance_timestep]
+    late_parasitological_failure_probability[treated_with_drug] <- parameters$late_parasitological_failure_prob[[i]][resistance_timestep]
+    reinfection_during_prophylaxis_probability[treated_with_drug] <- parameters$reinfection_during_prophylaxis[[i]][resistance_timestep]
+    dt_slow_parasite_clearance[treated_with_drug] <- parameters$dt_slow_parasite_clearance[[i]]
+  }
+
+  resistance_parameters <- list()
+  resistance_parameters$artemisinin_resistance_proportion <- artemisinin_resistance_proportion
+  resistance_parameters$partner_drug_resistance_proportion <- partner_drug_resistance_proportion
+  resistance_parameters$slow_parasite_clearance_probability <- slow_parasite_clearance_probability
+  resistance_parameters$early_treatment_failure_probability <- early_treatment_failure_probability
+  resistance_parameters$late_clinical_failure_probability <- late_clinical_failure_probability
+  resistance_parameters$late_parasitological_failure_probability <- late_parasitological_failure_probability
+  resistance_parameters$reinfection_during_prophylaxis_probability <- reinfection_during_prophylaxis_probability
+  resistance_parameters$dt_slow_parasite_clearance <- dt_slow_parasite_clearance
+
+  if(any(c(length(resistance_parameters$artemisinin_resistance_proportion),
+           length(resistance_parameters$partner_drug_resistance_proportion), 
+           length(resistance_parameters$slow_parasite_clearance_probability), 
+           length(resistance_parameters$early_treatment_failure_probability), 
+           length(resistance_parameters$late_clinical_failure_probability), 
+           length(resistance_parameters$late_parasitological_failure_probability), 
+           length(resistance_parameters$reinfection_during_prophylaxis_probability),
+           length(resistance_parameters$dt_slow_parasite_clearance)) != length(drugs))) {
+    stop("Length of one or more resistance parameter vectors does not match length of drugs vector")
+  }
 
-  # Return the parameter list:
-  parameters
+  return(resistance_parameters)
 
 }

R/human_infection.R

@@ -269,8 +269,6 @@ calculate_treated <- function(
     renderer
 ) {
 
-  renderer$render('n_clin_infected', clinical_infections$size(), timestep)
-
   if(clinical_infections$size() == 0) {
     return(individual::Bitset$new(parameters$human_population))
   }
@@ -296,27 +294,18 @@ calculate_treated <- function(
     )
   ])
 
-  if(parameters$antimalarial_resistance == TRUE) {
-    antimalarial_resistance_drug_index <- as.numeric(parameters$antimalarial_resistance_drug)[drugs]
-    artemisinin_resistance_proportion <- vector()
-    early_treatment_failure_probability <- vector()
-    drug_indices <- list(); drug_index <- vector()
-
-    for(i in seq_along(parameters$antimalarial_resistance_drug)) {
-      drug_indices[[i]] <- which(drugs == i)
-      drug_index[i] <- which(parameters$antimalarial_resistance_drug == i)
-      matched_t <- match_timestep(ts = parameters$antimalarial_resistance_timesteps[[drug_index[i]]], t = timestep)
-      artemisinin_resistance_proportion[drug_indices[[i]]] <- parameters$prop_artemisinin_resistant[[drug_index[i]]][matched_t]
-      early_treatment_failure_probability[drug_indices[[i]]] <- parameters$early_treatment_failure_prob[[drug_index[i]]][matched_t]
-    }
-
-    unsuccessful_treatment_probability <- artemisinin_resistance_proportion * early_treatment_failure_probability
+  if(parameters$antimalarial_resistance) {
+    resistance_parameters <- get_antimalarial_resistance_parameters(
+      parameters = parameters,
+      drugs = drugs, 
+      timestep = timestep
+    )
+    unsuccessful_treatment_probability <- resistance_parameters$artemisinin_resistance_proportion * resistance_parameters$early_treatment_failure_probability
     susceptible_to_treatment_index <- bernoulli_multi_p(p = 1 - unsuccessful_treatment_probability)
-    drugs <- drugs[susceptible_to_treatment_index]
     susceptible_to_treatment <- bitset_at(seek_treatment, susceptible_to_treatment_index)
+    drugs <- drugs[susceptible_to_treatment_index]
     n_early_treatment_failure <- n_treat - susceptible_to_treatment$size()
     renderer$render('n_early_treatment_failure', n_early_treatment_failure, timestep)
-
   } else {
     susceptible_to_treatment <- seek_treatment
     n_early_treatment_failure <- n_treat - susceptible_to_treatment$size()

R/model.R

@@ -74,10 +74,9 @@
 #' susceptible
 #'  * net_usage: the number people protected by a bed net
 #'  * mosquito_deaths: number of adult female mosquitoes who die this timestep
-#'  * n_clin_infected: number of new clinically infected individuals in this timestep
 #'  * n_early_treatment_failure: number of clinically treated individuals who experienced early treatment failure in this timestep
 #'  * n_treat_eff_fail: number of clinically treated individuals who's treatment failed due to drug efficacy
-#'  * n_treat_success: number of newly successfully treated individuals in this timestep
+#'  * n_treat_success: number of successfully treated individuals in this timestep
 #'
 #' @param timesteps the number of timesteps to run the simulation for (in days)
 #' @param parameters a named list of parameters to use

R/parameters.R

@@ -207,6 +207,7 @@
 #' * late_clinical_failure_prob - vector of probabilities of late clinical failure for a given drug; default = NULL
 #' * late_parasitological_failure_prob - vector of probabilities of late parasitological failure for a given drug; default = NULL
 #' * reinfection_during_prophylaxis - vector of probabilities of reinfection during prophylaxis for a given drug; default = NULL
+#' * dt_slow_parasite_clearance - the delay for humans experiencing slow parasite clearance to move from state Tr to S; default = NULL
 #'
 #' rendering:
 #' All values are in timesteps and all ranges are inclusive