Fixes following the 3rd round of comments on the PR

R/antimalarial_resistance.R

@@ -100,13 +100,14 @@ get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep)
     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))
+  empty_vector <- numeric(length = length(drugs))
+  artemisinin_resistance_proportion <- empty_vector
+  partner_drug_resistance_proportion <- empty_vector
+  slow_parasite_clearance_probability <- empty_vector
+  early_treatment_failure_probability <- empty_vector
+  late_clinical_failure_probability <- empty_vector
+  late_parasitological_failure_probability <- empty_vector
+  reinfection_during_prophylaxis_probability <- empty_vector
   dt_slow_parasite_clearance <- rep(parameters$dt, length = length(drugs))
 
   for(i in seq_along(parameters$antimalarial_resistance_drug)) {
@@ -133,17 +134,6 @@ get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep)
   resistance_parameters$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(resistance_parameters)
 
 }

R/human_infection.R

@@ -304,18 +304,17 @@ calculate_treated <- function(
     susceptible_to_treatment_index <- bernoulli_multi_p(p = 1 - unsuccessful_treatment_probability)
     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$size()
-    renderer$render('n_early_treatment_failure', n_early_treatment_failure, timestep)
   }
 
+  n_early_treatment_failure <- n_treat - susceptible_to_treatment$size()
   successfully_treated_index <- bernoulli_multi_p(parameters$drug_efficacy[drugs])
   successfully_treated <- bitset_at(susceptible_to_treatment, successfully_treated_index)
   successfully_treated_drugs <- drugs[successfully_treated_index]
   n_treat_eff_fail <- susceptible_to_treatment$size() - length(successfully_treated_index)
+
+  renderer$render('n_early_treatment_failure', n_early_treatment_failure, timestep)
   renderer$render('n_treat_eff_fail', n_treat_eff_fail, timestep)
   renderer$render('n_treat_success', successfully_treated$size(), timestep)
 

vignettes/Antimalarial_Resistance.Rmd

@@ -16,16 +16,11 @@ knitr::opts_chunk$set(
 
 
 ```{r setup}
-
 # Load the requisite packages:
-#library(malariasimulation)
-
-# Use devtools to load the updated malariasimulation:
-devtools::load_all("C:/Users/trb216/OneDrive - Imperial College London/Desktop/malariasimulation/malariasimulation.Rproj")
+library(malariasimulation)
 
 # Set colour palette:
 cols <- c("#E69F00", "#56B4E9", "#009E73", "#CC79A7","#F0E442", "#0072B2", "#D55E00")
-
 ```
 
 ## Introduction