Amendments made in response to 3rd round of PR requests

R/antimalarial_resistance.R

@@ -100,6 +100,7 @@ get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep)
     stop("Error: Antimalarial resistance has not been parameterised; antimalarial_resistance = FALSE")
   }
 
+<<<<<<< HEAD
   empty_vector <- numeric(length = length(drugs))
   artemisinin_resistance_proportion <- empty_vector
   partner_drug_resistance_proportion <- empty_vector
@@ -108,6 +109,15 @@ get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep)
   late_clinical_failure_probability <- empty_vector
   late_parasitological_failure_probability <- empty_vector
   reinfection_during_prophylaxis_probability <- empty_vector
+=======
+  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))
+>>>>>>> 4d75b2eb152ccb7a56e74322e6d733e21a32ee7f
   dt_slow_parasite_clearance <- rep(parameters$dt, length = length(drugs))
 
   for(i in seq_along(parameters$antimalarial_resistance_drug)) {
@@ -134,6 +144,20 @@ get_antimalarial_resistance_parameters <- function(parameters, drugs, timestep)
   resistance_parameters$reinfection_during_prophylaxis_probability <- reinfection_during_prophylaxis_probability
   resistance_parameters$dt_slow_parasite_clearance <- dt_slow_parasite_clearance
 
+<<<<<<< HEAD
+=======
+  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")
+  }
+
+>>>>>>> 4d75b2eb152ccb7a56e74322e6d733e21a32ee7f
   return(resistance_parameters)
 
 }

R/human_infection.R

@@ -129,9 +129,10 @@ calculate_infections <- function(
 
   # calculate vaccine efficacy
   vaccine_efficacy <- rep(0, length(source_vector))
-  vaccine_times <- variables$pev_timestep$get_values(source_vector)
-  vaccinated <- vaccine_times > -1
+  vaccine_times <- variables$last_eff_pev_timestep$get_values(source_vector)
   pev_profile <- variables$pev_profile$get_values(source_vector)
+  # get vector of individuals who have received their 3rd dose
+  vaccinated <- vaccine_times > -1
   pev_profile <- pev_profile[vaccinated]
   if (length(vaccinated) > 0) {
     antibodies <- calculate_pev_antibodies(
@@ -304,17 +305,31 @@ 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]
+<<<<<<< HEAD
   } else {
     susceptible_to_treatment <- seek_treatment
   }
 
   n_early_treatment_failure <- n_treat - susceptible_to_treatment$size()
+=======
+    n_early_treatment_failure <- n_treat - susceptible_to_treatment$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$render('n_early_treatment_failure', n_early_treatment_failure, timestep)
+  }
+
+>>>>>>> 4d75b2eb152ccb7a56e74322e6d733e21a32ee7f
   successfully_treated_index <- bernoulli_multi_p(parameters$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)
+<<<<<<< HEAD
 
   renderer$render('n_early_treatment_failure', n_early_treatment_failure, timestep)
+=======
+>>>>>>> 4d75b2eb152ccb7a56e74322e6d733e21a32ee7f
   renderer$render('n_treat_eff_fail', n_treat_eff_fail, timestep)
   renderer$render('n_treat_success', successfully_treated$size(), timestep)
 

vignettes/Antimalarial_Resistance.Rmd

@@ -16,11 +16,24 @@ knitr::opts_chunk$set(
 
 
 ```{r setup}
+<<<<<<< HEAD
 # Load the requisite packages:
 library(malariasimulation)
 
 # Set colour palette:
 cols <- c("#E69F00", "#56B4E9", "#009E73", "#CC79A7","#F0E442", "#0072B2", "#D55E00")
+=======
+
+# 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")
+
+# Set colour palette:
+cols <- c("#E69F00", "#56B4E9", "#009E73", "#CC79A7","#F0E442", "#0072B2", "#D55E00")
+
+>>>>>>> 4d75b2eb152ccb7a56e74322e6d733e21a32ee7f
 ```
 
 ## Introduction