Merge pull request #250 from mrc-ide/vivax_subpatent_duration

Vivax subpatent duration

R/disease_progression.R

@@ -84,3 +84,37 @@ update_to_asymptomatic_infection <- function(
     )
   }
 }
+
+#' @title Sub-patent progression for vivax model
+#' @description
+#' randomly selects individuals to clear sub-patent infections based on impact of
+#' individual immunity to detectability
+#'
+#' @param state the human state variable
+#' @param variables the available human variables
+#' @param parameters model parameters
+#' @noRd
+create_subpatent_progression_process <- function(
+  state,
+  variables,
+  parameters
+  ){
+  function(timestep) {
+    ## Get recovery rates for each subpatent individual
+    subpatent_index <- state$get_index_of("U")
+    rate <- anti_parasite_immunity(
+      parameters$du_min, parameters$du_max, parameters$au50, parameters$ku,
+      variables$id$get_values(index = subpatent_index),
+      variables$idm$get_values(index = subpatent_index))
+    ## Get individuals who are going to change
+    to_move <- subpatent_index$sample(1/rate)
+    # update individuals and infectivity
+    update_infection(
+      state,
+      to_state = "S",
+      infectivity = variables$infectivity,
+      new_infectivity = 0,
+      to_move
+    )
+  }
+}

R/human_infection.R

@@ -53,14 +53,33 @@ simulate_infection <- function(
       parameters$ud
     )
   }
+
+  if(parameters$parasite == "falciparum"){
+    clinical_infections <- calculate_clinical_infections(
+      variables,
+      infected_humans,
+      parameters,
+      renderer,
+      timestep
+    )
+  } else if (parameters$parasite == "vivax"){
+    patent_infections <- calculate_patent_infections(
+      variables,
+      infected_humans,
+      parameters,
+      renderer,
+      timestep
+    )
+
+    clinical_infections <- calculate_clinical_infections(
+      variables,
+      patent_infections,
+      parameters,
+      renderer,
+      timestep
+    )
+  }
 
-  clinical_infections <- calculate_clinical_infections(
-    variables,
-    infected_humans,
-    parameters,
-    renderer,
-    timestep
-  )
 
   update_severe_disease(
     timestep,
@@ -175,15 +194,51 @@ calculate_infections <- function(
   infected
 }
 
-#' @title Calculate clinical infections
+#' @title Calculate patent infections (vivax only)
 #' @description
-#' Sample clinical infections from all infections
+#' Sample patent infections from all infections
 #' @param variables a list of all of the model variables
 #' @param infections bitset of infected humans
 #' @param parameters model parameters
 #' @param renderer model render
 #' @param timestep current timestep
 #' @noRd
+calculate_patent_infections <- function(
+    variables,
+    infections,
+    parameters,
+    renderer,
+    timestep
+) {
+  id <- variables$id$get_values(infections)
+  idm <- variables$idm$get_values(infections)
+  philm <- anti_parasite_immunity(
+    min = parameters$du_min, max = parameters$du_max, a50 = parameters$au50,
+    k = parameters$ku, id = id, idm = idm)
+  patent_infections <- bitset_at(infections, bernoulli_multi_p(philm))
+  incidence_renderer(
+    variables$birth,
+    renderer,
+    patent_infections,
+    infections,
+    philm,
+    'inc_patent_',
+    parameters$patent_incidence_rendering_min_ages,
+    parameters$patent_incidence_rendering_max_ages,
+    timestep
+  )
+  patent_infections
+}
+
+#' @title Calculate clinical infections
+#' @description
+#' Sample clinical infections from all infections or patent infections (vivax)
+#' @param variables a list of all of the model variables
+#' @param infections bitset of infected/patent humans
+#' @param parameters model parameters
+#' @param renderer model render
+#' @param timestep current timestep
+#' @noRd
 calculate_clinical_infections <- function(
   variables,
   infections,
@@ -458,3 +513,9 @@ blood_immunity <- function(ib, parameters) {
       (1 + (ib / parameters$ib0) ** parameters$kb)
   )
 }
+
+# Implemented from White et al., 2018 - Supplementary Information
+anti_parasite_immunity <- function(min, max, a50, k, id, idm){
+  min + (max - min) / (
+    1 + ((id + idm) / a50) ** k)
+}

R/model.R

@@ -29,22 +29,28 @@
 #'  * n: number of humans between an inclusive age range at this timestep. This
 #' defaults to n_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * n_detect: number of humans with an infection detectable by microscopy between an inclusive age range at this timestep. This
-#' defaults to n_detect_730_3650. Other age ranges can be set with
+#'  * n_detect_pcr: number of humans with an infection detectable by pcr between an inclusive age range at this timestep. This
+#' defaults to n_detect_pcr_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * p_detect: the sum of probabilities of detection by microscopy between an
+#'  * n_detect_lm: number of humans with an infection detectable by light microscopy between an inclusive age range at this timestep. This
+#' defaults to n_detect_lm_730_3650. Other age ranges can be set with
+#' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
+#'  * p_detect_lm: the sum of probabilities of detection by light microscopy between an
 #' inclusive age range at this timestep. This
-#' defaults to p_detect_730_3650. Other age ranges can be set with
+#' defaults to p_detect_lm_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * n_severe: number of humans with a severe infection between an inclusive
-#' age range at this timestep. Age ranges can be set with
-#' severe_prevalence_rendering_min_ages and severe_prevalence_rendering_max_ages parameters.
 #'  * n_inc: number of new infections for humans between an inclusive age range at this timestep.
 #' incidence columns can be set with
 #' incidence_rendering_min_ages and incidence_rendering_max_ages parameters.
 #'  * p_inc: sum of probabilities of infection for humans between an inclusive age range at this timestep.
 #' incidence columns can be set with
 #' incidence_rendering_min_ages and incidence_rendering_max_ages parameters.
+#'  * n_inc_patent: number of new patent infections for humans between an inclusive age range at this timestep. 
+#' patent incidence columns can be set with
+#' patent_incidence_rendering_min_ages and patent_incidence_rendering_max_ages parameters.
+#'  * p_inc_patent: sub of probabilities of patent infection for humans between an inclusive age range at this timestep. 
+#' patent incidence columns can be set with
+#' patent_incidence_rendering_min_ages and patent_incidence_rendering_max_ages parameters.
 #'  * n_inc_clinical: number of new clinical infections for humans between an inclusive age range at this timestep. 
 #' clinical incidence columns can be set with
 #' clinical_incidence_rendering_min_ages and clinical_incidence_rendering_max_ages parameters.

R/mortality_processes.R

@@ -69,6 +69,11 @@ sample_maternal_immunity <- function(variables, target, timestep, parameters) {
         birth_ivm <- variables$ica$get_values(mothers) * parameters$pvm
         variables$icm$queue_update(birth_icm, target_group)
         variables$ivm$queue_update(birth_ivm, target_group)
+
+        if(parameters$parasite == "vivax"){
+          birth_idm <- variables$id$get_values(mothers) * parameters$pcm
+          variables$idm$queue_update(birth_idm, target_group)
+        }
       }
     }
   }