#169 move probability functionality

R/seroprevalence_data.R

@@ -146,53 +146,7 @@ prepare_bin_data <- function(serodata,
   return(serodata_bin)
 }
 
-#' Computes the probability of being seropositive for age-varying
-#' force-of-infection including seroreversion
-#'
-#' @param ages Integer indicating the ages of the exposed cohorts
-#' @param foi Numeric atomic vector corresponding to the age-varying
-#' force-of-infection to simulate from
-#' @param mu Seroreversion rate
-#' @return probability of being seropositive for age-varying FoI
-#' including seroreversion
-probability_exact_time_varying <- function(
-    ages,
-    foi,
-    mu = 0
-) {
-  n_ages <- length(ages)
-  exposure_matrix <- matrix(0, nrow = n_ages, ncol = n_ages)
-  for (k in 1:n_ages) {
-    exposure_matrix[k, (n_ages - ages[k] + 1):n_ages] <- 1
-  }
-  probabilities <-
-    (foi / (foi + mu)) * (1 - exp(-drop(exposure_matrix %*% (foi + mu))))
-  return(probabilities)
-}
 
-#' Returns the probability of being seropositive for age-varying
-#' force-of-infection including seroreversion
-#'
-#' @param age Integer corresponding to the age of the exposed cohort
-#' @param foi Numeric atomic vector corresponding to the age-varying FoI to
-#' simulate from
-#' @param mu Seroreversion rate
-#' @return probability of being seropositive for age-varying FoI
-#' including seroreversion
-probability_exact_age_varying <- function(
-    age,
-    foi,
-    mu = 0
-) {
-  probability <- 0
-  # solves ODE exactly within pieces
-  for (i in 1:age) {
-    probability <-
-    (1 / (foi[i] + mu)) *
-    (foi[i] + exp(-(foi[i] + mu)) * (probability * (foi[i] + mu) - foi[i]))
-  }
-  return(probability)
-}
 
 #' Generate probabilities of being previously exposed to a
 #' pathogen given a historical force-of-infection.

R/simulate_serosurvey.R

@@ -0,0 +1,47 @@
+#' Computes the probability of being seropositive for age-varying
+#' force-of-infection including seroreversion
+#'
+#' @param ages Integer indicating the ages of the exposed cohorts
+#' @param foi Numeric atomic vector corresponding to the age-varying
+#' force-of-infection to simulate from
+#' @param mu Seroreversion rate
+#' @return probability of being seropositive for age-varying FoI
+#' including seroreversion
+probability_exact_time_varying <- function(
+    ages,
+    foi,
+    mu = 0
+) {
+  n_ages <- length(ages)
+  exposure_matrix <- matrix(0, nrow = n_ages, ncol = n_ages)
+  for (k in 1:n_ages) {
+    exposure_matrix[k, (n_ages - ages[k] + 1):n_ages] <- 1
+  }
+  probabilities <-
+    (foi / (foi + mu)) * (1 - exp(-drop(exposure_matrix %*% (foi + mu))))
+  return(probabilities)
+}
+
+#' Returns the probability of being seropositive for age-varying
+#' force-of-infection including seroreversion
+#'
+#' @param age Integer corresponding to the age of the exposed cohort
+#' @param foi Numeric atomic vector corresponding to the age-varying FoI to
+#' simulate from
+#' @param mu Seroreversion rate
+#' @return probability of being seropositive for age-varying FoI
+#' including seroreversion
+probability_exact_age_varying <- function(
+    age,
+    foi,
+    mu = 0
+) {
+  probability <- 0
+  # solves ODE exactly within pieces
+  for (i in 1:age) {
+    probability <-
+      (1 / (foi[i] + mu)) *
+      (foi[i] + exp(-(foi[i] + mu)) * (probability * (foi[i] + mu) - foi[i]))
+  }
+  return(probability)
+}