Infect dist

R/get_infect_mat.R

@@ -43,8 +43,8 @@
 #' @export
 get_infect_mat <- function(alpha = 0.2, R = 2.5, kappa = 0.5, eta = 0.5, nu = 4,
                            t_ds = 3, t_da = 3, t_qcs = 3, t_qca = 3, t_qhs = 3,
-                           t_qha = 3, t_q = 3, t_incubation = 5.5, offset = -2.31,
-                           shape = 1.65, rate = 0.5) {
+                           t_qha = 3, t_q = 3, t_incubation = 5.5, offset = -12.27,
+                           shape = 21.13, rate = 1.592) {
   is_probability(alpha)
   is_probability(eta)
   is_positive(R)
@@ -70,23 +70,23 @@ get_infect_mat <- function(alpha = 0.2, R = 2.5, kappa = 0.5, eta = 0.5, nu = 4,
 
   gamma_qcs <- get_prop_infect_time(
     t_qcs,
-    shape = second_gen_shape, rate = rate, offset = 0
+    shape = second_gen_shape, rate = rate, offset = offset
   )
   gamma_qca <- get_prop_infect_time(
     t_qca,
-    shape = second_gen_shape, rate = rate, offset = 0
+    shape = second_gen_shape, rate = rate, offset = offset
   )
   gamma_qhs <- get_prop_infect_time(
     t_qhs,
-    shape = second_gen_shape, rate = rate, offset = 0
+    shape = second_gen_shape, rate = rate, offset = offset
   )
   gamma_qha <- get_prop_infect_time(
     t_qha,
-    shape = second_gen_shape, rate = rate, offset = 0
+    shape = second_gen_shape, rate = rate, offset = offset
   )
   gamma_q <- get_prop_infect_time(
     t_q,
-    shape = second_gen_shape, rate = rate, offset = 0
+    shape = second_gen_shape, rate = rate, offset = offset
   )
 
   R_s <- R / ((alpha * kappa) - alpha + 1)

R/get_prop_infect_time.R

@@ -2,21 +2,23 @@
 #'
 #' Calculates the proportion of the infections period reduced given the
 #' distribution of infectiousness and time from symptom onset to isolation.
-#' Infectious period is assumed to be gamma distributed.
+#' Infectious period is assumed to be gamma distributed. Defaults derived
+#' from a correction of He et al. (2020) where the incubation period was 
+#' assumed to be 5.5 days and the generation time 6.5 days.
 #'
 #' @param delay Numeric greater than 0. Time from symptom onset to isolation
 #' @param offset Numeric. Offset of infectiousness compared to symptom onset.
-#'     Default is -2.31.
+#'     Default is -12.27.
 #' @param shape Numeric. Shape of the gamma distribution of infectious period.
-#'    Default is 1.65.
+#'    Default is 21.13.
 #' @param rate Numeric. Rate of the gamma distribution of infectious period.
-#'    Default is 0.5.
+#'    Default is 1.592.
 #'
 #' @return Numeric. Proportion of infectious period reduced given the
 #'   distribution of infectiousness and time from symptom onset to isolation.
 #' @export
-get_prop_infect_time <- function(delay, offset = -2.31,
-                                 shape = 1.65, rate = 0.5) {
+get_prop_infect_time <- function(delay, offset = -12.27,
+                                 shape = 21.13, rate = 1.592) {
   if (delay < offset) {
     return(0)
   }

R/get_r_effective_df.R

@@ -98,8 +98,8 @@ get_r_effective_df <- function(alpha = 0.2, R = 2.5, kappa = 0.5, eta = 0.5, nu
                                omega_h = 0.5,
                                omega_q = 0.5,
                                quarantine_days = Inf,
-                               rho_s = 0.1, rho_a = 0.05, offset = -2.31,
-                               shape = 1.65, rate = 0.5,
+                               rho_s = 0.1, rho_a = 0.05, offset = -12.27,
+                               shape = 21.13, rate = 1.592,
                                stoch = FALSE, theta = NULL, n_inf = NULL, n_iter = NULL) {
   if (length(n_iter) > 1 | length(stoch) > 1) {
     stop_glue(

tests/testthat/test-get_r_effective.R

@@ -156,7 +156,7 @@ test_that("get_r_effective works, change incubation", {
 })
 
 test_that("get_r_effective works, change shape of gamma", {
-  param <- 4
+  param <- 30
   dqc <- c(
     Ds = 0.2, Da = 0.1, Qcds = 0.1, Qhds = 0.1, Qcda = 0.1, Qhda = 0.1,
     Qq = 0.15, Cs = 0.1, Ca = 0.05

tests/testthat/test-get_r_effective_df.R

@@ -2,7 +2,7 @@ test_that("get_r_effective_df works", {
   r <- get_r_effective_df(quarantine_days = Inf)
   expect_equal(nrow(r), 1)
   expect_equal(ncol(r), 20)
-  expect_equal(round(r$r_effective, 3), 2.362)
+  expect_equal(round(r$r_effective, 3), 2.359)
 })
 
 test_that("get_r_effective_df works with stochastic arguments", {