From 22112d443e345ae2e46dfc68ce23590746e7bbe9 Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Mon, 4 Sep 2023 17:45:26 +0100
Subject: [PATCH] Rename serial_sampler argument to serial_dist

---
 R/simulate.r                  | 10 +++++-----
 man/simulate_tree_from_pop.Rd |  8 ++++----
 tests/testthat/tests-sim.r    |  2 +-
 vignettes/epichains.Rmd       |  4 ++--
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/simulate.r b/R/simulate.r
index ea109275..49a294c7 100644
--- a/R/simulate.r
+++ b/R/simulate.r
@@ -300,7 +300,7 @@ simulate_summary <- function(nchains, statistic = c("size", "length"),
 #' secondary cases. Ignored if \code{offspring == "pois"}. Must be > 1 to
 #' avoid division by 0 when calculating the size. See details and
 #'  \code{?rnbinom} for details on the parameterisation in Ecology.
-#' @param serial_sampler The serial interval. A function that takes one
+#' @param serial_dist The serial interval. A function that takes one
 #' parameter (`n`), the number of serial intervals to randomly sample. Value
 #' must be >= 0.
 #' @param initial_immune The number of initial immunes in the population.
@@ -334,20 +334,20 @@ simulate_summary <- function(nchains, statistic = c("size", "length"),
 #' # Simulate with poisson offspring
 #' simulate_tree_from_pop(
 #'   pop = 100, offspring_dist = "pois",
-#'   offspring_mean = 0.5, serial_sampler = function(x) 3
+#'   offspring_mean = 0.5, serial_dist = function(x) 3
 #' )
 #'
 #' # Simulate with negative binomial offspring
 #' simulate_tree_from_pop(
 #'   pop = 100, offspring_dist = "nbinom",
-#'   offspring_mean = 0.5, offspring_disp = 1.1, serial_sampler = function(x) 3
+#'   offspring_mean = 0.5, offspring_disp = 1.1, serial_dist = function(x) 3
 #' )
 #' @export
 simulate_tree_from_pop <- function(pop,
                                    offspring_dist = c("pois", "nbinom"),
                                    offspring_mean,
                                    offspring_disp,
-                                   serial_sampler,
+                                   serial_dist,
                                    initial_immune = 0,
                                    t0 = 0,
                                    tf = Inf) {
@@ -418,7 +418,7 @@ simulate_tree_from_pop <- function(pop,
     ## add to df
     if (n_offspring > 0) {
       ## draw serial times
-      new_times <- serial_sampler(n_offspring)
+      new_times <- serial_dist(n_offspring)
 
       if (any(new_times < 0)) {
         stop("Serial interval must be >= 0.")
diff --git a/man/simulate_tree_from_pop.Rd b/man/simulate_tree_from_pop.Rd
index c24aca50..019efc27 100644
--- a/man/simulate_tree_from_pop.Rd
+++ b/man/simulate_tree_from_pop.Rd
@@ -10,7 +10,7 @@ simulate_tree_from_pop(
   offspring_dist = c("pois", "nbinom"),
   offspring_mean,
   offspring_disp,
-  serial_sampler,
+  serial_dist,
   initial_immune = 0,
   t0 = 0,
   tf = Inf
@@ -32,7 +32,7 @@ secondary cases. Ignored if \code{offspring == "pois"}. Must be > 1 to
 avoid division by 0 when calculating the size. See details and
 \code{?rnbinom} for details on the parameterisation in Ecology.}
 
-\item{serial_sampler}{The serial interval. A function that takes one
+\item{serial_dist}{The serial interval. A function that takes one
 parameter (\code{n}), the number of serial intervals to randomly sample. Value
 must be >= 0.}
 
@@ -75,13 +75,13 @@ simulate_tree_from_pop() has a couple of key different from simulate_tree():
 # Simulate with poisson offspring
 simulate_tree_from_pop(
   pop = 100, offspring_dist = "pois",
-  offspring_mean = 0.5, serial_sampler = function(x) 3
+  offspring_mean = 0.5, serial_dist = function(x) 3
 )
 
 # Simulate with negative binomial offspring
 simulate_tree_from_pop(
   pop = 100, offspring_dist = "nbinom",
-  offspring_mean = 0.5, offspring_disp = 1.1, serial_sampler = function(x) 3
+  offspring_mean = 0.5, offspring_disp = 1.1, serial_dist = function(x) 3
 )
 }
 \author{
diff --git a/tests/testthat/tests-sim.r b/tests/testthat/tests-sim.r
index 30dca41a..9b5868d0 100644
--- a/tests/testthat/tests-sim.r
+++ b/tests/testthat/tests-sim.r
@@ -15,7 +15,7 @@ test_that("Simulators output epichains objects", {
       offspring_dist = "nbinom",
       offspring_mean = 0.5,
       offspring_disp = 1.1,
-      serial_sampler = function(x) 3
+      serial_dist = function(x) 3
     ),
     "epichains"
   )
diff --git a/vignettes/epichains.Rmd b/vignettes/epichains.Rmd
index 1089f456..68c21807 100644
--- a/vignettes/epichains.Rmd
+++ b/vignettes/epichains.Rmd
@@ -91,7 +91,7 @@ tree_from_pop_pois <- simulate_tree_from_pop(
   pop = 1000,
   offspring_dist = "pois",
   offspring_mean = 0.5,
-  serial_sampler = function(x) 3
+  serial_dist = function(x) 3
 )
 
 tree_from_pop_pois # print the output
@@ -102,7 +102,7 @@ tree_from_pop_nbinom <- simulate_tree_from_pop(
   offspring_dist = "nbinom",
   offspring_mean = 0.5,
   offspring_disp = 1.1,
-  serial_sampler = function(x) 3
+  serial_dist = function(x) 3
 )
 
 tree_from_pop_nbinom # print the output