From ea049df2875a8fcc960c3a8b7326fa13472bc8f6 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 14 Dec 2023 11:29:59 +0000
Subject: [PATCH] removed num_init_infect default value from
 probability_contain and updated examples

---
 R/probability_contain.R    | 20 ++++++++++++++++++--
 man/probability_contain.Rd | 20 ++++++++++++++++++--
 2 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/R/probability_contain.R b/R/probability_contain.R
index db16c7d..9a499e8 100644
--- a/R/probability_contain.R
+++ b/R/probability_contain.R
@@ -22,10 +22,26 @@
 #' Nature, 438(7066), 355-359. \doi{10.1038/nature04153}
 #'
 #' @examples
-#' probability_contain(R = 1.5, k = 0.5, control = 1)
+#' # population-level control measures
+#' probability_contain(R = 1.5, k = 0.5, num_init_infect = 1, pop_control = 0.1)
+#'
+#' # individual-level control measures
+#' probability_contain(R = 1.5, k = 0.5, num_init_infect = 1, ind_control = 0.1)
+#'
+#' # both levels of control measures
+#' probability_contain(
+#'   R = 1.5,
+#'   k = 0.5,
+#'   num_init_infect = 1,
+#'   ind_control = 0.1,
+#'   pop_control = 0.1
+#' )
+#'
+#' # multi initial infections with population-level control measures
+#' probability_contain(R = 1.5, k = 0.5, num_init_infect = 5, pop_control = 0.1)
 probability_contain <- function(R,
                                 k,
-                                num_init_infect = 1,
+                                num_init_infect,
                                 ind_control = 0,
                                 pop_control = 0,
                                 stochastic = FALSE,
diff --git a/man/probability_contain.Rd b/man/probability_contain.Rd
index 6575f10..ce0d711 100644
--- a/man/probability_contain.Rd
+++ b/man/probability_contain.Rd
@@ -7,7 +7,7 @@
 probability_contain(
   R,
   k,
-  num_init_infect = 1,
+  num_init_infect,
   ind_control = 0,
   pop_control = 0,
   stochastic = FALSE,
@@ -51,7 +51,23 @@ Containment is defined as the size of the transmission chain
 not reaching the \code{case_threshold} (default = 100).
 }
 \examples{
-probability_contain(R = 1.5, k = 0.5, control = 1)
+# population-level control measures
+probability_contain(R = 1.5, k = 0.5, num_init_infect = 1, pop_control = 0.1)
+
+# individual-level control measures
+probability_contain(R = 1.5, k = 0.5, num_init_infect = 1, ind_control = 0.1)
+
+# both levels of control measures
+probability_contain(
+  R = 1.5,
+  k = 0.5,
+  num_init_infect = 1,
+  ind_control = 0.1,
+  pop_control = 0.1
+)
+
+# multi initial infections with population-level control measures
+probability_contain(R = 1.5, k = 0.5, num_init_infect = 5, pop_control = 0.1)
 }
 \references{
 Lloyd-Smith, J. O., Schreiber, S. J., Kopp, P. E., & Getz, W. M. (2005)