From 4fd9b0dcf699f257b70d4559710dc6bbc7734fde Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 5 Apr 2024 17:29:37 +0100
Subject: [PATCH 01/11] added onset_to_recovery to sim_linelist and
 sim_outbreak, WIP #36

---
 R/sim_linelist.R    | 21 ++++++++++++++++-----
 R/sim_outbreak.R    |  7 ++++++-
 man/sim_linelist.Rd | 16 ++++++++++++----
 man/sim_outbreak.Rd | 16 ++++++++++++----
 4 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/R/sim_linelist.R b/R/sim_linelist.R
index f0a67d63..7495c546 100644
--- a/R/sim_linelist.R
+++ b/R/sim_linelist.R
@@ -33,10 +33,16 @@
 #' infectious period.
 #' @param prob_infect A single `numeric` for the probability of a secondary
 #' contact being infected by an infected primary contact.
-#' @param onset_to_hosp An `<epidist>` object or anonymous function for
-#' the onset to hospitalisation delay distribution.
-#' @param onset_to_death An `<epidist>` object or anonymous function for
-#' the onset to death delay distribution.
+#' @param onset_to_hosp An `<epidist>` object, an anonymous function for
+#' the onset to hospitalisation delay distribution, or `NA` to not simulate
+#' hospitalisation (admission) dates.
+#' @param onset_to_death An `<epidist>` object, an anonymous function for
+#' the onset to death delay distribution, or `NA` to not simulate dates for
+#' individuals that died.
+#' @param onset_to_recovery An `<epidist>` object, an anonymous function for
+#' the onset to death delay distribution, or `NA` to not simulate dates for
+#' individuals that recovered. Default is `NA` so by default cases that
+#' recover get an `NA` in the `$date_outcome` line list column.
 #' @param hosp_risk Either a single `numeric` for the hospitalisation risk of
 #' everyone in the population, or a `<data.frame>` with age specific
 #' hospitalisation risks Default is 20% hospitalisation (`0.2`) for the entire
@@ -151,6 +157,7 @@ sim_linelist <- function(contact_distribution,
                          prob_infect,
                          onset_to_hosp,
                          onset_to_death,
+                         onset_to_recovery = NA,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,
                          non_hosp_death_risk = 0.05,
@@ -171,13 +178,15 @@ sim_linelist <- function(contact_distribution,
       contact_distribution = contact_distribution,
       infect_period = infect_period,
       onset_to_hosp = onset_to_hosp,
-      onset_to_death = onset_to_death
+      onset_to_death = onset_to_death,
+      onset_to_recovery = onset_to_recovery
     )
   )
   contact_distribution <- funcs$contact_distribution
   infect_period <- funcs$infect_period
   onset_to_hosp <- funcs$onset_to_hosp
   onset_to_death <- funcs$onset_to_death
+  onset_to_recovery <- funcs$onset_to_recovery
 
   .check_sim_input(
     sim_type = "linelist",
@@ -188,6 +197,7 @@ sim_linelist <- function(contact_distribution,
     outbreak_size = outbreak_size,
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     add_names = add_names,
     add_ct = add_ct,
     case_type_probs = case_type_probs,
@@ -241,6 +251,7 @@ sim_linelist <- function(contact_distribution,
     prob_infect = prob_infect,
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     hosp_risk = hosp_risk,
     hosp_death_risk = hosp_death_risk,
     non_hosp_death_risk = non_hosp_death_risk,
diff --git a/R/sim_outbreak.R b/R/sim_outbreak.R
index 6da600d6..3f4d169e 100644
--- a/R/sim_outbreak.R
+++ b/R/sim_outbreak.R
@@ -58,6 +58,7 @@ sim_outbreak <- function(contact_distribution,
                          prob_infect,
                          onset_to_hosp,
                          onset_to_death,
+                         onset_to_recovery = NA,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,
                          non_hosp_death_risk = 0.05,
@@ -83,13 +84,15 @@ sim_outbreak <- function(contact_distribution,
       contact_distribution = contact_distribution,
       infect_period = infect_period,
       onset_to_hosp = onset_to_hosp,
-      onset_to_death = onset_to_death
+      onset_to_death = onset_to_death,
+      onset_to_recovery = onset_to_recovery
     )
   )
   contact_distribution <- funcs$contact_distribution
   infect_period <- funcs$infect_period
   onset_to_hosp <- funcs$onset_to_hosp
   onset_to_death <- funcs$onset_to_death
+  onset_to_recovery <- funcs$onset_to_recovery
 
   .check_sim_input(
     sim_type = "outbreak",
@@ -100,6 +103,7 @@ sim_outbreak <- function(contact_distribution,
     outbreak_size = outbreak_size,
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     add_names = add_names,
     add_ct = add_ct,
     case_type_probs = case_type_probs,
@@ -154,6 +158,7 @@ sim_outbreak <- function(contact_distribution,
     prob_infect = prob_infect,
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     hosp_risk = hosp_risk,
     hosp_death_risk = hosp_death_risk,
     non_hosp_death_risk = non_hosp_death_risk,
diff --git a/man/sim_linelist.Rd b/man/sim_linelist.Rd
index 318aa2a6..03a371d4 100644
--- a/man/sim_linelist.Rd
+++ b/man/sim_linelist.Rd
@@ -10,6 +10,7 @@ sim_linelist(
   prob_infect,
   onset_to_hosp,
   onset_to_death,
+  onset_to_recovery = NA,
   hosp_risk = 0.2,
   hosp_death_risk = 0.5,
   non_hosp_death_risk = 0.05,
@@ -39,11 +40,18 @@ infectious period.}
 \item{prob_infect}{A single \code{numeric} for the probability of a secondary
 contact being infected by an infected primary contact.}
 
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
+
+\item{onset_to_recovery}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that recovered. Default is \code{NA} so by default cases that
+recover get an \code{NA} in the \verb{$date_outcome} line list column.}
 
 \item{hosp_risk}{Either a single \code{numeric} for the hospitalisation risk of
 everyone in the population, or a \verb{<data.frame>} with age specific
diff --git a/man/sim_outbreak.Rd b/man/sim_outbreak.Rd
index 34bf1ead..ed2e5bca 100644
--- a/man/sim_outbreak.Rd
+++ b/man/sim_outbreak.Rd
@@ -10,6 +10,7 @@ sim_outbreak(
   prob_infect,
   onset_to_hosp,
   onset_to_death,
+  onset_to_recovery = NA,
   hosp_risk = 0.2,
   hosp_death_risk = 0.5,
   non_hosp_death_risk = 0.05,
@@ -41,11 +42,18 @@ infectious period.}
 \item{prob_infect}{A single \code{numeric} for the probability of a secondary
 contact being infected by an infected primary contact.}
 
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
+
+\item{onset_to_recovery}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that recovered. Default is \code{NA} so by default cases that
+recover get an \code{NA} in the \verb{$date_outcome} line list column.}
 
 \item{hosp_risk}{Either a single \code{numeric} for the hospitalisation risk of
 everyone in the population, or a \verb{<data.frame>} with age specific

From db3c7370f2f2fcd708d4afaf9305aa1f3132f704 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 5 Apr 2024 17:30:09 +0100
Subject: [PATCH 02/11] added onset_to_recovery to as_function, WIP #36

---
 R/utils.R          | 16 +++++++++++++---
 man/as_function.Rd |  2 +-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index bccd936d..2e64d9ff 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -103,7 +103,7 @@ is_na <- function(x) {
 #'
 #' @param x A named list containing either `<epidist>`, `function` or `NA`.
 #' Named list elements are: `"contact_distribution"`, `"infect_period"`,
-#' `"onset_to_hosp"`, `"onset_to_death"`.
+#' `"onset_to_hosp"`, `"onset_to_death"`, `"onset_to_recovery".`
 #'
 #' @return A list of `function`s.
 #' @keywords internal
@@ -112,7 +112,8 @@ as_function <- function(x) {
     "Input delay distributions need to be either functions or <epidist>" =
       inherits(x$contact_distribution, c("function", "epidist")) &&
       inherits(x$infect_period, c("function", "epidist")),
-    "onset_to_hosp and onset_to_death need to be a function, <epidist> or NA" =
+    "onset_to_hosp, onset_to_death and onset_to_recovery need to be a function,
+    <epidist> or NA" =
       inherits(x$onset_to_hosp, c("function", "epidist")) ||
       is_na(x$onset_to_hosp) &&
       inherits(x$onset_to_death, c("function", "epidist")) ||
@@ -134,12 +135,21 @@ as_function <- function(x) {
   } else {
     onset_to_death <- as.function(x$onset_to_death, func_type = "generate")
   }
+  if (is_na(x$onset_to_recovery)) {
+    # function to generate NA instead of recovery times
+    onset_to_recovery <- function(x) rep(NA, times = x)
+  } else {
+    onset_to_recovery <- as.function(
+      x$onset_to_recovery, func_type = "generate"
+    )
+  }
 
   # return list of functions
   list(
     contact_distribution = contact_distribution,
     infect_period = infect_period,
     onset_to_hosp = onset_to_hosp,
-    onset_to_death = onset_to_death
+    onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery
   )
 }
diff --git a/man/as_function.Rd b/man/as_function.Rd
index 2986d0c6..e6178d0d 100644
--- a/man/as_function.Rd
+++ b/man/as_function.Rd
@@ -9,7 +9,7 @@ as_function(x)
 \arguments{
 \item{x}{A named list containing either \verb{<epidist>}, \code{function} or \code{NA}.
 Named list elements are: \code{"contact_distribution"}, \code{"infect_period"},
-\code{"onset_to_hosp"}, \code{"onset_to_death"}.}
+\code{"onset_to_hosp"}, \code{"onset_to_death"}, \verb{"onset_to_recovery".}}
 }
 \value{
 A list of \code{function}s.

From fab9a9040493d300a8a02e6587272fc6c580010c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 5 Apr 2024 17:31:04 +0100
Subject: [PATCH 03/11] renamed and updated .add_deaths to .add_outcome, WIP
 #36

---
 R/add_cols.R        | 53 +++++++++++++++++++++++----------------------
 man/dot-add_date.Rd | 25 ++++++++++++++++-----
 2 files changed, 46 insertions(+), 32 deletions(-)

diff --git a/R/add_cols.R b/R/add_cols.R
index a5299b29..9d77b98b 100644
--- a/R/add_cols.R
+++ b/R/add_cols.R
@@ -118,60 +118,61 @@ NULL
 }
 
 #' @name .add_date
-.add_deaths <- function(.data,
-                        onset_to_death,
-                        hosp_death_risk,
-                        non_hosp_death_risk) {
+.add_outcome <- function(.data,
+                         onset_to_death,
+                         onset_to_recovery,
+                         hosp_death_risk,
+                         non_hosp_death_risk) {
   infected_idx <- .data$infected == "infected"
   num_infected <- sum(infected_idx)
-  .data$deaths <- NA_real_
-  .data$deaths[infected_idx] <- .data$time[infected_idx] +
-    onset_to_death(num_infected)
+  .data$outcome <- "contact"
+  .data$outcome_time <- NA_real_
+  .data$outcome[infected_idx] <- "recovered"
+  .data$outcome_time[infected_idx] <- .data$time[infected_idx] +
+    onset_to_recovery(num_infected)
+  hosp_idx <- !is.na(.data$hospitalisation)
+  non_hosp_idx <- is.na(.data$hospitalisation)
 
-  apply_death_risk <- function(.data, risk, hosp = TRUE) {
+  apply_death_risk <- function(.data, risk, idx) {
     if (!is_na(risk)) {
       if (is.numeric(risk)) {
         # size is converted to an integer internally in sample()
         pop_sample <- sample(
-          which(infected_idx),
+          which(idx),
           replace = FALSE,
-          size = (1 - risk) * num_infected
+          size = risk * sum(idx)
         )
-        .data$deaths[pop_sample] <- NA_real_
+        .data$outcome[pop_sample] <- "died"
+        .data$outcome_time[pop_sample] <- .data$time[pop_sample] +
+          onset_to_death(length(pop_sample))
       } else {
         for (i in seq_len(nrow(risk))) {
           age_bracket <- risk$min_age[i]:risk$max_age[i]
-          if (hosp) {
-            age_group <- which(
-              .data$age %in% age_bracket & !is.na(.data$hospitalisation)
-            )
-          } else {
-            age_group <- which(
-              .data$age %in% age_bracket & is.na(.data$hospitalisation)
-            )
-          }
-          not_hosp_death_prob <- 1 - risk$risk[i]
+          age_group <- which(.data$age %in% age_bracket & idx)
           # size is converted to an integer internally in sample()
           age_group_sample <- sample(
             age_group,
             replace = FALSE,
-            size = not_hosp_death_prob * length(age_group)
+            size = risk$risk[i] * length(age_group)
           )
-          .data$deaths[age_group_sample] <- NA_real_
+          .data$outcome[age_group_sample] <- "died"
+          .data$outcome_time[age_group_sample] <- .data$time[age_group_sample] +
+            onset_to_death(length(age_group_sample))
         }
       }
     }
     .data
   }
 
-  .data <- apply_death_risk(.data, risk = hosp_death_risk, hosp = TRUE)
-  .data <- apply_death_risk(.data, risk = non_hosp_death_risk, hosp = FALSE)
+  .data <- apply_death_risk(.data, risk = hosp_death_risk, idx = hosp_idx)
+  .data <- apply_death_risk(
+    .data, risk = non_hosp_death_risk, idx = non_hosp_idx
+  )
 
   # return data
   .data
 }
 
-
 #' Add line list information as column to infectious history `<data.frame>`
 #'
 #' @param .data A `<data.frame>` containing the infectious history from a
diff --git a/man/dot-add_date.Rd b/man/dot-add_date.Rd
index 6a5a1506..64e77276 100644
--- a/man/dot-add_date.Rd
+++ b/man/dot-add_date.Rd
@@ -4,7 +4,7 @@
 \alias{.add_date}
 \alias{.add_date_contact}
 \alias{.add_hospitalisation}
-\alias{.add_deaths}
+\alias{.add_outcome}
 \title{Add event date as column to infectious history \verb{<data.frame>}}
 \usage{
 .add_date_contact(
@@ -17,7 +17,13 @@
 
 .add_hospitalisation(.data, onset_to_hosp, hosp_risk)
 
-.add_deaths(.data, onset_to_death, hosp_death_risk, non_hosp_death_risk)
+.add_outcome(
+  .data,
+  onset_to_death,
+  onset_to_recovery,
+  hosp_death_risk,
+  non_hosp_death_risk
+)
 }
 \arguments{
 \item{.data}{A \verb{<data.frame>} containing the infectious history from a
@@ -35,8 +41,9 @@ given in the \code{distribution} argument.}
 
 \item{outbreak_start_date}{A \code{date} for the start of the outbreak.}
 
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
 \item{hosp_risk}{Either a single \code{numeric} for the hospitalisation risk of
 everyone in the population, or a \verb{<data.frame>} with age specific
@@ -44,8 +51,14 @@ hospitalisation risks Default is 20\% hospitalisation (\code{0.2}) for the entir
 population. If the \code{onset_to_hosp} argument is set to \code{NA} this argument
 should also be set to \code{NA}. See details and examples for more information.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
+
+\item{onset_to_recovery}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that recovered. Default is \code{NA} so by default cases that
+recover get an \code{NA} in the \verb{$date_outcome} line list column.}
 
 \item{hosp_death_risk}{Either a single \code{numeric} for the death risk for
 hospitalised individuals across the population, or a \verb{<data.frame>} with age

From d342165b9e955a84d4270deb9ed48a3cace6c7b2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 5 Apr 2024 17:31:54 +0100
Subject: [PATCH 04/11] updated .sim_internal to call .add_outcome and use
 outcome columns, WIP #36

---
 R/sim_internal.R        |  8 +++++---
 man/dot-sim_internal.Rd | 16 ++++++++++++----
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/R/sim_internal.R b/R/sim_internal.R
index af8cc44b..9f97bf53 100644
--- a/R/sim_internal.R
+++ b/R/sim_internal.R
@@ -17,6 +17,7 @@
                           prob_infect,
                           onset_to_hosp = NULL,
                           onset_to_death = NULL,
+                          onset_to_recovery = NULL,
                           hosp_risk = NULL,
                           hosp_death_risk = NULL,
                           non_hosp_death_risk = NULL,
@@ -109,20 +110,21 @@
       onset_to_hosp = onset_to_hosp,
       hosp_risk = hosp_risk
     )
-    .data <- .add_deaths(
+    .data <- .add_outcome(
       .data = .data,
       onset_to_death = onset_to_death,
+      onset_to_recovery = onset_to_recovery,
       hosp_death_risk = hosp_death_risk,
       non_hosp_death_risk = non_hosp_death_risk
     )
 
     # add hospitalisation and death dates
     .data$date_admission <- .data$hospitalisation + outbreak_start_date
-    .data$date_death <- .data$deaths + outbreak_start_date
+    .data$date_outcome <- .data$outcome_time + outbreak_start_date
 
     linelist_cols <- c(
       "id", "case_type", "sex", "age", "date_onset", "date_admission",
-      "date_death", "date_first_contact", "date_last_contact"
+      "outcome", "date_outcome", "date_first_contact", "date_last_contact"
     )
 
     if (add_names) {
diff --git a/man/dot-sim_internal.Rd b/man/dot-sim_internal.Rd
index a8bba1d2..04668f25 100644
--- a/man/dot-sim_internal.Rd
+++ b/man/dot-sim_internal.Rd
@@ -12,6 +12,7 @@ within \pkg{simulist}}
   prob_infect,
   onset_to_hosp = NULL,
   onset_to_death = NULL,
+  onset_to_recovery = NULL,
   hosp_risk = NULL,
   hosp_death_risk = NULL,
   non_hosp_death_risk = NULL,
@@ -45,11 +46,18 @@ infectious period.}
 \item{prob_infect}{A single \code{numeric} for the probability of a secondary
 contact being infected by an infected primary contact.}
 
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
+
+\item{onset_to_recovery}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that recovered. Default is \code{NA} so by default cases that
+recover get an \code{NA} in the \verb{$date_outcome} line list column.}
 
 \item{hosp_risk}{Either a single \code{numeric} for the hospitalisation risk of
 everyone in the population, or a \verb{<data.frame>} with age specific

From fb136cbd8d149538f415b751cc9411e521eb23cd Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 5 Apr 2024 17:33:09 +0100
Subject: [PATCH 05/11] added onset_to_recovery to .check_sim_input and updated
 .cross_check_sim_input to return compound warnings or errors, WIP #36

---
 R/checkers.R                     | 70 ++++++++++++++++++++------------
 man/dot-check_sim_input.Rd       | 16 ++++++--
 man/dot-cross_check_sim_input.Rd | 10 +++--
 3 files changed, 63 insertions(+), 33 deletions(-)

diff --git a/R/checkers.R b/R/checkers.R
index 2dfea006..0fdefa6f 100644
--- a/R/checkers.R
+++ b/R/checkers.R
@@ -121,6 +121,7 @@
                              outbreak_size,
                              onset_to_hosp = NULL,
                              onset_to_death = NULL,
+                             onset_to_recovery = NULL,
                              add_names = NULL,
                              add_ct = NULL,
                              case_type_probs = NULL,
@@ -146,6 +147,7 @@
   if (sim_type %in% c("linelist", "outbreak")) {
     .check_func_req_args(onset_to_hosp)
     .check_func_req_args(onset_to_death)
+    .check_func_req_args(onset_to_recovery)
     checkmate::assert_logical(add_names, len = 1)
     checkmate::assert_logical(add_ct, len = 1)
     checkmate::assert_numeric(case_type_probs, len = 3, lower = 0, upper = 1)
@@ -250,59 +252,77 @@
   onset_to_hosp_eval <- onset_to_hosp(1)
   onset_to_death_eval <- onset_to_death(1)
 
+  msg <- character(0)
   # risks can only be NA when the onset to event is also NA
   if (!is_na(onset_to_hosp_eval) && is_na(hosp_risk)) {
-    stop(
+    msg <- c(msg, paste(
       "hosp_risk is set to NA but onset_to_hosp is specified \n",
-      "set hosp_risk to numeric value",
-      call. = FALSE
-    )
+      "set hosp_risk to numeric value"
+    ))
   }
   if (!is_na(onset_to_death_eval)) {
     if (is_na(hosp_death_risk)) {
-      stop(
+      msg <- c(msg, paste(
         "hosp_death_risk is set to NA but onset_to_death is specified \n",
-        "set hosp_death_risk to numeric value",
-        call. = FALSE
-      )
+        "set hosp_death_risk to numeric value"
+      ))
     }
     if (is_na(non_hosp_death_risk)) {
-      stop(
+      msg <- c(msg, paste(
         "non_hosp_death_risk is set to NA but onset_to_death is specified \n",
-        "set non_hosp_death_risk to numeric value",
-        call. = FALSE
-      )
+        "set non_hosp_death_risk to numeric value"
+      ))
     }
   }
+  if (length(msg) > 0) {
+    stop(
+      "Some onset-to-event and their corresponding risk are incompatible:\n",
+      sprintf("  - %s\n", msg),
+      call. = FALSE
+    )
+  }
 
   if (is_na(onset_to_hosp_eval) && checkmate::test_number(hosp_risk) ||
       is_na(onset_to_hosp_eval) && is.data.frame(hosp_risk)) {
-    warning(
+    msg <- c(msg, paste(
       "onset_to_hosp is set to NA but hosp_risk is specified \n",
-      "hosp_risk is being ignored, set hosp_risk to NA when ",
-      "onset_to_hosp is NA",
-      call. = FALSE
-    )
+      "hosp_risk is being ignored, set hosp_risk to NA when",
+      "onset_to_hosp is NA"
+    ))
+  }
+  if (is_na(onset_to_hosp_eval) && checkmate::test_number(hosp_death_risk) ||
+      is_na(onset_to_hosp_eval) && is.data.frame(hosp_death_risk)) {
+    msg <- c(msg, paste(
+      "onset_to_hosp is set to NA but hosp_death_risk is specified \n",
+      "hosp_death_risk is being ignored, set hosp_death_risk to NA when",
+      "onset_to_hosp is NA"
+    ))
   }
   if (is_na(onset_to_death_eval) && checkmate::test_number(hosp_death_risk) ||
       is_na(onset_to_death_eval) && is.data.frame(hosp_death_risk)) {
-    warning(
+    msg <- c(msg, paste(
       "onset_to_death is set to NA but hosp_death_risk is specified \n",
-      "hosp_death_risk is being ignored, set hosp_death_risk to NA when ",
-      "onset_to_death is NA",
-      call. = FALSE
-    )
+      "hosp_death_risk is being ignored, set hosp_death_risk to NA when",
+      "onset_to_death is NA"
+    ))
   }
   if (is_na(onset_to_death_eval) &&
       checkmate::test_number(non_hosp_death_risk) ||
       is_na(onset_to_death_eval) &&
       is.data.frame(non_hosp_death_risk)) {
-    warning(
+    msg <- c(msg, paste(
       "onset_to_death is set to NA but non_hosp_death_risk is specified \n",
-      "non_hosp_death_risk is being ignored, set non_hosp_death_risk to NA ",
-      "when onset_to_death is NA",
+      "non_hosp_death_risk is being ignored, set non_hosp_death_risk to NA",
+      "when onset_to_death is NA"
+    ))
+  }
+  if (length(msg) > 0) {
+    warning(
+      "Some onset-to-event and their corresponding risk are incompatible:\n",
+      sprintf("  - %s\n", msg),
       call. = FALSE
     )
   }
+
   invisible(onset_to_hosp)
 }
diff --git a/man/dot-check_sim_input.Rd b/man/dot-check_sim_input.Rd
index 9171f037..3f4904de 100644
--- a/man/dot-check_sim_input.Rd
+++ b/man/dot-check_sim_input.Rd
@@ -13,6 +13,7 @@
   outbreak_size,
   onset_to_hosp = NULL,
   onset_to_death = NULL,
+  onset_to_recovery = NULL,
   add_names = NULL,
   add_ct = NULL,
   case_type_probs = NULL,
@@ -56,11 +57,18 @@ many iterations (internally) then the function errors, whereas if the
 maximum outbreak size is exceeded the function returns the data early and a
 warning stating how many cases and contacts are returned.}
 
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
+
+\item{onset_to_recovery}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that recovered. Default is \code{NA} so by default cases that
+recover get an \code{NA} in the \verb{$date_outcome} line list column.}
 
 \item{add_names}{A \code{logical} boolean for whether to add names to each row
 of the line list. Default is \code{TRUE}.}
diff --git a/man/dot-cross_check_sim_input.Rd b/man/dot-cross_check_sim_input.Rd
index ecdf66f0..1f354975 100644
--- a/man/dot-cross_check_sim_input.Rd
+++ b/man/dot-cross_check_sim_input.Rd
@@ -14,11 +14,13 @@ compatible with hospitalisation and death risks}
 )
 }
 \arguments{
-\item{onset_to_hosp}{An \verb{<epidist>} object or anonymous function for
-the onset to hospitalisation delay distribution.}
+\item{onset_to_hosp}{An \verb{<epidist>} object, an anonymous function for
+the onset to hospitalisation delay distribution, or \code{NA} to not simulate
+hospitalisation (admission) dates.}
 
-\item{onset_to_death}{An \verb{<epidist>} object or anonymous function for
-the onset to death delay distribution.}
+\item{onset_to_death}{An \verb{<epidist>} object, an anonymous function for
+the onset to death delay distribution, or \code{NA} to not simulate dates for
+individuals that died.}
 
 \item{hosp_risk}{Either a single \code{numeric} for the hospitalisation risk of
 everyone in the population, or a \verb{<data.frame>} with age specific

From 7c4539a80c5dee36c5ac266432c3accac3c290ed Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Mon, 8 Apr 2024 17:46:59 +0100
Subject: [PATCH 06/11] add tidyr to Suggests in DESCRIPTION

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7ea2ab98..563e8987 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,6 +32,7 @@ Imports:
 Suggests: 
     bookdown,
     dplyr,
+    tidyr,
     epicontacts (>= 1.1.3),
     ggplot2,
     incidence2 (>= 2.1.0),

From 00e11e4c31f403bd881c8ea1851cd87a02b874f1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Mon, 8 Apr 2024 17:47:34 +0100
Subject: [PATCH 07/11] added data reshaping (base R and tidyverse) to fix
 vis-linelist vignette

---
 vignettes/vis-linelist.Rmd | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/vignettes/vis-linelist.Rmd b/vignettes/vis-linelist.Rmd
index 0ac8bb89..637b8b9d 100644
--- a/vignettes/vis-linelist.Rmd
+++ b/vignettes/vis-linelist.Rmd
@@ -127,6 +127,40 @@ plot(weekly)
 ```
  
 To visualise the onset, hospitalisation and death incidence in the same plot they can be jointly specified to the `date_index` argument of `incidence2::incidence()`. 
+
+First the outcome data needs to be pivoted from long data to wide data to be input into `incidence2::incidence()`.
+
+### Reshape line list data {.tabset}
+
+#### Base R
+
+```{r, reshape-linelist-base-r, eval=FALSE}
+# this can also be achieved with the reshape() function but the user interface
+# for that function is complicated so here we just create the columns manually
+linelist$date_death <- linelist$date_outcome
+linelist$date_death[linelist$outcome == "recovered"] <- NA
+linelist$date_recovery <- linelist$date_outcome
+linelist$date_recovery[linelist$outcome == "died"] <- NA
+```
+
+#### Tidyverse
+
+```{r, reshape-linelist-tidyverse, message=FALSE}
+library(tidyr)
+library(dplyr)
+linelist <- linelist %>% 
+  tidyr::pivot_wider(
+    names_from = outcome, 
+    values_from = date_outcome
+  )
+linelist <- linelist %>%
+  dplyr::rename(
+    date_death = died, 
+    date_recovery = recovered
+  )
+```
+
+## {-}
  
 ```{r, plot-onset-hospitalisation, fig.cap="Figure 4: Daily incidence of cases from symptom onset and incidence of hospitalisations and deaths.", fig.width = 8, fig.height = 5}
 daily <- incidence(
@@ -238,7 +272,7 @@ outbreak$contacts <- outbreak$contacts[outbreak$contacts$was_case == "Y", ]
 
 #### Tidyverse
 
-```{r, subset-linelist-tidyverse, message=FALSE}
+```{r, subset-linelist-tidyverse}
 library(dplyr)
 outbreak$contacts <- outbreak$contacts %>%
   dplyr::filter(was_case == "Y")

From 5fe308342ff9cef06e22ee34dfe615c1e86ffcd3 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 8 Apr 2024 16:50:47 +0000
Subject: [PATCH 08/11] Update CITATION.cff

---
 CITATION.cff | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/CITATION.cff b/CITATION.cff
index bda8d13b..8c91cec8 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -163,6 +163,22 @@ references:
     email: davis@posit.co
     orcid: https://orcid.org/0000-0003-4777-038X
   year: '2024'
+- type: software
+  title: tidyr
+  abstract: 'tidyr: Tidy Messy Data'
+  notes: Suggests
+  url: https://tidyr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=tidyr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Vaughan
+    given-names: Davis
+    email: davis@posit.co
+  - family-names: Girlich
+    given-names: Maximilian
+  year: '2024'
 - type: software
   title: epicontacts
   abstract: 'epicontacts: Handling, Visualisation and Analysis of Epidemiological

From b8f9f33aa81e5ac295750bf501c531a6ab2d22e6 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 10 Apr 2024 12:15:39 +0100
Subject: [PATCH 09/11] updated testdata and testdata README

---
 tests/testthat/testdata/README.md             |   2 +-
 tests/testthat/testdata/pre_ct.rds            | Bin 1687 -> 1583 bytes
 .../testdata/pre_date_first_contact.rds       | Bin 854 -> 759 bytes
 .../testdata/pre_date_last_contact.rds        | Bin 757 -> 671 bytes
 tests/testthat/testdata/pre_death.rds         | Bin 1095 -> 0 bytes
 .../testthat/testdata/pre_hospitalisation.rds | Bin 1002 -> 893 bytes
 tests/testthat/testdata/pre_names.rds         | Bin 1210 -> 1171 bytes
 tests/testthat/testdata/pre_outcome.rds       | Bin 0 -> 966 bytes
 8 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 tests/testthat/testdata/pre_death.rds
 create mode 100644 tests/testthat/testdata/pre_outcome.rds

diff --git a/tests/testthat/testdata/README.md b/tests/testthat/testdata/README.md
index a25b50ed..c245e72d 100644
--- a/tests/testthat/testdata/README.md
+++ b/tests/testthat/testdata/README.md
@@ -5,7 +5,7 @@ The {simulist} R package contains test data files in order to test internal func
 * "pre_date_last_contact"
 * "pre_date_first_contact"
 * "pre_hospitalisation"
-* "pre_death"
+* "pre_outcome"
 * "pre_names"
 * "pre_ct"
 
diff --git a/tests/testthat/testdata/pre_ct.rds b/tests/testthat/testdata/pre_ct.rds
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diff --git a/tests/testthat/testdata/pre_date_last_contact.rds b/tests/testthat/testdata/pre_date_last_contact.rds
index 42e503335f2e6da86037f11102e757b42b80e862..6bbadfeed3d1bb322ba89d3920606b7d4cf41443 100644
GIT binary patch
delta 597
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delta 684
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diff --git a/tests/testthat/testdata/pre_death.rds b/tests/testthat/testdata/pre_death.rds
deleted file mode 100644
index 07c92573a30d498f1b071d3110f72f6f3397a9f4..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/tests/testthat/testdata/pre_hospitalisation.rds b/tests/testthat/testdata/pre_hospitalisation.rds
index 3521406ff9527d69c7851382c60079e808979961..1c5ef33c46523301822eb794fba776d703af0c48 100644
GIT binary patch
literal 893
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literal 1002
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diff --git a/tests/testthat/testdata/pre_names.rds b/tests/testthat/testdata/pre_names.rds
index 23c11553f127d18d68c021ebe71b9f1c875a8c26..e21da405222cb7544646dff8cdf4ad6da2d86738 100644
GIT binary patch
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diff --git a/tests/testthat/testdata/pre_outcome.rds b/tests/testthat/testdata/pre_outcome.rds
new file mode 100644
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GIT binary patch
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From a2a6eed576e21e1169c26a83fe64dc167264141a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 10 Apr 2024 12:17:14 +0100
Subject: [PATCH 10/11] updated tests and snapshots with onset-to-recovery,
 relates #36

---
 tests/testthat/_snaps/sim_linelist.md | 416 +++++++++++-----------
 tests/testthat/_snaps/sim_outbreak.md | 480 +++++++++++++-------------
 tests/testthat/test-add_cols.R        |  44 ++-
 tests/testthat/test-checkers.R        |  67 +++-
 tests/testthat/test-sim_linelist.R    |  62 ++--
 5 files changed, 556 insertions(+), 513 deletions(-)

diff --git a/tests/testthat/_snaps/sim_linelist.md b/tests/testthat/_snaps/sim_linelist.md
index 93c5f1d2..7b4b5ae4 100644
--- a/tests/testthat/_snaps/sim_linelist.md
+++ b/tests/testthat/_snaps/sim_linelist.md
@@ -4,32 +4,32 @@
       sim_linelist(contact_distribution = contact_distribution, infect_period = infect_period,
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death)
     Output
-         id         case_name case_type sex age date_onset date_admission date_death
-      1   1  Isaiah Patterson  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael John suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3    Lorenzo Gaynor confirmed   m   1 2023-01-01           <NA>       <NA>
-      4   5      Cass Milburn confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6         Hope Cobb  probable   f  22 2023-01-01           <NA>       <NA>
-      6   8     Wyona Lenahan  probable   f  28 2023-01-01           <NA>       <NA>
-      7  11    Bishr al-Jamil confirmed   m  46 2023-01-01     2023-01-13       <NA>
-      8  12  Viviana Martinez  probable   f  67 2023-01-01           <NA>       <NA>
-      9  13 Mudrik al-Youssef  probable   m  86 2023-01-01     2023-01-01       <NA>
-      10 18      Kylie Rieger confirmed   f  60 2023-01-02           <NA>       <NA>
-      11 20   Vincent Edwards  probable   m  49 2023-01-02           <NA>       <NA>
-      12 22      Michiyo Hong suspected   f   7 2023-01-02     2023-01-02       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05       NA
-      3          2022-12-30        2023-01-02     25.6
-      4          2022-12-29        2023-01-02     25.6
-      5          2023-01-01        2023-01-03       NA
-      6          2023-01-03        2023-01-04       NA
-      7          2023-01-04        2023-01-05     25.6
-      8          2023-01-01        2023-01-04       NA
-      9          2022-12-31        2023-01-03       NA
-      10         2022-12-30        2023-01-03     25.6
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03       NA
+         id                 case_name case_type sex age date_onset date_admission
+      1   1               Damion Hamm confirmed   m  35 2023-01-01           <NA>
+      2   2         Ignacio Hernandez confirmed   m  43 2023-01-01           <NA>
+      3   3            Bryce Donnelly confirmed   m   1 2023-01-01           <NA>
+      4   5             David Arrieta confirmed   m  78 2023-01-01           <NA>
+      5   6 Kristina Vazquez Pallares confirmed   f  22 2023-01-01           <NA>
+      6   8          Nusaiba el-Farah suspected   f  28 2023-01-01           <NA>
+      7  11    Dominic Kills In Sight  probable   m  46 2023-01-01     2023-01-13
+      8  12              Violet Watts confirmed   f  67 2023-01-01           <NA>
+      9  13       Khristopher Cunniff confirmed   m  86 2023-01-01     2023-01-01
+      10 18               Paige Reich  probable   f  60 2023-01-02           <NA>
+      11 20           Jackson Carlson confirmed   m  49 2023-01-02           <NA>
+      12 22           Cassandra Smith suspected   f   7 2023-01-02     2023-01-02
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>     25.6
+      2  recovered         <NA>         2022-12-30        2023-01-05     25.6
+      3  recovered         <NA>         2022-12-30        2023-01-02     25.6
+      4  recovered         <NA>         2022-12-29        2023-01-02     25.6
+      5  recovered         <NA>         2023-01-01        2023-01-03     25.6
+      6  recovered         <NA>         2023-01-03        2023-01-04       NA
+      7  recovered         <NA>         2023-01-04        2023-01-05       NA
+      8  recovered         <NA>         2023-01-01        2023-01-04     25.6
+      9  recovered         <NA>         2022-12-31        2023-01-03     25.6
+      10 recovered         <NA>         2022-12-30        2023-01-03       NA
+      11 recovered         <NA>         2023-01-01        2023-01-04     25.6
+      12      died   2023-01-16         2023-01-01        2023-01-03       NA
 
 # sim_linelist works as expected with age-strat risks
 
@@ -39,32 +39,32 @@
         hosp_risk = age_dep_hosp_risk, hosp_death_risk = age_dep_hosp_death_risk,
         non_hosp_death_risk = age_dep_non_hosp_death_risk)
     Output
-         id          case_name case_type sex age date_onset date_admission date_death
-      1   1      Donald Childs  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael Duran suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3          Cass Root  probable   m   1 2023-01-01     2023-01-11 2023-01-19
-      4   5   Mudrik al-Hallal confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6       Erika Sierra confirmed   f  22 2023-01-01           <NA>       <NA>
-      6   8      Jennifer Hong confirmed   f  28 2023-01-01           <NA>       <NA>
-      7  11    Raashid el-Huda suspected   m  46 2023-01-01           <NA>       <NA>
-      8  12      Kayla Johnson suspected   f  67 2023-01-01           <NA>       <NA>
-      9  13 Dominic Montgomery  probable   m  86 2023-01-01     2023-01-01 2023-01-10
-      10 18    Giovana Segarra suspected   f  60 2023-01-02           <NA>       <NA>
-      11 20    Vincent Edwards suspected   m  49 2023-01-02     2023-01-09 2023-01-21
-      12 22        Kiona Dalke  probable   f   7 2023-01-02           <NA>       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05       NA
-      3          2022-12-30        2023-01-02       NA
-      4          2022-12-29        2023-01-02     23.1
-      5          2023-01-01        2023-01-03     23.1
-      6          2023-01-03        2023-01-04     23.1
-      7          2023-01-04        2023-01-05       NA
-      8          2023-01-01        2023-01-04       NA
-      9          2022-12-31        2023-01-03       NA
-      10         2022-12-30        2023-01-03       NA
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03       NA
+         id             case_name case_type sex age date_onset date_admission
+      1   1    David Garcia Mayen  probable   m  35 2023-01-01           <NA>
+      2   2   Rory Kills In Sight confirmed   m  43 2023-01-01           <NA>
+      3   3      Sheldon Martinez confirmed   m   1 2023-01-01     2023-01-11
+      4   5         Bryce Cunniff  probable   m  78 2023-01-01           <NA>
+      5   6        Lien Whitworth confirmed   f  22 2023-01-01           <NA>
+      6   8         Tiffany Weiss suspected   f  28 2023-01-01           <NA>
+      7  11    Cleatus Kacprowicz  probable   m  46 2023-01-01           <NA>
+      8  12          Taylor Moore confirmed   f  67 2023-01-01           <NA>
+      9  13         Tyler Carlson confirmed   m  86 2023-01-01     2023-01-01
+      10 18      Grayson Lovelace confirmed   f  60 2023-01-02           <NA>
+      11 20 Abdul Maalik al-Ishak suspected   m  49 2023-01-02     2023-01-09
+      12 22         Kendra Newton confirmed   f   7 2023-01-02           <NA>
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>       NA
+      2  recovered         <NA>         2022-12-30        2023-01-05       25
+      3  recovered         <NA>         2022-12-30        2023-01-02       25
+      4  recovered         <NA>         2022-12-29        2023-01-02       NA
+      5  recovered         <NA>         2023-01-01        2023-01-03       25
+      6  recovered         <NA>         2023-01-03        2023-01-04       NA
+      7  recovered         <NA>         2023-01-04        2023-01-05       NA
+      8  recovered         <NA>         2023-01-01        2023-01-04       25
+      9  recovered         <NA>         2022-12-31        2023-01-03       25
+      10 recovered         <NA>         2022-12-30        2023-01-03       25
+      11 recovered         <NA>         2023-01-01        2023-01-04       NA
+      12 recovered         <NA>         2023-01-01        2023-01-03       25
 
 # sim_linelist works as expected without Ct
 
@@ -73,32 +73,32 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
         add_ct = FALSE)
     Output
-         id         case_name case_type sex age date_onset date_admission date_death
-      1   1  Isaiah Patterson  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael John suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3    Lorenzo Gaynor confirmed   m   1 2023-01-01           <NA>       <NA>
-      4   5      Cass Milburn confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6         Hope Cobb  probable   f  22 2023-01-01           <NA>       <NA>
-      6   8     Wyona Lenahan  probable   f  28 2023-01-01           <NA>       <NA>
-      7  11    Bishr al-Jamil confirmed   m  46 2023-01-01     2023-01-13       <NA>
-      8  12  Viviana Martinez  probable   f  67 2023-01-01           <NA>       <NA>
-      9  13 Mudrik al-Youssef  probable   m  86 2023-01-01     2023-01-01       <NA>
-      10 18      Kylie Rieger confirmed   f  60 2023-01-02           <NA>       <NA>
-      11 20   Vincent Edwards  probable   m  49 2023-01-02           <NA>       <NA>
-      12 22      Michiyo Hong suspected   f   7 2023-01-02     2023-01-02       <NA>
-         date_first_contact date_last_contact
-      1                <NA>              <NA>
-      2          2022-12-30        2023-01-05
-      3          2022-12-30        2023-01-02
-      4          2022-12-29        2023-01-02
-      5          2023-01-01        2023-01-03
-      6          2023-01-03        2023-01-04
-      7          2023-01-04        2023-01-05
-      8          2023-01-01        2023-01-04
-      9          2022-12-31        2023-01-03
-      10         2022-12-30        2023-01-03
-      11         2023-01-01        2023-01-04
-      12         2023-01-01        2023-01-03
+         id                 case_name case_type sex age date_onset date_admission
+      1   1               Damion Hamm confirmed   m  35 2023-01-01           <NA>
+      2   2         Ignacio Hernandez confirmed   m  43 2023-01-01           <NA>
+      3   3            Bryce Donnelly confirmed   m   1 2023-01-01           <NA>
+      4   5             David Arrieta confirmed   m  78 2023-01-01           <NA>
+      5   6 Kristina Vazquez Pallares confirmed   f  22 2023-01-01           <NA>
+      6   8          Nusaiba el-Farah suspected   f  28 2023-01-01           <NA>
+      7  11    Dominic Kills In Sight  probable   m  46 2023-01-01     2023-01-13
+      8  12              Violet Watts confirmed   f  67 2023-01-01           <NA>
+      9  13       Khristopher Cunniff confirmed   m  86 2023-01-01     2023-01-01
+      10 18               Paige Reich  probable   f  60 2023-01-02           <NA>
+      11 20           Jackson Carlson confirmed   m  49 2023-01-02           <NA>
+      12 22           Cassandra Smith suspected   f   7 2023-01-02     2023-01-02
+           outcome date_outcome date_first_contact date_last_contact
+      1  recovered         <NA>               <NA>              <NA>
+      2  recovered         <NA>         2022-12-30        2023-01-05
+      3  recovered         <NA>         2022-12-30        2023-01-02
+      4  recovered         <NA>         2022-12-29        2023-01-02
+      5  recovered         <NA>         2023-01-01        2023-01-03
+      6  recovered         <NA>         2023-01-03        2023-01-04
+      7  recovered         <NA>         2023-01-04        2023-01-05
+      8  recovered         <NA>         2023-01-01        2023-01-04
+      9  recovered         <NA>         2022-12-31        2023-01-03
+      10 recovered         <NA>         2022-12-30        2023-01-03
+      11 recovered         <NA>         2023-01-01        2023-01-04
+      12      died   2023-01-16         2023-01-01        2023-01-03
 
 # sim_linelist works as expected with anonymous
 
@@ -107,32 +107,32 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
         add_names = FALSE)
     Output
-         id case_type sex age date_onset date_admission date_death date_first_contact
-      1   1  probable   m  35 2023-01-01           <NA>       <NA>               <NA>
-      2   2 confirmed   m  43 2023-01-01           <NA>       <NA>         2022-12-30
-      3   3 confirmed   m   1 2023-01-01           <NA>       <NA>         2022-12-30
-      4   5 confirmed   m  78 2023-01-01           <NA>       <NA>         2022-12-29
-      5   6 confirmed   f  22 2023-01-01           <NA>       <NA>         2023-01-01
-      6   8 suspected   f  28 2023-01-01           <NA>       <NA>         2023-01-03
-      7  11 confirmed   m  46 2023-01-01     2023-01-13       <NA>         2023-01-04
-      8  12 suspected   f  67 2023-01-01           <NA>       <NA>         2023-01-01
-      9  13 confirmed   m  86 2023-01-01     2023-01-01       <NA>         2022-12-31
-      10 18 confirmed   f  60 2023-01-02           <NA>       <NA>         2022-12-30
-      11 20 confirmed   m  49 2023-01-02           <NA>       <NA>         2023-01-01
-      12 22 confirmed   f   7 2023-01-02     2023-01-02       <NA>         2023-01-01
-         date_last_contact ct_value
-      1               <NA>       NA
-      2         2023-01-05       26
-      3         2023-01-02       26
-      4         2023-01-02       26
-      5         2023-01-03       26
-      6         2023-01-04       NA
-      7         2023-01-05       26
-      8         2023-01-04       NA
-      9         2023-01-03       26
-      10        2023-01-03       26
-      11        2023-01-04       26
-      12        2023-01-03       26
+         id case_type sex age date_onset date_admission   outcome date_outcome
+      1   1 confirmed   m  35 2023-01-01           <NA> recovered         <NA>
+      2   2 confirmed   m  43 2023-01-01           <NA> recovered         <NA>
+      3   3 confirmed   m   1 2023-01-01           <NA> recovered         <NA>
+      4   5 confirmed   m  78 2023-01-01           <NA> recovered         <NA>
+      5   6 suspected   f  22 2023-01-01           <NA> recovered         <NA>
+      6   8  probable   f  28 2023-01-01           <NA> recovered         <NA>
+      7  11 confirmed   m  46 2023-01-01     2023-01-13 recovered         <NA>
+      8  12 confirmed   f  67 2023-01-01           <NA> recovered         <NA>
+      9  13  probable   m  86 2023-01-01     2023-01-01 recovered         <NA>
+      10 18  probable   f  60 2023-01-02           <NA> recovered         <NA>
+      11 20 confirmed   m  49 2023-01-02           <NA> recovered         <NA>
+      12 22 confirmed   f   7 2023-01-02     2023-01-02      died   2023-01-16
+         date_first_contact date_last_contact ct_value
+      1                <NA>              <NA>     25.7
+      2          2022-12-30        2023-01-05     25.7
+      3          2022-12-30        2023-01-02     25.7
+      4          2022-12-29        2023-01-02     25.7
+      5          2023-01-01        2023-01-03       NA
+      6          2023-01-03        2023-01-04       NA
+      7          2023-01-04        2023-01-05     25.7
+      8          2023-01-01        2023-01-04     25.7
+      9          2022-12-31        2023-01-03       NA
+      10         2022-12-30        2023-01-03       NA
+      11         2023-01-01        2023-01-04     25.7
+      12         2023-01-01        2023-01-03     25.7
 
 # sim_linelist works as expected with age structure
 
@@ -141,32 +141,32 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
         population_age = age_struct)
     Output
-         id          case_name case_type sex age date_onset date_admission date_death
-      1   1 Ghaamid el-Ishmael suspected   m  44 2023-01-01           <NA>       <NA>
-      2   2   Faatih el-Kaiser confirmed   m  13 2023-01-01           <NA>       <NA>
-      3   3   Brandon Galligan confirmed   m  22 2023-01-01     2023-01-09       <NA>
-      4   5      Aiman el-Riaz suspected   m  85 2023-01-01           <NA>       <NA>
-      5   6     Katelyn Catlin confirmed   f  41 2023-01-01           <NA>       <NA>
-      6   8       Lynsey Duron confirmed   f  89 2023-01-01     2023-01-02       <NA>
-      7  11      Travis Foster confirmed   m  69 2023-01-01           <NA>       <NA>
-      8  12       Jacy Cousins confirmed   f  23 2023-01-01           <NA>       <NA>
-      9  13        Khoa Murray confirmed   m   9 2023-01-01           <NA>       <NA>
-      10 18     Maria Eberhart  probable   f  62 2023-01-02           <NA>       <NA>
-      11 20        John Flores suspected   m  52 2023-01-02     2023-01-15       <NA>
-      12 22        Erin Payson confirmed   f  76 2023-01-02           <NA>       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05     25.1
-      3          2022-12-30        2023-01-02     25.1
-      4          2022-12-29        2023-01-02       NA
-      5          2023-01-01        2023-01-03     25.1
-      6          2023-01-03        2023-01-04     25.1
-      7          2023-01-04        2023-01-05     25.1
-      8          2023-01-01        2023-01-04     25.1
-      9          2022-12-31        2023-01-03     25.1
-      10         2022-12-30        2023-01-03       NA
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03     25.1
+         id         case_name case_type sex age date_onset date_admission   outcome
+      1   1        Mark Beard confirmed   m  44 2023-01-01           <NA> recovered
+      2   2   Brian Mccracken confirmed   m  13 2023-01-01           <NA> recovered
+      3   3     Jesus Garduno confirmed   m  22 2023-01-01     2023-01-09      died
+      4   5   Taalib al-Naqvi confirmed   m  85 2023-01-01           <NA> recovered
+      5   6       Kelly Geist confirmed   f  41 2023-01-01           <NA> recovered
+      6   8    Madison Krause suspected   f  89 2023-01-01     2023-01-02 recovered
+      7  11   Jonathon Lujano  probable   m  69 2023-01-01           <NA> recovered
+      8  12      Ashlan Allen confirmed   f  23 2023-01-01           <NA> recovered
+      9  13 Dhaahir el-Hariri confirmed   m   9 2023-01-01           <NA> recovered
+      10 18       Korren Hart  probable   f  62 2023-01-02           <NA> recovered
+      11 20        Isaac Huff confirmed   m  52 2023-01-02     2023-01-15 recovered
+      12 22      Ryanna Watts suspected   f  76 2023-01-02           <NA> recovered
+         date_outcome date_first_contact date_last_contact ct_value
+      1          <NA>               <NA>              <NA>     25.6
+      2          <NA>         2022-12-30        2023-01-05     25.6
+      3    2023-01-09         2022-12-30        2023-01-02     25.6
+      4          <NA>         2022-12-29        2023-01-02     25.6
+      5          <NA>         2023-01-01        2023-01-03     25.6
+      6          <NA>         2023-01-03        2023-01-04       NA
+      7          <NA>         2023-01-04        2023-01-05       NA
+      8          <NA>         2023-01-01        2023-01-04     25.6
+      9          <NA>         2022-12-31        2023-01-03     25.6
+      10         <NA>         2022-12-30        2023-01-03       NA
+      11         <NA>         2023-01-01        2023-01-04     25.6
+      12         <NA>         2023-01-01        2023-01-03       NA
 
 # sim_linelist works as expected with age-strat risks & age struct
 
@@ -175,32 +175,32 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
         hosp_risk = age_dep_hosp_risk, population_age = age_struct)
     Output
-         id              case_name case_type sex age date_onset date_admission
-      1   1           Corey Marten  probable   m  44 2023-01-01           <NA>
-      2   2         Sean Natarelli confirmed   m  13 2023-01-01           <NA>
-      3   3         Collin Stimack suspected   m  22 2023-01-01           <NA>
-      4   5        Nicholas Orgill confirmed   m  85 2023-01-01     2023-01-01
-      5   6            Hope Arshad suspected   f  41 2023-01-01           <NA>
-      6   8         Shanta Holiday  probable   f  89 2023-01-01           <NA>
-      7  11 Anthony Zapata Morales  probable   m  69 2023-01-01           <NA>
-      8  12         Chandra Kilian suspected   f  23 2023-01-01           <NA>
-      9  13       Bradford Coffman confirmed   m   9 2023-01-01           <NA>
-      10 18          Kanani Nguyen confirmed   f  62 2023-01-02           <NA>
-      11 20            Codie North  probable   m  52 2023-01-02           <NA>
-      12 22           Annie Carter  probable   f  76 2023-01-02           <NA>
-         date_death date_first_contact date_last_contact ct_value
-      1        <NA>               <NA>              <NA>       NA
-      2        <NA>         2022-12-30        2023-01-05     24.1
-      3        <NA>         2022-12-30        2023-01-02       NA
-      4        <NA>         2022-12-29        2023-01-02     24.1
-      5        <NA>         2023-01-01        2023-01-03       NA
-      6        <NA>         2023-01-03        2023-01-04       NA
-      7        <NA>         2023-01-04        2023-01-05       NA
-      8        <NA>         2023-01-01        2023-01-04       NA
-      9        <NA>         2022-12-31        2023-01-03     24.1
-      10       <NA>         2022-12-30        2023-01-03     24.1
-      11       <NA>         2023-01-01        2023-01-04       NA
-      12       <NA>         2023-01-01        2023-01-03       NA
+         id          case_name case_type sex age date_onset date_admission   outcome
+      1   1       Taylor Swift  probable   m  44 2023-01-01           <NA> recovered
+      2   2      Devion Thomas confirmed   m  13 2023-01-01           <NA> recovered
+      3   3      Dustin Bellow confirmed   m  22 2023-01-01           <NA> recovered
+      4   5   Shabaan el-Laham confirmed   m  85 2023-01-01     2023-01-01 recovered
+      5   6  Nadheera el-Wakim confirmed   f  41 2023-01-01           <NA> recovered
+      6   8      Mariah Makris confirmed   f  89 2023-01-01           <NA> recovered
+      7  11 Devyn Garcia Mayen confirmed   m  69 2023-01-01           <NA> recovered
+      8  12       Kaylynn Grip suspected   f  23 2023-01-01           <NA> recovered
+      9  13     Bryce Lehmkuhl  probable   m   9 2023-01-01           <NA> recovered
+      10 18      Aaliyah Trent confirmed   f  62 2023-01-02           <NA> recovered
+      11 20     Ignacio Abeyta confirmed   m  52 2023-01-02           <NA> recovered
+      12 22  Tiffany Wolfchief  probable   f  76 2023-01-02           <NA> recovered
+         date_outcome date_first_contact date_last_contact ct_value
+      1          <NA>               <NA>              <NA>       NA
+      2          <NA>         2022-12-30        2023-01-05     24.9
+      3          <NA>         2022-12-30        2023-01-02     24.9
+      4          <NA>         2022-12-29        2023-01-02     24.9
+      5          <NA>         2023-01-01        2023-01-03     24.9
+      6          <NA>         2023-01-03        2023-01-04     24.9
+      7          <NA>         2023-01-04        2023-01-05     24.9
+      8          <NA>         2023-01-01        2023-01-04       NA
+      9          <NA>         2022-12-31        2023-01-03       NA
+      10         <NA>         2022-12-30        2023-01-03     24.9
+      11         <NA>         2023-01-01        2023-01-04     24.9
+      12         <NA>         2023-01-01        2023-01-03       NA
 
 # sim_linelist works as expected with modified config
 
@@ -210,32 +210,32 @@
         config = create_config(last_contact_distribution = "geom",
           last_contact_distribution_params = c(prob = 0.5)))
     Output
-         id          case_name case_type sex age date_onset date_admission date_death
-      1   1       Lily Camacho confirmed   f  20 2023-01-01           <NA>       <NA>
-      2   2     Justin Apodaca suspected   m  24 2023-01-01           <NA> 2023-01-10
-      3   3       Sad el-Irani suspected   m  51 2023-01-01     2023-01-07       <NA>
-      4   5   Tristan Benjamin  probable   m  16 2023-01-01           <NA>       <NA>
-      5   6     Treven Cornejo suspected   m  83 2023-01-01           <NA>       <NA>
-      6   8    Kevin Contreras suspected   m  48 2023-01-01           <NA>       <NA>
-      7  11    Luqmaan el-Ozer  probable   m  77 2023-01-01     2023-01-01       <NA>
-      8  12      Royse Beltran confirmed   m  90 2023-01-01           <NA>       <NA>
-      9  13   Halle Batchelder confirmed   f  66 2023-01-01           <NA>       <NA>
-      10 18 Morgan Grant-Perry confirmed   f  31 2023-01-02     2023-01-02       <NA>
-      11 20     Matthew Chavez confirmed   m  46 2023-01-02           <NA>       <NA>
-      12 22      Martin Gaspar confirmed   m  75 2023-01-02           <NA>       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>     24.7
-      2          2022-12-30        2023-01-01       NA
-      3          2022-12-31        2023-01-02       NA
-      4          2022-12-30        2023-01-02       NA
-      5          2022-12-31        2023-01-01       NA
-      6          2022-12-31        2023-01-01       NA
-      7          2022-12-30        2023-01-02       NA
-      8          2022-12-30        2023-01-01     24.7
-      9          2022-12-29        2023-01-01     24.7
-      10         2022-12-30        2023-01-01     24.7
-      11         2022-12-30        2023-01-01     24.7
-      12         2022-12-30        2023-01-02     24.7
+         id               case_name case_type sex age date_onset date_admission
+      1   1      Lilibeth Depoyster suspected   f  20 2023-01-01           <NA>
+      2   2       Mubarak el-Othman confirmed   m  24 2023-01-01           <NA>
+      3   3          Tae Woo Karman confirmed   m  51 2023-01-01     2023-01-07
+      4   5       Raakaan el-Vaziri suspected   m  16 2023-01-01           <NA>
+      5   6         Jaasim al-Shams confirmed   m  83 2023-01-01           <NA>
+      6   8          Jared Chambers confirmed   m  48 2023-01-01           <NA>
+      7  11          Muneer al-Miah confirmed   m  77 2023-01-01     2023-01-01
+      8  12 Abdul Khaliq al-Youssef confirmed   m  90 2023-01-01           <NA>
+      9  13         Cheyenne Garcia confirmed   f  66 2023-01-01           <NA>
+      10 18       Shaakira al-Gaber  probable   f  31 2023-01-02     2023-01-02
+      11 20          Miguel Stimack suspected   m  46 2023-01-02           <NA>
+      12 22          Benito Casarez confirmed   m  75 2023-01-02           <NA>
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>       NA
+      2  recovered         <NA>         2022-12-30        2023-01-01     25.1
+      3       died   2023-01-10         2022-12-31        2023-01-02     25.1
+      4  recovered         <NA>         2022-12-30        2023-01-02       NA
+      5  recovered         <NA>         2022-12-31        2023-01-01     25.1
+      6  recovered         <NA>         2022-12-31        2023-01-01     25.1
+      7  recovered         <NA>         2022-12-30        2023-01-02     25.1
+      8  recovered         <NA>         2022-12-30        2023-01-01     25.1
+      9  recovered         <NA>         2022-12-29        2023-01-01     25.1
+      10 recovered         <NA>         2022-12-30        2023-01-01       NA
+      11 recovered         <NA>         2022-12-30        2023-01-01       NA
+      12 recovered         <NA>         2022-12-30        2023-01-02     25.1
 
 # sim_linelist works as expected with modified config parameters
 
@@ -244,30 +244,30 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
         config = create_config(last_contact_distribution_params = c(lambda = 5)))
     Output
-         id         case_name case_type sex age date_onset date_admission date_death
-      1   1  Isaiah Patterson  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael John suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3    Lorenzo Gaynor confirmed   m   1 2023-01-01           <NA>       <NA>
-      4   5      Cass Milburn confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6         Hope Cobb  probable   f  22 2023-01-01           <NA>       <NA>
-      6   8     Wyona Lenahan  probable   f  28 2023-01-01           <NA>       <NA>
-      7  11    Bishr al-Jamil confirmed   m  46 2023-01-01     2023-01-13       <NA>
-      8  12  Viviana Martinez  probable   f  67 2023-01-01           <NA>       <NA>
-      9  13 Mudrik al-Youssef  probable   m  86 2023-01-01     2023-01-01       <NA>
-      10 18      Kylie Rieger confirmed   f  60 2023-01-02           <NA>       <NA>
-      11 20   Vincent Edwards  probable   m  49 2023-01-02           <NA>       <NA>
-      12 22      Michiyo Hong suspected   f   7 2023-01-02     2023-01-02       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2023-01-01        2023-01-07       NA
-      3          2022-12-31        2023-01-03     25.6
-      4          2022-12-31        2023-01-04     25.6
-      5          2023-01-02        2023-01-04       NA
-      6          2023-01-06        2023-01-07       NA
-      7          2023-01-07        2023-01-08     25.6
-      8          2023-01-03        2023-01-06       NA
-      9          2023-01-02        2023-01-05       NA
-      10         2023-01-01        2023-01-05     25.6
-      11         2023-01-04        2023-01-07       NA
-      12         2023-01-03        2023-01-05       NA
+         id                 case_name case_type sex age date_onset date_admission
+      1   1               Damion Hamm confirmed   m  35 2023-01-01           <NA>
+      2   2         Ignacio Hernandez confirmed   m  43 2023-01-01           <NA>
+      3   3            Bryce Donnelly confirmed   m   1 2023-01-01           <NA>
+      4   5             David Arrieta confirmed   m  78 2023-01-01           <NA>
+      5   6 Kristina Vazquez Pallares confirmed   f  22 2023-01-01           <NA>
+      6   8          Nusaiba el-Farah suspected   f  28 2023-01-01           <NA>
+      7  11    Dominic Kills In Sight  probable   m  46 2023-01-01     2023-01-13
+      8  12              Violet Watts confirmed   f  67 2023-01-01           <NA>
+      9  13       Khristopher Cunniff confirmed   m  86 2023-01-01     2023-01-01
+      10 18               Paige Reich  probable   f  60 2023-01-02           <NA>
+      11 20           Jackson Carlson confirmed   m  49 2023-01-02           <NA>
+      12 22           Cassandra Smith suspected   f   7 2023-01-02     2023-01-02
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>     25.6
+      2  recovered         <NA>         2023-01-01        2023-01-07     25.6
+      3  recovered         <NA>         2022-12-31        2023-01-03     25.6
+      4  recovered         <NA>         2022-12-31        2023-01-04     25.6
+      5  recovered         <NA>         2023-01-02        2023-01-04     25.6
+      6  recovered         <NA>         2023-01-06        2023-01-07       NA
+      7  recovered         <NA>         2023-01-07        2023-01-08       NA
+      8  recovered         <NA>         2023-01-03        2023-01-06     25.6
+      9  recovered         <NA>         2023-01-02        2023-01-05     25.6
+      10 recovered         <NA>         2023-01-01        2023-01-05       NA
+      11 recovered         <NA>         2023-01-04        2023-01-07     25.6
+      12      died   2023-01-16         2023-01-03        2023-01-05       NA
 
diff --git a/tests/testthat/_snaps/sim_outbreak.md b/tests/testthat/_snaps/sim_outbreak.md
index 3e9f72bc..73a8984f 100644
--- a/tests/testthat/_snaps/sim_outbreak.md
+++ b/tests/testthat/_snaps/sim_outbreak.md
@@ -5,56 +5,138 @@
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death)
     Output
       $linelist
-         id         case_name case_type sex age date_onset date_admission date_death
-      1   1  Isaiah Patterson  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael John suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3    Lorenzo Gaynor confirmed   m   1 2023-01-01           <NA>       <NA>
-      4   5      Cass Milburn confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6         Hope Cobb  probable   f  22 2023-01-01           <NA>       <NA>
-      6   8     Wyona Lenahan  probable   f  28 2023-01-01           <NA>       <NA>
-      7  11    Bishr al-Jamil confirmed   m  46 2023-01-01     2023-01-13       <NA>
-      8  12  Viviana Martinez  probable   f  67 2023-01-01           <NA>       <NA>
-      9  13 Mudrik al-Youssef  probable   m  86 2023-01-01     2023-01-01       <NA>
-      10 18      Kylie Rieger confirmed   f  60 2023-01-02           <NA>       <NA>
-      11 20   Vincent Edwards  probable   m  49 2023-01-02           <NA>       <NA>
-      12 22      Michiyo Hong suspected   f   7 2023-01-02     2023-01-02       <NA>
+         id                 case_name case_type sex age date_onset date_admission
+      1   1               Damion Hamm confirmed   m  35 2023-01-01           <NA>
+      2   2         Ignacio Hernandez confirmed   m  43 2023-01-01           <NA>
+      3   3            Bryce Donnelly confirmed   m   1 2023-01-01           <NA>
+      4   5             David Arrieta confirmed   m  78 2023-01-01           <NA>
+      5   6 Kristina Vazquez Pallares confirmed   f  22 2023-01-01           <NA>
+      6   8          Nusaiba el-Farah suspected   f  28 2023-01-01           <NA>
+      7  11    Dominic Kills In Sight  probable   m  46 2023-01-01     2023-01-13
+      8  12              Violet Watts confirmed   f  67 2023-01-01           <NA>
+      9  13       Khristopher Cunniff confirmed   m  86 2023-01-01     2023-01-01
+      10 18               Paige Reich  probable   f  60 2023-01-02           <NA>
+      11 20           Jackson Carlson confirmed   m  49 2023-01-02           <NA>
+      12 22           Cassandra Smith suspected   f   7 2023-01-02     2023-01-02
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>     25.6
+      2  recovered         <NA>         2022-12-30        2023-01-05     25.6
+      3  recovered         <NA>         2022-12-30        2023-01-02     25.6
+      4  recovered         <NA>         2022-12-29        2023-01-02     25.6
+      5  recovered         <NA>         2023-01-01        2023-01-03     25.6
+      6  recovered         <NA>         2023-01-03        2023-01-04       NA
+      7  recovered         <NA>         2023-01-04        2023-01-05       NA
+      8  recovered         <NA>         2023-01-01        2023-01-04     25.6
+      9  recovered         <NA>         2022-12-31        2023-01-03     25.6
+      10 recovered         <NA>         2022-12-30        2023-01-03       NA
+      11 recovered         <NA>         2023-01-01        2023-01-04     25.6
+      12      died   2023-01-16         2023-01-01        2023-01-03       NA
+      
+      $contacts
+                              from                        to age sex
+      1                Damion Hamm         Ignacio Hernandez  43   m
+      2                Damion Hamm            Bryce Donnelly   1   m
+      3          Ignacio Hernandez             Ashlan Krause  29   f
+      4          Ignacio Hernandez             David Arrieta  78   m
+      5             Bryce Donnelly Kristina Vazquez Pallares  22   f
+      6             Bryce Donnelly         Morgan Vermillion  70   m
+      7             Bryce Donnelly          Nusaiba el-Farah  28   f
+      8              David Arrieta               Ryanna Hart  37   f
+      9  Kristina Vazquez Pallares               Shan Klutke  61   f
+      10          Nusaiba el-Farah    Dominic Kills In Sight  46   m
+      11          Nusaiba el-Farah              Violet Watts  67   f
+      12          Nusaiba el-Farah       Khristopher Cunniff  86   m
+      13    Dominic Kills In Sight              Tyler Kelley  71   m
+      14    Dominic Kills In Sight             Janayva Allen  51   f
+      15    Dominic Kills In Sight          Sheldon Martinez  44   m
+      16              Violet Watts             Lien Saldanha  49   f
+      17       Khristopher Cunniff               Paige Reich  60   f
+      18       Khristopher Cunniff           Brianna Pollard  56   f
+      19       Khristopher Cunniff           Jackson Carlson  49   m
+      20       Khristopher Cunniff      Raynaldo Santistevan  50   m
+      21               Paige Reich           Cassandra Smith   7   f
+         date_first_contact date_last_contact was_case           status
+      1          2022-12-30        2023-01-05        Y             case
+      2          2022-12-30        2023-01-02        Y             case
+      3          2022-12-27        2023-01-03        N   under_followup
+      4          2022-12-29        2023-01-02        Y             case
+      5          2023-01-01        2023-01-03        Y             case
+      6          2022-12-30        2023-01-02        N   under_followup
+      7          2023-01-03        2023-01-04        Y             case
+      8          2023-01-06        2023-01-06        N lost_to_followup
+      9          2023-01-01        2023-01-05        N   under_followup
+      10         2023-01-04        2023-01-05        Y             case
+      11         2023-01-01        2023-01-04        Y             case
+      12         2022-12-31        2023-01-03        Y             case
+      13         2022-12-28        2023-01-05        N   under_followup
+      14         2023-01-01        2023-01-04        N   under_followup
+      15         2023-01-02        2023-01-05        N lost_to_followup
+      16         2023-01-02        2023-01-03        N   under_followup
+      17         2022-12-30        2023-01-03        Y             case
+      18         2023-01-06        2023-01-09        N lost_to_followup
+      19         2023-01-01        2023-01-04        Y             case
+      20         2023-01-01        2023-01-03        N          unknown
+      21         2023-01-01        2023-01-03        Y             case
+      
+
+# sim_outbreak works as expected with add_names = FALSE
+
+    Code
+      sim_outbreak(contact_distribution = contact_distribution, infect_period = infect_period,
+        prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
+        add_names = FALSE)
+    Output
+      $linelist
+         id case_type sex age date_onset date_admission   outcome date_outcome
+      1   1 confirmed   m  35 2023-01-01           <NA> recovered         <NA>
+      2   2 confirmed   m  43 2023-01-01           <NA> recovered         <NA>
+      3   3 confirmed   m   1 2023-01-01           <NA> recovered         <NA>
+      4   5 confirmed   m  78 2023-01-01           <NA> recovered         <NA>
+      5   6 suspected   f  22 2023-01-01           <NA> recovered         <NA>
+      6   8  probable   f  28 2023-01-01           <NA> recovered         <NA>
+      7  11 confirmed   m  46 2023-01-01     2023-01-13 recovered         <NA>
+      8  12 confirmed   f  67 2023-01-01           <NA> recovered         <NA>
+      9  13  probable   m  86 2023-01-01     2023-01-01 recovered         <NA>
+      10 18  probable   f  60 2023-01-02           <NA> recovered         <NA>
+      11 20 confirmed   m  49 2023-01-02           <NA> recovered         <NA>
+      12 22 confirmed   f   7 2023-01-02     2023-01-02      died   2023-01-16
          date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05       NA
-      3          2022-12-30        2023-01-02     25.6
-      4          2022-12-29        2023-01-02     25.6
+      1                <NA>              <NA>     25.7
+      2          2022-12-30        2023-01-05     25.7
+      3          2022-12-30        2023-01-02     25.7
+      4          2022-12-29        2023-01-02     25.7
       5          2023-01-01        2023-01-03       NA
       6          2023-01-03        2023-01-04       NA
-      7          2023-01-04        2023-01-05     25.6
-      8          2023-01-01        2023-01-04       NA
+      7          2023-01-04        2023-01-05     25.7
+      8          2023-01-01        2023-01-04     25.7
       9          2022-12-31        2023-01-03       NA
-      10         2022-12-30        2023-01-03     25.6
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03       NA
+      10         2022-12-30        2023-01-03       NA
+      11         2023-01-01        2023-01-04     25.7
+      12         2023-01-01        2023-01-03     25.7
       
       $contacts
-                      from                to age sex date_first_contact
-      1   Isaiah Patterson      Michael John  43   m         2022-12-30
-      2   Isaiah Patterson    Lorenzo Gaynor   1   m         2022-12-30
-      3       Michael John      Alyssa Davis  29   f         2022-12-27
-      4       Michael John      Cass Milburn  78   m         2022-12-29
-      5     Lorenzo Gaynor         Hope Cobb  22   f         2023-01-01
-      6     Lorenzo Gaynor    Donald Simmons  70   m         2022-12-30
-      7     Lorenzo Gaynor     Wyona Lenahan  28   f         2023-01-03
-      8       Cass Milburn      Jasra al-Dib  37   f         2023-01-06
-      9          Hope Cobb    Courtney Senff  61   f         2023-01-01
-      10     Wyona Lenahan    Bishr al-Jamil  46   m         2023-01-04
-      11     Wyona Lenahan  Viviana Martinez  67   f         2023-01-01
-      12     Wyona Lenahan Mudrik al-Youssef  86   m         2022-12-31
-      13    Bishr al-Jamil  Jareer al-Hallal  71   m         2022-12-28
-      14    Bishr al-Jamil   Jennifer Nguyen  51   f         2023-01-01
-      15    Bishr al-Jamil     Hector Abeyta  44   m         2023-01-02
-      16  Viviana Martinez     Chandra Musil  49   f         2023-01-02
-      17 Mudrik al-Youssef      Kylie Rieger  60   f         2022-12-30
-      18 Mudrik al-Youssef  Alexandra Arshad  56   f         2023-01-06
-      19 Mudrik al-Youssef   Vincent Edwards  49   m         2023-01-01
-      20 Mudrik al-Youssef    Avery Johnston  50   m         2023-01-01
-      21      Kylie Rieger      Michiyo Hong   7   f         2023-01-01
+                           from                        to age sex date_first_contact
+      1            John Sheldon    Abdul Maalik al-Sarwar  43   m         2022-12-30
+      2            John Sheldon                Jeffrey Le   1   m         2022-12-30
+      3  Abdul Maalik al-Sarwar             Taylor Graves  29   f         2022-12-27
+      4  Abdul Maalik al-Sarwar             Grayson Black  78   m         2022-12-29
+      5              Jeffrey Le             Carolyn Moore  22   f         2023-01-01
+      6              Jeffrey Le              Tyler Kelley  70   m         2022-12-30
+      7              Jeffrey Le         Cheyenne Sayavong  28   f         2023-01-03
+      8           Grayson Black         Mercedes Lovelace  37   f         2023-01-06
+      9           Carolyn Moore Chantelle Vazquez-Luevano  61   f         2023-01-01
+      10      Cheyenne Sayavong           Jackson Carlson  46   m         2023-01-04
+      11      Cheyenne Sayavong                 Kendra To  67   f         2023-01-01
+      12      Cheyenne Sayavong           Rushdi al-Bahri  86   m         2022-12-31
+      13        Jackson Carlson          Bassaam el-Laham  71   m         2022-12-28
+      14        Jackson Carlson               Megan Hayes  51   f         2023-01-01
+      15        Jackson Carlson          John Khanthavong  44   m         2023-01-02
+      16              Kendra To         Amanda Larochelle  49   f         2023-01-02
+      17        Rushdi al-Bahri         Dominique Raymond  60   f         2022-12-30
+      18        Rushdi al-Bahri            Natalie Newton  56   f         2023-01-06
+      19        Rushdi al-Bahri          Qaaid al-Chahine  49   m         2023-01-01
+      20        Rushdi al-Bahri     Abdul Kader el-Jabour  50   m         2023-01-01
+      21      Dominique Raymond             Susana Varela   7   f         2023-01-01
          date_last_contact was_case           status
       1         2023-01-05        Y             case
       2         2023-01-02        Y             case
@@ -68,10 +150,10 @@
       10        2023-01-05        Y             case
       11        2023-01-04        Y             case
       12        2023-01-03        Y             case
-      13        2023-01-05        N lost_to_followup
-      14        2023-01-04        N          unknown
-      15        2023-01-05        N          unknown
-      16        2023-01-03        N   under_followup
+      13        2023-01-05        N   under_followup
+      14        2023-01-04        N   under_followup
+      15        2023-01-05        N   under_followup
+      16        2023-01-03        N lost_to_followup
       17        2023-01-03        Y             case
       18        2023-01-09        N   under_followup
       19        2023-01-04        Y             case
@@ -79,64 +161,65 @@
       21        2023-01-03        Y             case
       
 
-# sim_outbreak works as expected with add_names = FALSE
+# sim_outbreak works as expected with age-strat risks
 
     Code
       sim_outbreak(contact_distribution = contact_distribution, infect_period = infect_period,
         prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
-        add_names = FALSE)
+        hosp_risk = age_dep_hosp_risk, hosp_death_risk = age_dep_hosp_death_risk,
+        non_hosp_death_risk = age_dep_non_hosp_death_risk)
     Output
       $linelist
-         id case_type sex age date_onset date_admission date_death date_first_contact
-      1   1  probable   m  35 2023-01-01           <NA>       <NA>               <NA>
-      2   2 confirmed   m  43 2023-01-01           <NA>       <NA>         2022-12-30
-      3   3 confirmed   m   1 2023-01-01           <NA>       <NA>         2022-12-30
-      4   5 confirmed   m  78 2023-01-01           <NA>       <NA>         2022-12-29
-      5   6 confirmed   f  22 2023-01-01           <NA>       <NA>         2023-01-01
-      6   8 suspected   f  28 2023-01-01           <NA>       <NA>         2023-01-03
-      7  11 confirmed   m  46 2023-01-01     2023-01-13       <NA>         2023-01-04
-      8  12 suspected   f  67 2023-01-01           <NA>       <NA>         2023-01-01
-      9  13 confirmed   m  86 2023-01-01     2023-01-01       <NA>         2022-12-31
-      10 18 confirmed   f  60 2023-01-02           <NA>       <NA>         2022-12-30
-      11 20 confirmed   m  49 2023-01-02           <NA>       <NA>         2023-01-01
-      12 22 confirmed   f   7 2023-01-02     2023-01-02       <NA>         2023-01-01
-         date_last_contact ct_value
-      1               <NA>       NA
-      2         2023-01-05       26
-      3         2023-01-02       26
-      4         2023-01-02       26
-      5         2023-01-03       26
-      6         2023-01-04       NA
-      7         2023-01-05       26
-      8         2023-01-04       NA
-      9         2023-01-03       26
-      10        2023-01-03       26
-      11        2023-01-04       26
-      12        2023-01-03       26
+         id             case_name case_type sex age date_onset date_admission
+      1   1    David Garcia Mayen  probable   m  35 2023-01-01           <NA>
+      2   2   Rory Kills In Sight confirmed   m  43 2023-01-01           <NA>
+      3   3      Sheldon Martinez confirmed   m   1 2023-01-01     2023-01-11
+      4   5         Bryce Cunniff  probable   m  78 2023-01-01           <NA>
+      5   6        Lien Whitworth confirmed   f  22 2023-01-01           <NA>
+      6   8         Tiffany Weiss suspected   f  28 2023-01-01           <NA>
+      7  11    Cleatus Kacprowicz  probable   m  46 2023-01-01           <NA>
+      8  12          Taylor Moore confirmed   f  67 2023-01-01           <NA>
+      9  13         Tyler Carlson confirmed   m  86 2023-01-01     2023-01-01
+      10 18      Grayson Lovelace confirmed   f  60 2023-01-02           <NA>
+      11 20 Abdul Maalik al-Ishak suspected   m  49 2023-01-02     2023-01-09
+      12 22         Kendra Newton confirmed   f   7 2023-01-02           <NA>
+           outcome date_outcome date_first_contact date_last_contact ct_value
+      1  recovered         <NA>               <NA>              <NA>       NA
+      2  recovered         <NA>         2022-12-30        2023-01-05       25
+      3  recovered         <NA>         2022-12-30        2023-01-02       25
+      4  recovered         <NA>         2022-12-29        2023-01-02       NA
+      5  recovered         <NA>         2023-01-01        2023-01-03       25
+      6  recovered         <NA>         2023-01-03        2023-01-04       NA
+      7  recovered         <NA>         2023-01-04        2023-01-05       NA
+      8  recovered         <NA>         2023-01-01        2023-01-04       25
+      9  recovered         <NA>         2022-12-31        2023-01-03       25
+      10 recovered         <NA>         2022-12-30        2023-01-03       25
+      11 recovered         <NA>         2023-01-01        2023-01-04       NA
+      12 recovered         <NA>         2023-01-01        2023-01-03       25
       
       $contacts
-                        from                      to age sex date_first_contact
-      1  Christopher Chaffin            Kevin Cooper  43   m         2022-12-30
-      2  Christopher Chaffin       Austin Loughridge   1   m         2022-12-30
-      3         Kevin Cooper           Michiyo Smith  29   f         2022-12-27
-      4         Kevin Cooper         Khaleel el-Huda  78   m         2022-12-29
-      5    Austin Loughridge       Samantha Gonzalez  22   f         2023-01-01
-      6    Austin Loughridge       Benjamin Mcdonald  70   m         2022-12-30
-      7    Austin Loughridge           Tea Slaughter  28   f         2023-01-03
-      8      Khaleel el-Huda            Audreon Hill  37   f         2023-01-06
-      9    Samantha Gonzalez        Dieu Linh Batara  61   f         2023-01-01
-      10       Tea Slaughter       Travis Montgomery  46   m         2023-01-04
-      11       Tea Slaughter         Hishma el-Hamid  67   f         2023-01-01
-      12       Tea Slaughter           Jose Gonzales  86   m         2022-12-31
-      13   Travis Montgomery            Efren Abeyta  71   m         2022-12-28
-      14   Travis Montgomery        Giovana Quintero  51   f         2023-01-01
-      15   Travis Montgomery       Zayyaan el-Radwan  44   m         2023-01-02
-      16     Hishma el-Hamid       Kiona Fitzsimmons  49   f         2023-01-02
-      17       Jose Gonzales         Danita Anderson  60   f         2022-12-30
-      18       Jose Gonzales          Arwa el-Moussa  56   f         2023-01-06
-      19       Jose Gonzales Enrique Salas Dominguez  49   m         2023-01-01
-      20       Jose Gonzales            Charles Graf  50   m         2023-01-01
-      21     Danita Anderson         Cheyenne Miller   7   f         2023-01-01
+                        from                    to age sex date_first_contact
+      1   David Garcia Mayen   Rory Kills In Sight  43   m         2022-12-30
+      2   David Garcia Mayen      Sheldon Martinez   1   m         2022-12-30
+      3  Rory Kills In Sight       Violet Harrison  29   f         2022-12-27
+      4  Rory Kills In Sight         Bryce Cunniff  78   m         2022-12-29
+      5     Sheldon Martinez        Lien Whitworth  22   f         2023-01-01
+      6     Sheldon Martinez    Khristopher Kelley  70   m         2022-12-30
+      7     Sheldon Martinez         Tiffany Weiss  28   f         2023-01-03
+      8        Bryce Cunniff  Caroline Hergenreter  37   f         2023-01-06
+      9       Lien Whitworth    Cassandra Sayavong  61   f         2023-01-01
+      10       Tiffany Weiss    Cleatus Kacprowicz  46   m         2023-01-04
+      11       Tiffany Weiss          Taylor Moore  67   f         2023-01-01
+      12       Tiffany Weiss         Tyler Carlson  86   m         2022-12-31
+      13  Cleatus Kacprowicz       Raynaldo Abeyta  71   m         2022-12-28
+      14  Cleatus Kacprowicz       Carolyn Raymond  51   f         2023-01-01
+      15  Cleatus Kacprowicz        Jelani Sheldon  44   m         2023-01-02
+      16        Taylor Moore           Harleigh To  49   f         2023-01-02
+      17       Tyler Carlson      Grayson Lovelace  60   f         2022-12-30
+      18       Tyler Carlson Angel Vazquez-Luevano  56   f         2023-01-06
+      19       Tyler Carlson Abdul Maalik al-Ishak  49   m         2023-01-01
+      20       Tyler Carlson             Joewid Le  50   m         2023-01-01
+      21    Grayson Lovelace         Kendra Newton   7   f         2023-01-01
          date_last_contact was_case           status
       1         2023-01-05        Y             case
       2         2023-01-02        Y             case
@@ -145,105 +228,22 @@
       5         2023-01-03        Y             case
       6         2023-01-02        N   under_followup
       7         2023-01-04        Y             case
-      8         2023-01-06        N   under_followup
-      9         2023-01-05        N   under_followup
+      8         2023-01-06        N lost_to_followup
+      9         2023-01-05        N          unknown
       10        2023-01-05        Y             case
       11        2023-01-04        Y             case
       12        2023-01-03        Y             case
-      13        2023-01-05        N          unknown
-      14        2023-01-04        N lost_to_followup
-      15        2023-01-05        N lost_to_followup
-      16        2023-01-03        N          unknown
+      13        2023-01-05        N   under_followup
+      14        2023-01-04        N   under_followup
+      15        2023-01-05        N   under_followup
+      16        2023-01-03        N   under_followup
       17        2023-01-03        Y             case
-      18        2023-01-09        N          unknown
+      18        2023-01-09        N lost_to_followup
       19        2023-01-04        Y             case
       20        2023-01-03        N   under_followup
       21        2023-01-03        Y             case
       
 
-# sim_outbreak works as expected with age-strat risks
-
-    Code
-      sim_outbreak(contact_distribution = contact_distribution, infect_period = infect_period,
-        prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
-        hosp_risk = age_dep_hosp_risk, hosp_death_risk = age_dep_hosp_death_risk,
-        non_hosp_death_risk = age_dep_non_hosp_death_risk)
-    Output
-      $linelist
-         id          case_name case_type sex age date_onset date_admission date_death
-      1   1      Donald Childs  probable   m  35 2023-01-01           <NA>       <NA>
-      2   2      Michael Duran suspected   m  43 2023-01-01           <NA>       <NA>
-      3   3          Cass Root  probable   m   1 2023-01-01     2023-01-11 2023-01-19
-      4   5   Mudrik al-Hallal confirmed   m  78 2023-01-01           <NA>       <NA>
-      5   6       Erika Sierra confirmed   f  22 2023-01-01           <NA>       <NA>
-      6   8      Jennifer Hong confirmed   f  28 2023-01-01           <NA>       <NA>
-      7  11    Raashid el-Huda suspected   m  46 2023-01-01           <NA>       <NA>
-      8  12      Kayla Johnson suspected   f  67 2023-01-01           <NA>       <NA>
-      9  13 Dominic Montgomery  probable   m  86 2023-01-01     2023-01-01 2023-01-10
-      10 18    Giovana Segarra suspected   f  60 2023-01-02           <NA>       <NA>
-      11 20    Vincent Edwards suspected   m  49 2023-01-02     2023-01-09 2023-01-21
-      12 22        Kiona Dalke  probable   f   7 2023-01-02           <NA>       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05       NA
-      3          2022-12-30        2023-01-02       NA
-      4          2022-12-29        2023-01-02     23.1
-      5          2023-01-01        2023-01-03     23.1
-      6          2023-01-03        2023-01-04     23.1
-      7          2023-01-04        2023-01-05       NA
-      8          2023-01-01        2023-01-04       NA
-      9          2022-12-31        2023-01-03       NA
-      10         2022-12-30        2023-01-03       NA
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03       NA
-      
-      $contacts
-                       from                      to age sex date_first_contact
-      1       Donald Childs           Michael Duran  43   m         2022-12-30
-      2       Donald Childs               Cass Root   1   m         2022-12-30
-      3       Michael Duran        Kaitlynne Rieger  29   f         2022-12-27
-      4       Michael Duran        Mudrik al-Hallal  78   m         2022-12-29
-      5           Cass Root            Erika Sierra  22   f         2023-01-01
-      6           Cass Root         Jareer al-Safar  70   m         2022-12-30
-      7           Cass Root           Jennifer Hong  28   f         2023-01-03
-      8    Mudrik al-Hallal        Kaitlin Gonzalez  37   f         2023-01-06
-      9        Erika Sierra       Marissa Slaughter  61   f         2023-01-01
-      10      Jennifer Hong         Raashid el-Huda  46   m         2023-01-04
-      11      Jennifer Hong           Kayla Johnson  67   f         2023-01-01
-      12      Jennifer Hong      Dominic Montgomery  86   m         2022-12-31
-      13    Raashid el-Huda          Lorenzo Gaynor  71   m         2022-12-28
-      14    Raashid el-Huda            Michiyo Tran  51   f         2023-01-01
-      15    Raashid el-Huda          Avery Johnston  44   m         2023-01-02
-      16      Kayla Johnson Marzooqa el-Abdelrahman  49   f         2023-01-02
-      17 Dominic Montgomery         Giovana Segarra  60   f         2022-12-30
-      18 Dominic Montgomery       Kaylie Shangreaux  56   f         2023-01-06
-      19 Dominic Montgomery         Vincent Edwards  49   m         2023-01-01
-      20 Dominic Montgomery             Ethan Black  50   m         2023-01-01
-      21    Giovana Segarra             Kiona Dalke   7   f         2023-01-01
-         date_last_contact was_case         status
-      1         2023-01-05        Y           case
-      2         2023-01-02        Y           case
-      3         2023-01-03        N under_followup
-      4         2023-01-02        Y           case
-      5         2023-01-03        Y           case
-      6         2023-01-02        N under_followup
-      7         2023-01-04        Y           case
-      8         2023-01-06        N under_followup
-      9         2023-01-05        N under_followup
-      10        2023-01-05        Y           case
-      11        2023-01-04        Y           case
-      12        2023-01-03        Y           case
-      13        2023-01-05        N under_followup
-      14        2023-01-04        N under_followup
-      15        2023-01-05        N under_followup
-      16        2023-01-03        N under_followup
-      17        2023-01-03        Y           case
-      18        2023-01-09        N        unknown
-      19        2023-01-04        Y           case
-      20        2023-01-03        N under_followup
-      21        2023-01-03        Y           case
-      
-
 # sim_outbreak works as expected with age structure
 
     Code
@@ -252,56 +252,56 @@
         population_age = age_struct)
     Output
       $linelist
-         id          case_name case_type sex age date_onset date_admission date_death
-      1   1 Ghaamid el-Ishmael suspected   m  44 2023-01-01           <NA>       <NA>
-      2   2   Faatih el-Kaiser confirmed   m  13 2023-01-01           <NA>       <NA>
-      3   3   Brandon Galligan confirmed   m  22 2023-01-01     2023-01-09       <NA>
-      4   5      Aiman el-Riaz suspected   m  85 2023-01-01           <NA>       <NA>
-      5   6     Katelyn Catlin confirmed   f  41 2023-01-01           <NA>       <NA>
-      6   8       Lynsey Duron confirmed   f  89 2023-01-01     2023-01-02       <NA>
-      7  11      Travis Foster confirmed   m  69 2023-01-01           <NA>       <NA>
-      8  12       Jacy Cousins confirmed   f  23 2023-01-01           <NA>       <NA>
-      9  13        Khoa Murray confirmed   m   9 2023-01-01           <NA>       <NA>
-      10 18     Maria Eberhart  probable   f  62 2023-01-02           <NA>       <NA>
-      11 20        John Flores suspected   m  52 2023-01-02     2023-01-15       <NA>
-      12 22        Erin Payson confirmed   f  76 2023-01-02           <NA>       <NA>
-         date_first_contact date_last_contact ct_value
-      1                <NA>              <NA>       NA
-      2          2022-12-30        2023-01-05     25.1
-      3          2022-12-30        2023-01-02     25.1
-      4          2022-12-29        2023-01-02       NA
-      5          2023-01-01        2023-01-03     25.1
-      6          2023-01-03        2023-01-04     25.1
-      7          2023-01-04        2023-01-05     25.1
-      8          2023-01-01        2023-01-04     25.1
-      9          2022-12-31        2023-01-03     25.1
-      10         2022-12-30        2023-01-03       NA
-      11         2023-01-01        2023-01-04       NA
-      12         2023-01-01        2023-01-03     25.1
+         id         case_name case_type sex age date_onset date_admission   outcome
+      1   1        Mark Beard confirmed   m  44 2023-01-01           <NA> recovered
+      2   2   Brian Mccracken confirmed   m  13 2023-01-01           <NA> recovered
+      3   3     Jesus Garduno confirmed   m  22 2023-01-01     2023-01-09      died
+      4   5   Taalib al-Naqvi confirmed   m  85 2023-01-01           <NA> recovered
+      5   6       Kelly Geist confirmed   f  41 2023-01-01           <NA> recovered
+      6   8    Madison Krause suspected   f  89 2023-01-01     2023-01-02 recovered
+      7  11   Jonathon Lujano  probable   m  69 2023-01-01           <NA> recovered
+      8  12      Ashlan Allen confirmed   f  23 2023-01-01           <NA> recovered
+      9  13 Dhaahir el-Hariri confirmed   m   9 2023-01-01           <NA> recovered
+      10 18       Korren Hart  probable   f  62 2023-01-02           <NA> recovered
+      11 20        Isaac Huff confirmed   m  52 2023-01-02     2023-01-15 recovered
+      12 22      Ryanna Watts suspected   f  76 2023-01-02           <NA> recovered
+         date_outcome date_first_contact date_last_contact ct_value
+      1          <NA>               <NA>              <NA>     25.6
+      2          <NA>         2022-12-30        2023-01-05     25.6
+      3    2023-01-09         2022-12-30        2023-01-02     25.6
+      4          <NA>         2022-12-29        2023-01-02     25.6
+      5          <NA>         2023-01-01        2023-01-03     25.6
+      6          <NA>         2023-01-03        2023-01-04       NA
+      7          <NA>         2023-01-04        2023-01-05       NA
+      8          <NA>         2023-01-01        2023-01-04     25.6
+      9          <NA>         2022-12-31        2023-01-03     25.6
+      10         <NA>         2022-12-30        2023-01-03       NA
+      11         <NA>         2023-01-01        2023-01-04     25.6
+      12         <NA>         2023-01-01        2023-01-03       NA
       
       $contacts
-                       from                     to age sex date_first_contact
-      1  Ghaamid el-Ishmael       Faatih el-Kaiser  13   m         2022-12-30
-      2  Ghaamid el-Ishmael       Brandon Galligan  22   m         2022-12-30
-      3    Faatih el-Kaiser Carisa Flores-Gonzalez   5   f         2022-12-27
-      4    Faatih el-Kaiser          Aiman el-Riaz  85   m         2022-12-29
-      5    Brandon Galligan         Katelyn Catlin  41   f         2023-01-01
-      6    Brandon Galligan        Wajdi al-Demian   2   m         2022-12-30
-      7    Brandon Galligan           Lynsey Duron  89   f         2023-01-03
-      8       Aiman el-Riaz        Amaani al-Gaber  86   f         2023-01-06
-      9      Katelyn Catlin         Lilibeth Black  82   f         2023-01-01
-      10       Lynsey Duron          Travis Foster  69   m         2023-01-04
-      11       Lynsey Duron           Jacy Cousins  23   f         2023-01-01
-      12       Lynsey Duron            Khoa Murray   9   m         2022-12-31
-      13      Travis Foster          Raaid el-Diab  79   m         2022-12-28
-      14      Travis Foster       Marquaja Johnson  29   f         2023-01-01
-      15      Travis Foster      Mubarak el-Vaziri   4   m         2023-01-02
-      16       Jacy Cousins            Kayla Tudor  13   f         2023-01-02
-      17        Khoa Murray         Maria Eberhart  62   f         2022-12-30
-      18        Khoa Murray            Katja Muetz  24   f         2023-01-06
-      19        Khoa Murray            John Flores  52   m         2023-01-01
-      20        Khoa Murray             Bryce Sena  74   m         2023-01-01
-      21     Maria Eberhart            Erin Payson  76   f         2023-01-01
+                      from                to age sex date_first_contact
+      1         Mark Beard   Brian Mccracken  13   m         2022-12-30
+      2         Mark Beard     Jesus Garduno  22   m         2022-12-30
+      3    Brian Mccracken    Alivia Estrada   5   f         2022-12-27
+      4    Brian Mccracken   Taalib al-Naqvi  85   m         2022-12-29
+      5      Jesus Garduno       Kelly Geist  41   f         2023-01-01
+      6      Jesus Garduno      Umar al-Basa   2   m         2022-12-30
+      7      Jesus Garduno    Madison Krause  89   f         2023-01-03
+      8    Taalib al-Naqvi  Mawhiba al-Bilal  86   f         2023-01-06
+      9        Kelly Geist    Destiny Bailey  82   f         2023-01-01
+      10    Madison Krause   Jonathon Lujano  69   m         2023-01-04
+      11    Madison Krause      Ashlan Allen  23   f         2023-01-01
+      12    Madison Krause Dhaahir el-Hariri   9   m         2022-12-31
+      13   Jonathon Lujano      Andres Garza  79   m         2022-12-28
+      14   Jonathon Lujano     Nicole Wright  29   f         2023-01-01
+      15   Jonathon Lujano         Raj Ament   4   m         2023-01-02
+      16      Ashlan Allen    Turfa el-Farah  13   f         2023-01-02
+      17 Dhaahir el-Hariri       Korren Hart  62   f         2022-12-30
+      18 Dhaahir el-Hariri       Shan Klutke  24   f         2023-01-06
+      19 Dhaahir el-Hariri        Isaac Huff  52   m         2023-01-01
+      20 Dhaahir el-Hariri    Darienne Knost  74   m         2023-01-01
+      21       Korren Hart      Ryanna Watts  76   f         2023-01-01
          date_last_contact was_case           status
       1         2023-01-05        Y             case
       2         2023-01-02        Y             case
@@ -310,19 +310,19 @@
       5         2023-01-03        Y             case
       6         2023-01-02        N   under_followup
       7         2023-01-04        Y             case
-      8         2023-01-06        N   under_followup
-      9         2023-01-05        N          unknown
+      8         2023-01-06        N lost_to_followup
+      9         2023-01-05        N   under_followup
       10        2023-01-05        Y             case
       11        2023-01-04        Y             case
       12        2023-01-03        Y             case
       13        2023-01-05        N   under_followup
-      14        2023-01-04        N lost_to_followup
+      14        2023-01-04        N   under_followup
       15        2023-01-05        N lost_to_followup
       16        2023-01-03        N   under_followup
       17        2023-01-03        Y             case
       18        2023-01-09        N lost_to_followup
       19        2023-01-04        Y             case
-      20        2023-01-03        N   under_followup
+      20        2023-01-03        N          unknown
       21        2023-01-03        Y             case
       
 
diff --git a/tests/testthat/test-add_cols.R b/tests/testthat/test-add_cols.R
index ac82c659..c5d76efb 100644
--- a/tests/testthat/test-add_cols.R
+++ b/tests/testthat/test-add_cols.R
@@ -13,6 +13,8 @@ suppressMessages({
     epi_dist = "onset to death",
     single_epidist = TRUE
   ))
+
+  onset_to_recovery <- function(x) rep(NA, times = x)
 })
 
 test_that(".add_date_contact works as expected with contact_type = 'last'", {
@@ -173,42 +175,46 @@ test_that(".add_hospitalisation works as expected with age-strat risks", {
   )
 })
 
-test_that(".add_deaths works as expected", {
-  ll <- readRDS(file.path("testdata", "pre_death.rds"))
-  linelist <- .add_deaths(
+test_that(".add_outcome works as expected", {
+  ll <- readRDS(file.path("testdata", "pre_outcome.rds"))
+  linelist <- .add_outcome(
     .data = ll,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     hosp_death_risk = 0.5,
     non_hosp_death_risk = 0.5
   )
   expect_s3_class(linelist, class = "data.frame")
-  expect_type(linelist$deaths, type = "double")
-  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 1L))
+  expect_type(linelist$outcome, type = "character")
+  expect_type(linelist$outcome_time, type = "double")
+  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 2L))
   expect_identical(
     colnames(linelist),
-    c(colnames(ll), "deaths")
+    c(colnames(ll), "outcome", "outcome_time")
   )
 })
 
-test_that(".add_deaths works as expected with different parameter", {
-  ll <- readRDS(file.path("testdata", "pre_death.rds"))
-  linelist <- .add_deaths(
+test_that(".add_outcome works as expected with different parameter", {
+  ll <- readRDS(file.path("testdata", "pre_outcome.rds"))
+  linelist <- .add_outcome(
     .data = ll,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     hosp_death_risk = 0.9,
     non_hosp_death_risk = 0.1
   )
   expect_s3_class(linelist, class = "data.frame")
-  expect_type(linelist$deaths, type = "double")
-  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 1L))
+  expect_type(linelist$outcome, type = "character")
+  expect_type(linelist$outcome_time, type = "double")
+  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 2L))
   expect_identical(
     colnames(linelist),
-    c(colnames(ll), "deaths")
+    c(colnames(ll), "outcome", "outcome_time")
   )
 })
 
-test_that(".add_deaths works as expected with age-strat risks", {
-  ll <- readRDS(file.path("testdata", "pre_death.rds"))
+test_that(".add_outcome works as expected with age-strat risks", {
+  ll <- readRDS(file.path("testdata", "pre_outcome.rds"))
   age_dep_hosp_death_risk <- data.frame(
     min_age = c(1, 5, 80),
     max_age = c(4, 79, 90),
@@ -219,18 +225,20 @@ test_that(".add_deaths works as expected with age-strat risks", {
     max_age = c(4, 79, 90),
     risk = c(0.05, 0.025, 0.1)
   )
-  linelist <- .add_deaths(
+  linelist <- .add_outcome(
     .data = ll,
     onset_to_death = onset_to_death,
+    onset_to_recover = onset_to_recovery,
     hosp_death_risk = age_dep_hosp_death_risk,
     non_hosp_death_risk = age_dep_non_hosp_death_risk
   )
   expect_s3_class(linelist, class = "data.frame")
-  expect_type(linelist$deaths, type = "double")
-  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 1L))
+  expect_type(linelist$outcome, type = "character")
+  expect_type(linelist$outcome_time, type = "double")
+  expect_identical(dim(linelist), c(nrow(ll), ncol(ll) + 2L))
   expect_identical(
     colnames(linelist),
-    c(colnames(ll), "deaths")
+    c(colnames(ll), "outcome", "outcome_time")
   )
 })
 
diff --git a/tests/testthat/test-checkers.R b/tests/testthat/test-checkers.R
index d09df031..cab951fb 100644
--- a/tests/testthat/test-checkers.R
+++ b/tests/testthat/test-checkers.R
@@ -165,6 +165,14 @@ suppressMessages({
     epi_dist = "onset to death",
     single_epidist = TRUE
   ))
+
+  onset_to_recovery <- as.function(epiparameter::epidist(
+    disease = "COVID-19",
+    epi_dist = "onset to recovery",
+    prob_distribution = "lnorm",
+    prob_distribution_params = c(meanlog = 3, sdlog = 1)
+  ))
+
 })
 
 test_that(".check_sim_input works as expected", {
@@ -177,6 +185,7 @@ test_that(".check_sim_input works as expected", {
     outbreak_size = c(10, 1e4),
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
     add_ct = FALSE,
     case_type_probs = c(
@@ -206,6 +215,7 @@ test_that(".check_sim_input works as expected", {
     outbreak_size = c(10, 1e4),
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
     add_ct = FALSE,
     case_type_probs = c(
@@ -249,6 +259,7 @@ test_that(".check_sim_input works as expected with NA risks", {
     outbreak_size = c(10, 1e4),
     onset_to_hosp = onset_to_hosp,
     onset_to_death = onset_to_death,
+    onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
     add_ct = FALSE,
     case_type_probs = c(
@@ -361,22 +372,37 @@ test_that(".cross_check_sim_input warns as expected", {
       hosp_death_risk = 0.5,
       non_hosp_death_risk = 0.05
     ),
-    regexp = "(onset_to_hosp is set to NA)*(hosp_risk is being ignored)"
+    regexp = paste0(
+      "(onset_to_hosp is set to NA)*(hosp_risk is being ignored)*",
+      "(hosp_death_risk is being ignored)"
+    )
   )
-  # since testthat v3 these handle a single condition so nesting expect warning
-  # to check both warnings
+
   expect_warning(
-    expect_warning(
-      .cross_check_sim_input(
-        onset_to_hosp = onset_to_hosp,
-        onset_to_death = function(x) rep(NA, times = x),
-        hosp_risk = 0.2,
-        hosp_death_risk = 0.5,
-        non_hosp_death_risk = 0.05
-      ),
-      regexp = "(onset_to_death is)*(NA)*(hosp_death_risk is being ignored)"
+    .cross_check_sim_input(
+      onset_to_hosp = function(x) rep(NA, times = x),
+      onset_to_death = onset_to_death,
+      hosp_risk = 0.2,
+      hosp_death_risk = 0.5,
+      non_hosp_death_risk = 0.05
+    ),
+    regexp = paste0(
+      "(onset_to_hosp is set to NA)*(hosp_risk is being ignored)*",
+      "(hosp_death_risk is being ignored)"
+    )
+  )
+  expect_warning(
+    .cross_check_sim_input(
+      onset_to_hosp = onset_to_hosp,
+      onset_to_death = function(x) rep(NA, times = x),
+      hosp_risk = 0.2,
+      hosp_death_risk = 0.5,
+      non_hosp_death_risk = 0.05
     ),
-    regexp = "(onset_to_death is)*(NA)*(non_hosp_death_risk is being ignored)"
+    regexp = paste0(
+      "(onset_to_death is set to NA)*(hosp_death_risk is being ignored)*",
+      "(non_hosp_death_risk is being ignored)"
+    )
   )
   expect_error(
     .cross_check_sim_input(
@@ -386,7 +412,10 @@ test_that(".cross_check_sim_input warns as expected", {
       hosp_death_risk = 0.5,
       non_hosp_death_risk = 0.05
     ),
-    regexp = "(hosp_risk is set to NA)*(but onset_to_hosp is specified)"
+    regexp = paste0(
+      "(hosp_risk is set to NA)*(but onset_to_hosp is specified)*",
+      "(set hosp_risk to numeric value)"
+    )
   )
   expect_error(
     .cross_check_sim_input(
@@ -396,7 +425,10 @@ test_that(".cross_check_sim_input warns as expected", {
       hosp_death_risk = NA,
       non_hosp_death_risk = 0.05
     ),
-    regexp = "(hosp_death_risk is set to NA but onset_to_death is specified)"
+    regexp = paste0(
+      "(hosp_death_risk is set to NA)*(but onset_to_death is specified)*",
+      "(set hosp_death_risk to numeric value)"
+    )
   )
   expect_error(
     .cross_check_sim_input(
@@ -406,6 +438,9 @@ test_that(".cross_check_sim_input warns as expected", {
       hosp_death_risk = 0.5,
       non_hosp_death_risk = NA
     ),
-    regexp = "(non_hosp_death_risk is set to NA)*(onset_to_death is specified)"
+    regexp = paste0(
+      "(non_hosp_death_risk is set to NA)*(onset_to_death is specified)*",
+      "(set non_hosp_death_risk to numeric value)"
+    )
   )
 })
diff --git a/tests/testthat/test-sim_linelist.R b/tests/testthat/test-sim_linelist.R
index e5199435..7da1396f 100644
--- a/tests/testthat/test-sim_linelist.R
+++ b/tests/testthat/test-sim_linelist.R
@@ -296,35 +296,33 @@ test_that("sim_linelist warns when risks are given by onset-to-event is NA", {
     ),
     regexp = "(onset_to_hosp is set to NA)*(hosp_risk is being ignored)"
   )
-  # since testthat v3 these handle a single condition so nesting expect warning
-  # to check both warnings
   expect_warning(
-    expect_warning(
-      sim_linelist(
-        contact_distribution = contact_distribution,
-        infect_period = infect_period,
-        prob_infect = 0.5,
-        onset_to_hosp = onset_to_hosp,
-        onset_to_death = NA,
-        hosp_death_risk = 0.5
-      ),
-      regexp = "(onset_to_death is)*(NA)*(hosp_death_risk is being ignored)"
+    sim_linelist(
+      contact_distribution = contact_distribution,
+      infect_period = infect_period,
+      prob_infect = 0.5,
+      onset_to_hosp = onset_to_hosp,
+      onset_to_death = NA,
+      hosp_death_risk = 0.5
     ),
-    regexp = "(onset_to_death is)*(NA)*(non_hosp_death_risk is being ignored)"
+    regexp = paste0(
+      "(onset_to_death is set to NA)*(hosp_death_risk is being ignored)*",
+      "(non_hosp_death_risk is being ignored)"
+    )
   )
   expect_warning(
-    expect_warning(
-      sim_linelist(
-        contact_distribution = contact_distribution,
-        infect_period = infect_period,
-        prob_infect = 0.5,
-        onset_to_hosp = onset_to_hosp,
-        onset_to_death = NA,
-        non_hosp_death_risk = 0.02
-      ),
-      regexp = "(onset_to_death is)*(NA)*(hosp_death_risk is being ignored)"
+    sim_linelist(
+      contact_distribution = contact_distribution,
+      infect_period = infect_period,
+      prob_infect = 0.5,
+      onset_to_hosp = onset_to_hosp,
+      onset_to_death = NA,
+      non_hosp_death_risk = 0.02
     ),
-    regexp = "(onset_to_death is)*(NA)*(non_hosp_death_risk is being ignored)"
+    regexp = paste0(
+      "(onset_to_death is set to NA)*(hosp_death_risk is being ignored)*",
+      "(non_hosp_death_risk is being ignored)"
+    )
   )
 })
 
@@ -376,13 +374,15 @@ test_that("sim_linest date_admission column is NA when onset_to_hosp is NA", {
   )
   expect_true(all(is.na(ll$date_admission)))
 
-  ll <- sim_linelist(
-    contact_distribution = contact_distribution,
-    infect_period = infect_period,
-    prob_infect = 0.5,
-    onset_to_hosp = NA,
-    onset_to_death = onset_to_death,
-    hosp_risk = NA
+  ll <- suppressWarnings(
+    sim_linelist(
+      contact_distribution = contact_distribution,
+      infect_period = infect_period,
+      prob_infect = 0.5,
+      onset_to_hosp = NA,
+      onset_to_death = onset_to_death,
+      hosp_risk = NA
+    )
   )
   expect_true(all(is.na(ll$date_admission)))
 })

From e9935fef4151fba36ebd4638b2dba4794b465323 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 10 Apr 2024 12:37:18 +0100
Subject: [PATCH 11/11] linting

---
 vignettes/vis-linelist.Rmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/vignettes/vis-linelist.Rmd b/vignettes/vis-linelist.Rmd
index 637b8b9d..3d8252ae 100644
--- a/vignettes/vis-linelist.Rmd
+++ b/vignettes/vis-linelist.Rmd
@@ -148,14 +148,14 @@ linelist$date_recovery[linelist$outcome == "died"] <- NA
 ```{r, reshape-linelist-tidyverse, message=FALSE}
 library(tidyr)
 library(dplyr)
-linelist <- linelist %>% 
+linelist <- linelist %>%
   tidyr::pivot_wider(
-    names_from = outcome, 
+    names_from = outcome,
     values_from = date_outcome
   )
 linelist <- linelist %>%
   dplyr::rename(
-    date_death = died, 
+    date_death = died,
     date_recovery = recovered
   )
 ```