From 3c03d3f25a3816ea282b1831311645e43577e872 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 06:11:43 +1100
Subject: [PATCH 01/17] feat: add dynamic target #52

---
 DESCRIPTION                                   |   1 +
 NAMESPACE                                     |   4 +
 NEWS.md                                       |   3 +-
 R/Target.R                                    | 105 ++++++++++++++++++
 R/Transition.R                                |  41 ++++---
 R/TransitionClassification.R                  |  27 +++--
 R/checkmate.R                                 |  81 ++++++++++++++
 man/Target.Rd                                 |  55 +++++++++
 man/Transition.Rd                             |   5 +
 man/TransitionClassification.Rd               |  26 +++--
 man/check_target.Rd                           |  47 ++++++++
 tests/testthat/test-Target.R                  |  12 ++
 .../testthat/test-TransitionClassification.R  |  55 +++++++++
 tests/testthat/test-checkmate.R               |  26 +++++
 14 files changed, 448 insertions(+), 40 deletions(-)
 create mode 100644 R/Target.R
 create mode 100644 man/Target.Rd
 create mode 100644 man/check_target.Rd
 create mode 100644 tests/testthat/test-Target.R
 create mode 100644 tests/testthat/test-checkmate.R

diff --git a/DESCRIPTION b/DESCRIPTION
index bcb3988d..f84c0908 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -81,6 +81,7 @@ Collate:
     'Network.R'
     'Population.R'
     'Pipeline.R'
+    'Target.R'
     'Transition.R'
     'TransitionClassification.R'
     'TransitionRegression.R'
diff --git a/NAMESPACE b/NAMESPACE
index 29d03d9e..9fd6ca3f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -41,6 +41,7 @@ export(alignment)
 export(assert_entity)
 export(assert_entity_ids)
 export(assert_required_models)
+export(assert_target)
 export(assert_transition_supported_model)
 export(assign_reference)
 export(check_entity)
@@ -48,6 +49,7 @@ export(check_entity_ids)
 export(check_module)
 export(check_module_version)
 export(check_required_models)
+export(check_target)
 export(check_transition_supported_model)
 export(combine_histories)
 export(create_scenario)
@@ -60,6 +62,7 @@ export(element_wise_expand_lists)
 export(expect_entity)
 export(expect_entity_ids)
 export(expect_required_models)
+export(expect_target)
 export(expect_transition_supported_model)
 export(get_active_scenario)
 export(get_all_module_files)
@@ -85,6 +88,7 @@ export(set_active_scenario)
 export(test_entity)
 export(test_entity_ids)
 export(test_required_models)
+export(test_target)
 export(test_transition_supported_model)
 export(trans)
 export(unnest_datatable)
diff --git a/NEWS.md b/NEWS.md
index 8a2101cd..4754224d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,7 +8,8 @@
 4. Added a `replace` method to `World` which basically `remove` and `add` in one call.
 5. Moved `$subset_ids()` from `Agent`  to `Entity`.
 6. `download_module()` and `set_active_scenario()` now have a `.basedir` argument which sets the base directory where their files will be created at. By default this is the root folder of the currently active R project (if you are using RStudio) which is determined by `here::here()`.
-7. Renamed `use_scenario` to `create_scenario` and `active_scenario` to `get_active_scenario`. 
+7. Renamed `use_scenario` to `create_scenario` and `active_scenario` to `get_active_scenario`.
+8. `TransitionClassification`'s target argument now accepts a dynamic target, see issue [#52] https://github.com/dymium-org/dymiumCore/issues/52. 
 
 ## BUG FIXES
 
diff --git a/R/Target.R b/R/Target.R
new file mode 100644
index 00000000..891f1434
--- /dev/null
+++ b/R/Target.R
@@ -0,0 +1,105 @@
+#' @title Target
+#'
+#' @usage NULL
+#' @include Generic.R
+#' @format [R6::R6Class] object inheriting [Generic].
+#'
+#' @description
+#'
+#' `Target` is to be used within `TransitionClassification` or supply to event
+#' functions. If the target is dynamic then its `get` will return its target
+#' value at the current time or its closest time to the current time.
+#'
+#' @section Construction:
+#'
+#' ```
+#' Target$new(x)
+#' ```
+#'
+#' * `x` :: any object that passes `check_target()`\cr
+#' A target object.
+#'
+#' @section Active Field (read-only):
+#'
+#'  * `data`:: a target object\cr
+#'  A target object.
+#'
+#'  * `dynamic`:: `logical(1)`\cr
+#'  A logical flag which indicates whether the target object is dynamic or not.
+#'
+#' @section Public Methods:
+#'
+#'  * `get(time = .get_sim_time())`\cr
+#'  (`integer(1)`) -> a named `list()`\cr
+#'  Get a alignment target as a named list.
+#'
+#' @aliases Models
+#'
+#' @examples
+#'
+#' TrgtStatic <- Target$new(list(yes = 10))
+#' TrgtStatic$data
+#' TrgtStatic$dynamic
+#' TrgtStatic$get()
+#'
+#' target_dynamic <- data.table(time = 1:10, yes = 1:10)
+#' TrgtDynamic <- Target$new(list(yes = 10))
+#' TrgtDynamic$data
+#' TrgtDynamic$dynamic
+#' TrgtDynamic$get()
+#' TrgtDynamic$get(1)
+#' TrgtDynamic$get(10)
+Target <- R6::R6Class(
+  classname = "Target",
+  inherit = dymiumCore::Generic,
+  public = list(
+    initialize = function(x) {
+      assert_target(x, null.ok = FALSE)
+
+      if (is.data.frame(x)) {
+
+        if (!is.data.table(x)) {
+          private$.data <- as.data.table(x)
+        } else {
+          private$.data <- data.table::copy(x)
+        }
+
+        if ("time" %in% names(x)) {
+          private$.dynamic <- TRUE
+        }
+      }
+
+      private$.data <- x
+
+      return(invisible(self))
+    },
+
+    get = function(time = .get_sim_time()) {
+      if (private$.dynamic) {
+        closest_time_index <- which.min(abs(private$.data[['time']] - time))
+        return(as.list(private$.data[closest_time_index, -c("time")]))
+      }
+
+      if (is.data.table(private$.data)) {
+        return(copy(private$.data))
+      }
+
+      return(private$.data)
+    }
+  ),
+
+  active = list(
+    data = function() {
+      base::get(".data", envir = private)
+    },
+    dynamic = function() {
+      base::get(".dynamic", envir = private)
+    }
+  ),
+
+  private = list(
+    .data = NULL,
+    .dynamic = FALSE
+  )
+
+)
diff --git a/R/Transition.R b/R/Transition.R
index b0ed9666..10ccad04 100644
--- a/R/Transition.R
+++ b/R/Transition.R
@@ -7,6 +7,12 @@
 #' Note that, to swap the run order of `filter()` and `mutate()` you need to change the
 #' `mutate_first` public field to `TRUE`.
 #'
+#' @note
+#'
+#' `target` can be static or dynamic depending on the data structure of it. A static
+#' target can be a named list or an integer value depending its usage in each
+#' event function.
+#'
 #' @section Construction:
 #'
 #' ```
@@ -82,13 +88,13 @@ Transition <- R6Class(
       # checks
       checkmate::assert_class(x, c("Agent"))
       checkmate::assert_subset(class(model)[[1]], choices = SupportedTransitionModels())
-      checkmate::assert_list(target, any.missing = FALSE, types = 'integerish', names = 'strict', null.ok = TRUE)
+      dymiumCore::assert_target(target, null.ok = TRUE)
       checkmate::assert_integerish(targeted_agents, lower = 1, any.missing = FALSE, null.ok = TRUE)
 
       # store inputs
       private$.AgtObj <- x
       private$.model <- model
-      private$.target <- target
+      private$.target <- .pick_target(target)
       private$.targeted_agents <- targeted_agents
 
       # run the steps ------
@@ -245,22 +251,11 @@ Transition <- R6Class(
     simulate = function() {
 
       # expect a vector
+      lg$warn("Transition is not meant not be used directly! It only gives an incorrect \\
+               simulation result for internal testing purposes! Please use \\
+               TransitionClassification or TransitonRegression instead.")
       response <- rep(1, nrow(private$.sim_data)) # dummy
 
-      # response <- switch(
-      #   EXPR = class(private$.model)[[1]],
-      #   "train" = simulate_train(self, private),
-      #   "data.table" = simulate_datatable(self, private),
-      #   "list" = simulate_list(self, private),
-      #   "NULL" = simulate_numeric(self, private),
-      #   stop(
-      #     glue::glue(
-      #       "{class(self)[[1]]} class doesn't have an implementation of {class(private$.model)} \\
-      #       class. Please kindly request this in dymiumCore's Github issue or send in a PR! :)"
-      #     )
-      #   )
-      # )
-
       response
     },
 
@@ -337,9 +332,21 @@ Transition <- R6Class(
  )
 )
 
-
 # Functions ---------------------------------------------------------------
 
+.pick_target <- function(target) {
+  if (!is.data.frame(target)) {
+    return(target)
+  }
+  if (!is.data.table(target)) {
+    target <- as.data.table(target)
+  }
+  current_sim_time <- .get_sim_time()
+
+  index_closest_time <- which.min(abs(target[['time']] - current_sim_time))
+
+  return(as.list(target[index_closest_time, -c("time")]))
+}
 
 #' Get all object classes that are supported by Transition
 #'
diff --git a/R/TransitionClassification.R b/R/TransitionClassification.R
index 375e7cf4..4f3eff51 100644
--- a/R/TransitionClassification.R
+++ b/R/TransitionClassification.R
@@ -21,6 +21,19 @@
 #'
 #' To get the simulation result use `$get_result()`.
 #'
+#' @note
+#'
+#' `target` is used ensures that the aggregate outcome of the transition matches
+#'  a macro-level outcome as defined in `target`. This is known as 'alignment' see,
+#'  Li, J., & O'Donoghue, C. (2012). Evaluating binary alignment
+#'  methods in microsimulation models. For example, in a transition where the probabilistic
+#'  model predicts only two outcomes, a binary model, "yes" and "no". If the target
+#'  is a list of yes = 10 and no = 20 (i.e. `r list(yes = 10, no = 20)`), this will
+#'  ensure that there will be 10 decision makers whom select 'yes' and 20 decision makers
+#'  that select 'no'. However, this doesn't mean that all decision makers have
+#'  an equal odd of select 'yes' or 'no', the odd is still to be determined by the given
+#'  probalistic model. See [alignment] for more detail.
+#'
 #' @section Construction:
 #'
 #' ```
@@ -35,17 +48,9 @@
 #'
 #' * `target` :: a named `list()`\cr
 #'  (Default as NULL).
-#'  A named list where the names of its elements correspond to the choices and
-#'  the values are the number of agents to choose those choices. This ensure that
-#'  the aggregate outcome of the transition matches a macro target. This is known
-#'  as 'alignment' see, Li, J., & O'Donoghue, C. (2012). Evaluating binary alignment
-#'  methods in microsimulation models. For example, in a transition where the probabilistic
-#'  model predicts only two outcomes, a binary model, "yes" and "no". If the target
-#'  is a list of yes = 10 and no = 20 (i.e. `r list(yes = 10, no = 20)`), this will
-#'  ensure that there will be 10 decision makers whom select 'yes' and 20 decision makers
-#'  that select 'no'. However, this doesn't mean that all decision makers have
-#'  an equal odd of select 'yes' or 'no', the odd is still to be determined by the given
-#'  probalistic model. See [alignment] for more detail.
+#'  `Target` or A named list where its names is a subset of to the choices in `model`
+#'  to be selected and its values are the number of agents to choose those choices.
+#'  See the note section for more details.
 #'
 #' * `targeted_agent` :: `integer()`\cr
 #'  (Default as NULL)
diff --git a/R/checkmate.R b/R/checkmate.R
index 8c441fbd..0d146bc1 100644
--- a/R/checkmate.R
+++ b/R/checkmate.R
@@ -171,3 +171,84 @@ test_required_models <- checkmate::makeTestFunction(check_required_models)
 #' @inheritParams checkmate::makeExpectation
 #' @rdname check_required_models
 expect_required_models <- checkmate::makeExpectationFunction(check_required_models)
+
+#' Check if argument is a valid target object
+#'
+#' A target object is either a named list that contains integer values (static target) or a
+#' data.frame that contains a 'time' column and other response columns (dynamic target). The type of
+#' of the target depends on its usage.
+#'
+#' Here is an example of a static target `list(yes=10, no=20)`. Here is an example
+#' of a dynamic target `data.frame(time = c(1,2,3), yes = c(10,11,12), no = c(20,21,22)`.
+#'
+#' @param x any object to check
+#' @param null.ok default as TRUE
+#'
+#' @return TRUE if `x` is a valid target object else throws an error.
+#'
+#' @export
+check_target <- function(x, null.ok = TRUE) {
+
+  if (is.null(x)) {
+    if (null.ok) {
+      return(TRUE)
+    } else {
+      msg = "`x` cannot be NULL."
+      return(msg)
+    }
+  }
+
+  checkmate::assert(
+    checkmate::check_list(
+      x = x,
+      any.missing = FALSE,
+      types = c('integerish'),
+      names = 'strict',
+      null.ok = FALSE
+    ),
+    checkmate::check_data_frame(
+      x = x,
+      any.missing = FALSE,
+      min.cols = 2,
+      col.names = "strict",
+      null.ok = null.ok
+    )
+  )
+
+  if (is.data.frame(x)) {
+    checkmate::assert_names(
+      x = names(x),
+      type = "strict",
+      must.include = "time"
+    )
+
+    checkmate::assert_integerish(
+      x$time,
+      lower = 1,
+      any.missing = FALSE,
+      min.len = 1,
+      null.ok = FALSE,
+      unique = TRUE,
+      .var.name = "`time` column"
+    )
+
+  }
+
+  return(TRUE)
+}
+
+#' @export
+#' @param add [checkmate::AssertCollection]\cr
+#'  Collection to store assertions. See [checkmate::AssertCollection].
+#' @inheritParams checkmate::makeAssertion
+#' @rdname check_target
+assert_target <- checkmate::makeAssertionFunction(check_target)
+
+#' @export
+#' @rdname check_target
+test_target <- checkmate::makeTestFunction(check_target)
+
+#' @export
+#' @inheritParams checkmate::makeExpectation
+#' @rdname check_target
+expect_target <- checkmate::makeExpectationFunction(check_target)
diff --git a/man/Target.Rd b/man/Target.Rd
new file mode 100644
index 00000000..eceaa91d
--- /dev/null
+++ b/man/Target.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Target.R
+\name{Target}
+\alias{Target}
+\alias{Models}
+\title{Target}
+\format{\link[R6:R6Class]{R6::R6Class} object inheriting \link{Generic}.}
+\description{
+\code{Target} is to be used within \code{TransitionClassification} or supply to event
+functions. If the target is dynamic then its \code{get} will return its target
+value at the current time or its closest time to the current time.
+}
+\section{Construction}{
+\preformatted{Target$new(x)
+}
+\itemize{
+\item \code{x} :: any object that passes \code{check_target()}\cr
+A target object.
+}
+}
+
+\section{Active Field (read-only)}{
+
+\itemize{
+\item \code{data}:: a target object\cr
+A target object.
+\item \code{dynamic}:: \code{logical(1)}\cr
+A logical flag which indicates whether the target object is dynamic or not.
+}
+}
+
+\section{Public Methods}{
+
+\itemize{
+\item \code{get(time = .get_sim_time())}\cr
+(\code{integer(1)}) -> a named \code{list()}\cr
+Get a alignment target as a named list.
+}
+}
+
+\examples{
+
+TrgtStatic <- Target$new(list(yes = 10))
+TrgtStatic$data
+TrgtStatic$dynamic
+TrgtStatic$get()
+
+target_dynamic <- data.table(time = 1:10, yes = 1:10)
+TrgtDynamic <- Target$new(list(yes = 10))
+TrgtDynamic$data
+TrgtDynamic$dynamic
+TrgtDynamic$get()
+TrgtDynamic$get(1)
+TrgtDynamic$get(10)
+}
diff --git a/man/Transition.Rd b/man/Transition.Rd
index 812bea2b..ad2dbb1c 100644
--- a/man/Transition.Rd
+++ b/man/Transition.Rd
@@ -9,6 +9,11 @@ Work flow: \code{initialise()} -> \code{filter()} -> \code{mutate()} -> \code{si
 Note that, to swap the run order of \code{filter()} and \code{mutate()} you need to change the
 \code{mutate_first} public field to \code{TRUE}.
 }
+\note{
+\code{target} can be static or dynamic depending on the data structure of it. A static
+target can be a named list or an integer value depending its usage in each
+event function.
+}
 \section{Construction}{
 \preformatted{Transition$new(x, model, target = NULL, targeted_agents = NULL)
 }
diff --git a/man/TransitionClassification.Rd b/man/TransitionClassification.Rd
index a10b978f..9302f74e 100644
--- a/man/TransitionClassification.Rd
+++ b/man/TransitionClassification.Rd
@@ -43,6 +43,18 @@ To get the simulation result use \verb{$get_result()}.
 
 Create a \link{TransitionClassification} object.
 }
+\note{
+\code{target} is used ensures that the aggregate outcome of the transition matches
+a macro-level outcome as defined in \code{target}. This is known as 'alignment' see,
+Li, J., & O'Donoghue, C. (2012). Evaluating binary alignment
+methods in microsimulation models. For example, in a transition where the probabilistic
+model predicts only two outcomes, a binary model, "yes" and "no". If the target
+is a list of yes = 10 and no = 20 (i.e. \verb{r list(yes = 10, no = 20)}), this will
+ensure that there will be 10 decision makers whom select 'yes' and 20 decision makers
+that select 'no'. However, this doesn't mean that all decision makers have
+an equal odd of select 'yes' or 'no', the odd is still to be determined by the given
+probalistic model. See \link{alignment} for more detail.
+}
 \section{Construction}{
 \preformatted{TransitionClassification$new(x, model, target = NULL, targeted_agents = NULL)
 }
@@ -53,17 +65,9 @@ An \link{Entity} object or its inheritances.
 A model object to be used to simulate transition.
 \item \code{target} :: a named \code{list()}\cr
 (Default as NULL).
-A named list where the names of its elements correspond to the choices and
-the values are the number of agents to choose those choices. This ensure that
-the aggregate outcome of the transition matches a macro target. This is known
-as 'alignment' see, Li, J., & O'Donoghue, C. (2012). Evaluating binary alignment
-methods in microsimulation models. For example, in a transition where the probabilistic
-model predicts only two outcomes, a binary model, "yes" and "no". If the target
-is a list of yes = 10 and no = 20 (i.e. \verb{r list(yes = 10, no = 20)}), this will
-ensure that there will be 10 decision makers whom select 'yes' and 20 decision makers
-that select 'no'. However, this doesn't mean that all decision makers have
-an equal odd of select 'yes' or 'no', the odd is still to be determined by the given
-probalistic model. See \link{alignment} for more detail.
+\code{Target} or A named list where its names is a subset of to the choices in \code{model}
+to be selected and its values are the number of agents to choose those choices.
+See the note section for more details.
 \item \code{targeted_agent} :: \code{integer()}\cr
 (Default as NULL)
 An integer vector that contains agents' ids of the \link{Entity} in \code{x} to undergo
diff --git a/man/check_target.Rd b/man/check_target.Rd
new file mode 100644
index 00000000..3bd8f876
--- /dev/null
+++ b/man/check_target.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/checkmate.R
+\name{check_target}
+\alias{check_target}
+\alias{assert_target}
+\alias{test_target}
+\alias{expect_target}
+\title{Check if argument is a valid target object}
+\usage{
+check_target(x, null.ok = TRUE)
+
+assert_target(x, null.ok = TRUE, .var.name = checkmate::vname(x), add = NULL)
+
+test_target(x, null.ok = TRUE)
+
+expect_target(x, null.ok = TRUE, info = NULL, label = vname(x))
+}
+\arguments{
+\item{x}{any object to check}
+
+\item{null.ok}{default as TRUE}
+
+\item{.var.name}{[\code{character(1)}]\cr
+The custom name for \code{x} as passed to any \code{assert*} function.
+Defaults to a heuristic name lookup.}
+
+\item{add}{\link[checkmate:AssertCollection]{checkmate::AssertCollection}\cr
+Collection to store assertions. See \link[checkmate:AssertCollection]{checkmate::AssertCollection}.}
+
+\item{info}{[\code{character(1)}]\cr
+See \code{\link[testthat]{expect_that}}}
+
+\item{label}{[\code{character(1)}]\cr
+See \code{\link[testthat]{expect_that}}}
+}
+\value{
+TRUE if \code{x} is a valid target object else throws an error.
+}
+\description{
+A target object is either a named list that contains integer values (static target) or a
+data.frame that contains a 'time' column and other response columns (dynamic target). The type of
+of the target depends on its usage.
+}
+\details{
+Here is an example of a static target \code{list(yes=10, no=20)}. Here is an example
+of a dynamic target \verb{data.frame(time = c(1,2,3), yes = c(10,11,12), no = c(20,21,22)}.
+}
diff --git a/tests/testthat/test-Target.R b/tests/testthat/test-Target.R
new file mode 100644
index 00000000..61049a0c
--- /dev/null
+++ b/tests/testthat/test-Target.R
@@ -0,0 +1,12 @@
+test_that("Target", {
+  Tgt <- Target$new(list(yes = 10))
+  expect_equal(Tgt$data, list(yes = 10))
+  expect_equal(Trgt$get(), list(yes = 10))
+  expect_false(Tgt$dynamic)
+
+  target_dynamic <- data.table(time = 1:10, yes = 10)
+  TgtDy <- Target$new(target_dynamic)
+  expect_equal(TgtDy$get(), list(yes = 10))
+  expect_equal(TgtDy$data, target_dynamic)
+  expect_true(TgtDy$dynamic)
+})
diff --git a/tests/testthat/test-TransitionClassification.R b/tests/testthat/test-TransitionClassification.R
index 95b73c8d..f3118f44 100644
--- a/tests/testthat/test-TransitionClassification.R
+++ b/tests/testthat/test-TransitionClassification.R
@@ -241,3 +241,58 @@ test_that("update", {
   checkmate::assert_character(names(table(Ind$get_attr("test"))), min.len = 1, unique = TRUE, null.ok = FALSE)
 })
 
+
+test_that("dynamic target", {
+
+  create_toy_world()
+
+  model <- list(yes = 0.10, no = 0.90)
+
+  dynamic_target <-
+    data.table(
+      time = c(1:10),
+      yes = sample(1:20, 10, replace = TRUE),
+      no = sample(1:20, 10, replace = TRUE)
+    )
+
+  event_dynamic_target <- function(world, model, target) {
+
+    Ind <- world$get("Individual")
+
+    DynamicTrans <- TransitionClassification$new(Ind, model, target)
+
+    remove_ids <- DynamicTrans$get_result()[response == "yes", id]
+
+    if (length(remove_ids) > 0) {
+      Ind$remove(ids = remove_ids)
+    }
+
+    return(world)
+  }
+
+  Ind <- world$get("Individual")
+
+  n_ind_before <- Ind$n()
+
+  for (i in 1:10) {
+    world$start_iter(time_step = i, unit = "year") %>%
+      event_dynamic_target(., model, target = dynamic_target)
+  }
+
+  n_ind_after <- Ind$n()
+
+  expect_true(n_ind_after + sum(dynamic_target$yes) == n_ind_before)
+
+  # bad target, `nooo` is not a valid response
+  dynamic_target <-
+    data.table(
+      time = c(1:10),
+      yes = sample(1:20, 10, replace = TRUE),
+      no = sample(1:20, 10, replace = TRUE),
+      nooo = sample(1:20, 10, replace = TRUE)
+    )
+
+  expect_error(TransitionClassification$new(world$entities$Individual, model, dynamic_target),
+               regexp = "Must be a subset of set \\{yes,no\\}.")
+
+})
diff --git a/tests/testthat/test-checkmate.R b/tests/testthat/test-checkmate.R
new file mode 100644
index 00000000..0fd80294
--- /dev/null
+++ b/tests/testthat/test-checkmate.R
@@ -0,0 +1,26 @@
+test_that("check_target", {
+
+  expect_true(check_target(NULL))
+
+  expect_error(check_target(1))
+
+  expect_error(assert_target(1))
+
+  expect_error(assert_target(list(1)))
+
+  expect_true(check_target(list(yes = 1)))
+
+  expect_error(check_target(data.table(1)))
+
+  expect_error(check_target(data.table(time = 1:10)))
+
+  expect_error(check_target(data.table(time = 1:10)))
+
+  expect_error(check_target(data.table(time = rep(1, 10))),
+               regexp = "Contains duplicated values")
+
+  expect_error(check_target(data.table(time = paste(1:10))))
+
+  expect_true(check_target(data.table(time = 1:10, yes = 1:10)))
+
+})

From 658fed083d412ddcf51ad1c1c90a94ba75cca8b6 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 06:13:41 +1100
Subject: [PATCH 02/17] test: fix check_target

---
 tests/testthat/test-checkmate.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-checkmate.R b/tests/testthat/test-checkmate.R
index 0fd80294..5b992c18 100644
--- a/tests/testthat/test-checkmate.R
+++ b/tests/testthat/test-checkmate.R
@@ -10,17 +10,17 @@ test_that("check_target", {
 
   expect_true(check_target(list(yes = 1)))
 
-  expect_error(check_target(data.table(1)))
+  expect_error(check_target(data.frame(1)))
 
-  expect_error(check_target(data.table(time = 1:10)))
+  expect_error(check_target(data.frame(time = 1:10)))
 
-  expect_error(check_target(data.table(time = 1:10)))
+  expect_error(check_target(data.frame(time = 1:10)))
 
-  expect_error(check_target(data.table(time = rep(1, 10))),
-               regexp = "Contains duplicated values")
+  expect_error(check_target(data.frame(time = rep(1, 10))),
+               regexp = "Must have at least 2 cols, but has 1 cols")
 
-  expect_error(check_target(data.table(time = paste(1:10))))
+  expect_error(check_target(data.frame(time = paste(1:10))))
 
-  expect_true(check_target(data.table(time = 1:10, yes = 1:10)))
+  expect_true(check_target(data.frame(time = 1:10, yes = 1:10)))
 
 })

From 9aded756558700340d3fcb5c1d9ef28003f5aa56 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:00:22 +1100
Subject: [PATCH 03/17] feat: add print format for Target

---
 R/Target.R    | 23 ++++++++++++++++-------
 man/Target.Rd |  5 +++++
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/R/Target.R b/R/Target.R
index 891f1434..ac9a9808 100644
--- a/R/Target.R
+++ b/R/Target.R
@@ -37,15 +37,20 @@
 #'
 #' @examples
 #'
+#' # static target
 #' TrgtStatic <- Target$new(list(yes = 10))
 #' TrgtStatic$data
 #' TrgtStatic$dynamic
 #' TrgtStatic$get()
 #'
+#' # dynamic target
 #' target_dynamic <- data.table(time = 1:10, yes = 1:10)
 #' TrgtDynamic <- Target$new(list(yes = 10))
 #' TrgtDynamic$data
 #' TrgtDynamic$dynamic
+#'
+#' # if the `time` argument in `get()` is not specified then it will rely on
+#' # the time step from the simulation clock from `.get_sim_time()`.
 #' TrgtDynamic$get()
 #' TrgtDynamic$get(1)
 #' TrgtDynamic$get(10)
@@ -55,22 +60,17 @@ Target <- R6::R6Class(
   public = list(
     initialize = function(x) {
       assert_target(x, null.ok = FALSE)
-
       if (is.data.frame(x)) {
-
         if (!is.data.table(x)) {
           private$.data <- as.data.table(x)
         } else {
           private$.data <- data.table::copy(x)
         }
-
         if ("time" %in% names(x)) {
           private$.dynamic <- TRUE
         }
       }
-
       private$.data <- x
-
       return(invisible(self))
     },
 
@@ -79,12 +79,21 @@ Target <- R6::R6Class(
         closest_time_index <- which.min(abs(private$.data[['time']] - time))
         return(as.list(private$.data[closest_time_index, -c("time")]))
       }
-
       if (is.data.table(private$.data)) {
         return(copy(private$.data))
       }
-
       return(private$.data)
+    },
+
+    print = function() {
+      msg <- glue::glue("dynamic: {private$.dynamic}")
+      if (private$.dynamic) {
+        period <- c(min(private$.data[["time"]]),
+                    max(private$.data[["time"]]))
+        msg <- glue::glue(msg,
+                          "period: {period[1]} to {period[2]}", .sep = "\n- ")
+      }
+      super$print(msg)
     }
   ),
 
diff --git a/man/Target.Rd b/man/Target.Rd
index eceaa91d..44ed182f 100644
--- a/man/Target.Rd
+++ b/man/Target.Rd
@@ -40,15 +40,20 @@ Get a alignment target as a named list.
 
 \examples{
 
+# static target
 TrgtStatic <- Target$new(list(yes = 10))
 TrgtStatic$data
 TrgtStatic$dynamic
 TrgtStatic$get()
 
+# dynamic target
 target_dynamic <- data.table(time = 1:10, yes = 1:10)
 TrgtDynamic <- Target$new(list(yes = 10))
 TrgtDynamic$data
 TrgtDynamic$dynamic
+
+# if the `time` argument in `get()` is not specified then it will rely on
+# the time step from the simulation clock from `.get_sim_time()`.
 TrgtDynamic$get()
 TrgtDynamic$get(1)
 TrgtDynamic$get(10)

From fc7cd7f0e7e34a70e46add31e44ff1a47348b4b7 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:00:34 +1100
Subject: [PATCH 04/17] test: fix Target

---
 tests/testthat/test-Target.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-Target.R b/tests/testthat/test-Target.R
index 61049a0c..80feb0fb 100644
--- a/tests/testthat/test-Target.R
+++ b/tests/testthat/test-Target.R
@@ -1,7 +1,7 @@
 test_that("Target", {
   Tgt <- Target$new(list(yes = 10))
   expect_equal(Tgt$data, list(yes = 10))
-  expect_equal(Trgt$get(), list(yes = 10))
+  expect_equal(Tgt$get(), list(yes = 10))
   expect_false(Tgt$dynamic)
 
   target_dynamic <- data.table(time = 1:10, yes = 10)
@@ -9,4 +9,5 @@ test_that("Target", {
   expect_equal(TgtDy$get(), list(yes = 10))
   expect_equal(TgtDy$data, target_dynamic)
   expect_true(TgtDy$dynamic)
+  expect_target(TgtDy)
 })

From cb3b272f029bf8682c462b99cf378461815a9916 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:00:56 +1100
Subject: [PATCH 05/17] feat: use Target in the inner working of Transition

---
 R/Transition.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Transition.R b/R/Transition.R
index 10ccad04..ccb780e8 100644
--- a/R/Transition.R
+++ b/R/Transition.R
@@ -94,7 +94,7 @@ Transition <- R6Class(
       # store inputs
       private$.AgtObj <- x
       private$.model <- model
-      private$.target <- .pick_target(target)
+      private$.target <- Target$new(target)$get()
       private$.targeted_agents <- targeted_agents
 
       # run the steps ------

From 1571e88842a9281a7c90d0a40a3c25534bd35b9b Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:01:13 +1100
Subject: [PATCH 06/17] feat: add print format for Generic

---
 R/Generic.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/R/Generic.R b/R/Generic.R
index c307c3a5..8f478b67 100644
--- a/R/Generic.R
+++ b/R/Generic.R
@@ -99,6 +99,19 @@ Generic <- R6Class(
 
     class = function() {
       class(self)[[1]]
+    },
+
+    print = function(...) {
+      dots <- list(...)
+      .class_inheritance <- glue::glue_collapse(class(self), sep = " <- ")
+      message(
+        glue::glue(
+        "Class: {class(self)[[1]]}",
+        "Inheritance: {.class_inheritance}",
+        "{dots[[1]]}",
+        .sep = "\n- "
+        )
+      )
     }
   ),
 

From b17625c8b055e8500d0d8287b5e3c29acbd0ff17 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:01:58 +1100
Subject: [PATCH 07/17] feat: check_target knows Target

---
 R/checkmate.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/checkmate.R b/R/checkmate.R
index 0d146bc1..3f111c85 100644
--- a/R/checkmate.R
+++ b/R/checkmate.R
@@ -212,6 +212,11 @@ check_target <- function(x, null.ok = TRUE) {
       min.cols = 2,
       col.names = "strict",
       null.ok = null.ok
+    ),
+    checkmate::check_r6(
+      x = x,
+      classes = c("Target", "Generic"),
+      null.ok = null.ok
     )
   )
 

From a4dfc722b00346982338dac91e04330d195b63da Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:02:33 +1100
Subject: [PATCH 08/17] test: update TransitionClassifiication

---
 tests/testthat/test-TransitionClassification.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tests/testthat/test-TransitionClassification.R b/tests/testthat/test-TransitionClassification.R
index f3118f44..4b27ce09 100644
--- a/tests/testthat/test-TransitionClassification.R
+++ b/tests/testthat/test-TransitionClassification.R
@@ -255,6 +255,14 @@ test_that("dynamic target", {
       no = sample(1:20, 10, replace = TRUE)
     )
 
+  TargetDynamic <-
+    data.table(
+      time = c(1:10),
+      yes = sample(1:20, 10, replace = TRUE),
+      no = sample(1:20, 10, replace = TRUE)
+    ) %>%
+    Target$new(.)
+
   event_dynamic_target <- function(world, model, target) {
 
     Ind <- world$get("Individual")

From a1770199c3fe61bce1bb1c13d8639f7b8e742ca1 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:29:37 +1100
Subject: [PATCH 09/17] fix: Target did not accept NULL

---
 R/Target.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/Target.R b/R/Target.R
index ac9a9808..c9fdd1b5 100644
--- a/R/Target.R
+++ b/R/Target.R
@@ -17,7 +17,7 @@
 #' ```
 #'
 #' * `x` :: any object that passes `check_target()`\cr
-#' A target object.
+#' A target object or `NULL`.
 #'
 #' @section Active Field (read-only):
 #'
@@ -59,7 +59,7 @@ Target <- R6::R6Class(
   inherit = dymiumCore::Generic,
   public = list(
     initialize = function(x) {
-      assert_target(x, null.ok = FALSE)
+      assert_target(x, null.ok = TRUE)
       if (is.data.frame(x)) {
         if (!is.data.table(x)) {
           private$.data <- as.data.table(x)

From f7b9a4dc1a554cb47f42851bfcf5ee6941390e11 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:29:49 +1100
Subject: [PATCH 10/17] docs: update man

---
 man/Target.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/Target.Rd b/man/Target.Rd
index 44ed182f..82a15b74 100644
--- a/man/Target.Rd
+++ b/man/Target.Rd
@@ -15,7 +15,7 @@ value at the current time or its closest time to the current time.
 }
 \itemize{
 \item \code{x} :: any object that passes \code{check_target()}\cr
-A target object.
+A target object or \code{NULL}.
 }
 }
 

From bfae4ca3e5cc857c3c31011e744061d147c72a30 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:30:05 +1100
Subject: [PATCH 11/17] docs: update news

---
 NEWS.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 4754224d..1f22f317 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,14 +2,15 @@
 
 ## NEW FEATURES
 
-1. Added a `plot_relationship` method to `Household`. This uses `visNetwork` for plotting (added to Suggests). See #48 for its implementation detail.
+1. Add a `plot_relationship` method to `Household`. This uses `visNetwork` for plotting (added to Suggests). See #48 for its implementation detail.
 2. `inspect` now has a verbose option.
 3. `Transition` no longer removes the `NA` reponses when target is used.
-4. Added a `replace` method to `World` which basically `remove` and `add` in one call.
-5. Moved `$subset_ids()` from `Agent`  to `Entity`.
+4. Add a `replace` method to `World` which basically `remove` and `add` in one call.
+5. Move `$subset_ids()` from `Agent`  to `Entity`.
 6. `download_module()` and `set_active_scenario()` now have a `.basedir` argument which sets the base directory where their files will be created at. By default this is the root folder of the currently active R project (if you are using RStudio) which is determined by `here::here()`.
-7. Renamed `use_scenario` to `create_scenario` and `active_scenario` to `get_active_scenario`.
+7. Rename `use_scenario` to `create_scenario` and `active_scenario` to `get_active_scenario`.
 8. `TransitionClassification`'s target argument now accepts a dynamic target, see issue [#52] https://github.com/dymium-org/dymiumCore/issues/52. 
+9. Add a `Target` R6 class which acts as a wrapper for different types of target and make them work consistently in the `Transition` classes.
 
 ## BUG FIXES
 

From 977cb03e2d82bf5ae7a46575e36aca11b3e11ff2 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:30:35 +1100
Subject: [PATCH 12/17] test: fix check_target test

---
 tests/testthat/test-checkmate.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-checkmate.R b/tests/testthat/test-checkmate.R
index 5b992c18..2ee8ee8d 100644
--- a/tests/testthat/test-checkmate.R
+++ b/tests/testthat/test-checkmate.R
@@ -17,7 +17,7 @@ test_that("check_target", {
   expect_error(check_target(data.frame(time = 1:10)))
 
   expect_error(check_target(data.frame(time = rep(1, 10))),
-               regexp = "Must have at least 2 cols, but has 1 cols")
+               regexp = "Must have at least 2 cols, but has 1")
 
   expect_error(check_target(data.frame(time = paste(1:10))))
 

From 9596dbd9901f74e69ad78d024787480d6a3859b7 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:35:14 +1100
Subject: [PATCH 13/17] docs: export Target

---
 R/Target.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/Target.R b/R/Target.R
index c9fdd1b5..d5bca8e3 100644
--- a/R/Target.R
+++ b/R/Target.R
@@ -34,6 +34,7 @@
 #'  Get a alignment target as a named list.
 #'
 #' @aliases Models
+#' @export
 #'
 #' @examples
 #'

From 8a91ae435135701b2efd90f8704a90c7baf88bd2 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Mon, 27 Jan 2020 20:54:28 +1100
Subject: [PATCH 14/17] fix: checkmate::makeExpectation is missing

makeExpectation is imported to be used internally in our customised checkmate functions
---
 NAMESPACE              | 3 +++
 R/dymiumCore-package.R | 1 +
 2 files changed, 4 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 9fd6ca3f..b27b6671 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -31,6 +31,7 @@ export(Network)
 export(Pipeline)
 export(Population)
 export(SupportedTransitionModels)
+export(Target)
 export(Transition)
 export(TransitionClassification)
 export(TransitionRegression)
@@ -98,6 +99,8 @@ export(use_module_readme)
 export(validate_linkages)
 import(R6)
 import(data.table)
+importFrom(checkmate,makeExpectation)
+importFrom(checkmate,vname)
 importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_li)
diff --git a/R/dymiumCore-package.R b/R/dymiumCore-package.R
index 5ec0b0cb..9fc5c86b 100644
--- a/R/dymiumCore-package.R
+++ b/R/dymiumCore-package.R
@@ -11,6 +11,7 @@
 #' @name dymiumCore
 #' @import R6
 #' @import data.table
+#' @importFrom checkmate makeExpectation vname
 #' @importFrom glue glue glue_col glue_collapse
 #' @importFrom fs path dir_create path_ext_remove path_ext path_ext_set
 #' @importFrom usethis use_template use_directory

From 12c869aa7f081f981476cc07ade168b38191b589 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Tue, 28 Jan 2020 15:10:11 +1100
Subject: [PATCH 15/17] docs: fix wrong alias of Target

---
 R/Target.R    | 2 +-
 man/Target.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/Target.R b/R/Target.R
index d5bca8e3..99b90c20 100644
--- a/R/Target.R
+++ b/R/Target.R
@@ -33,7 +33,7 @@
 #'  (`integer(1)`) -> a named `list()`\cr
 #'  Get a alignment target as a named list.
 #'
-#' @aliases Models
+#' @aliases Targets
 #' @export
 #'
 #' @examples
diff --git a/man/Target.Rd b/man/Target.Rd
index 82a15b74..051ed871 100644
--- a/man/Target.Rd
+++ b/man/Target.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/Target.R
 \name{Target}
 \alias{Target}
-\alias{Models}
+\alias{Targets}
 \title{Target}
 \format{\link[R6:R6Class]{R6::R6Class} object inheriting \link{Generic}.}
 \description{

From 37842d49873ce918f3225927cc0bad0622ef78b6 Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Tue, 28 Jan 2020 15:10:39 +1100
Subject: [PATCH 16/17] test: fix Target tests

---
 tests/testthat/test-Target.R                   | 2 +-
 tests/testthat/test-TransitionClassification.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-Target.R b/tests/testthat/test-Target.R
index 80feb0fb..98feb3fe 100644
--- a/tests/testthat/test-Target.R
+++ b/tests/testthat/test-Target.R
@@ -4,7 +4,7 @@ test_that("Target", {
   expect_equal(Tgt$get(), list(yes = 10))
   expect_false(Tgt$dynamic)
 
-  target_dynamic <- data.table(time = 1:10, yes = 10)
+  target_dynamic <- data.table::data.table(time = 1:10, yes = 10)
   TgtDy <- Target$new(target_dynamic)
   expect_equal(TgtDy$get(), list(yes = 10))
   expect_equal(TgtDy$data, target_dynamic)
diff --git a/tests/testthat/test-TransitionClassification.R b/tests/testthat/test-TransitionClassification.R
index 4b27ce09..2f9a6ab5 100644
--- a/tests/testthat/test-TransitionClassification.R
+++ b/tests/testthat/test-TransitionClassification.R
@@ -256,7 +256,7 @@ test_that("dynamic target", {
     )
 
   TargetDynamic <-
-    data.table(
+    data.table::data.table(
       time = c(1:10),
       yes = sample(1:20, 10, replace = TRUE),
       no = sample(1:20, 10, replace = TRUE)

From fa79fecc6db26a2b879f18ba203c2f9450c1e5da Mon Sep 17 00:00:00 2001
From: amarin <17020181+asiripanich@users.noreply.github.com>
Date: Tue, 28 Jan 2020 15:15:43 +1100
Subject: [PATCH 17/17] feat: revamp the simulation clock

- use global option to store the clock time
- add functions to modify the clock
- `.dymium_options_msg()` shows the simulation time and every time during onload
- fix `get_active_scenario()` test to accept numeric due to the new clock time that get returned with the paths
---
 DESCRIPTION                    |  1 +
 R/World.R                      |  4 ++--
 R/clock.R                      | 19 +++++++++++++++++++
 R/utils-class.R                |  2 +-
 R/zzz.R                        | 22 ++++++----------------
 tests/testthat/test-scenario.R |  2 +-
 6 files changed, 30 insertions(+), 20 deletions(-)
 create mode 100644 R/clock.R

diff --git a/DESCRIPTION b/DESCRIPTION
index f84c0908..4110b065 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -90,6 +90,7 @@ Collate:
     'alignment.R'
     'checkmate.R'
     'checks.R'
+    'clock.R'
     'constants.R'
     'create-world.R'
     'data.R'
diff --git a/R/World.R b/R/World.R
index c19ab8ef..6014940a 100644
--- a/R/World.R
+++ b/R/World.R
@@ -299,7 +299,7 @@ World <- R6::R6Class(
     },
 
     get_time = function(x) {
-      get("sim_time", envir = .DMevn)
+      getOption("dymium.simulation_clock")
     },
 
     get_info = function() {
@@ -310,7 +310,7 @@ World <- R6::R6Class(
     # @param x An integer value.
     set_time = function(x) {
       checkmate::assert_integerish(x, lower = 0, len = 1)
-      assign("sim_time", as.integer(x), envir = .DMevn)
+      options(dymium.simulation_clock = x)
       invisible()
     },
 
diff --git a/R/clock.R b/R/clock.R
new file mode 100644
index 00000000..f35ee599
--- /dev/null
+++ b/R/clock.R
@@ -0,0 +1,19 @@
+clock_get <- function() {
+  return(getOption("dymium.simulation_clock"))
+}
+
+clock_reset <- function() {
+  clock_set(0)
+}
+
+clock_set <- function(x) {
+  checkmate::assert_number(
+    x,
+    lower = 0,
+    na.ok = FALSE,
+    finite = T,
+    null.ok = FALSE
+  )
+  options(dymium.simulation_clock = x)
+  return(invisible())
+}
diff --git a/R/utils-class.R b/R/utils-class.R
index d6c3ecff..742e5a99 100644
--- a/R/utils-class.R
+++ b/R/utils-class.R
@@ -35,7 +35,7 @@ is_dymium_class <- function(x) {
 #'
 #' .get_sim_time()
 .get_sim_time <- function() {
-  get("sim_time", envir = .DMevn)
+  getOption("dymium.simulation_clock")
 }
 
 
diff --git a/R/zzz.R b/R/zzz.R
index 3dbe4e45..1c526b4b 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,10 +1,8 @@
-# for storing variables that accessible and modifiable by all functions and objects
-.DMevn <- new.env(parent = emptyenv())
-
 .dymium_tempdir <- file.path(tempdir(), "scenario")
 
 .dymium_options <- function() {
   return(list(
+    simulation_clock = getOption('dymium.simulation_clock'),
     scenario_dir = getOption('dymium.scenario_dir'),
     output_dir = getOption('dymium.output_dir'),
     input_dir = getOption('dymium.input_dir')
@@ -12,14 +10,13 @@
 }
 
 .dymium_options_msg = function() {
-  # cli::cli_text(cli::rule(left = " {cli::symbol$info} dymium's options {cli::symbol$info} "))
   cli::cli_text(cli::rule(left = " * dymium's options * "))
   cli::cli_li(items = c(
-    "dymiun.scenario_dir: {getOption('dymium.scenario_dir')}",
-    "dymiun.input_dir: {getOption('dymium.input_dir')}",
-    "dymiun.output_dir: {getOption('dymium.output_dir')}"
+    "dymium.simulation_clock: {getOption('dymium.simulation_clock')}",
+    "dymium.scenario_dir: {getOption('dymium.scenario_dir')}",
+    "dymium.input_dir: {getOption('dymium.input_dir')}",
+    "dymium.output_dir: {getOption('dymium.output_dir')}"
   ))
-  # print("hello")
 }
 
 .onLoad <- function(libname, pkgname) {
@@ -32,6 +29,7 @@
   # set global options
   opts <- options()
   opts.dymium <- list(
+    dymium.simulation_clock = 0L,
     dymium.scenario_dir = file.path(.dymium_tempdir),
     dymium.input_dir = file.path(.dymium_tempdir, "inputs"),
     dymium.output_dir = file.path(.dymium_tempdir, "outputs")
@@ -39,13 +37,6 @@
   toset <- !(names(opts.dymium) %in% names(opts))
   if (any(toset)) options(opts.dymium[toset])
 
-  # setup package global variables
-  .DMevn[["sim_time"]] <- 0L
-
-  # create log file
-  # _dir.create(_dirname(opts.dymium$dymium.logFile), recursive = T, showWarnings = FALSE)
-  # file.create(opts.dymium$dymium.logFile)
-
   # setup logger
   assign("lg", lgr::get_logger_glue(name = pkgname), envir = parent.env(environment()))
 
@@ -73,7 +64,6 @@
   # print to console
   .dymium_options_msg()
 
-
   invisible()
 }
 
diff --git a/tests/testthat/test-scenario.R b/tests/testthat/test-scenario.R
index 1c5b6501..f52d52ba 100644
--- a/tests/testthat/test-scenario.R
+++ b/tests/testthat/test-scenario.R
@@ -1,5 +1,5 @@
 test_that("get_active_scenario", {
-  checkmate::expect_list(get_active_scenario(), types = "character")
+  checkmate::expect_list(get_active_scenario(), types = c("character", "numeric"), any.missing = FALSE)
   checkmate::expect_access(get_active_scenario()[['scenario_dir']])
   checkmate::expect_access(get_active_scenario()[['output_dir']])
   checkmate::expect_access(get_active_scenario()[['input_dir']])