calibrator without data

Author: stevencarlislewalker

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: macpan2
 Title: Fast and Flexible Compartmental Modelling
-Version: 1.16.1
+Version: 1.16.2
 Authors@R: c(
   person("Steve Walker", email="[email protected]", role=c("cre", "aut")),
   person("Weiguang Guan", role="aut"),

R/mp_cal_time.R

@@ -14,8 +14,8 @@
 #' time using a (1) \code{\link{Date}} vector, (2) \code{\link{character}}
 #' vector in YYYY-MM-DD format, or (3) \code{\link{integer}} vector that 
 #' counts the number of days since some reference. Otherwise please choose 
-#' 'steps' and convert your time column into integer values that represent 
-#' the time step that you would like in the model.
+#' 'steps', the default, and convert your time column into integer values that
+#' represent the time step that you would like in the model.
 #' @param time_column Name of the column that will identify the time at which
 #' particular values were observed.
 #' 
@@ -24,12 +24,21 @@
 #' @seealso [mp_sim_offset()]
 #' 
 #' @export
-mp_sim_bounds = function(sim_start, sim_end, time_scale, time_column = "time") {
+mp_sim_bounds = function(sim_start, sim_end, time_scale = "steps", time_column = "time") {
   self = Base()
   self$sim_start = sim_start
   self$sim_end = sim_end
   self$time_scale = time_scale
   self$time_column = time_column
+  self$extend = function(steps_to_extend) {
+    new_obj = mp_sim_offset(
+        self$sim_start_offset
+      , self$sim_end_offset + steps_to_extend
+      , self$time_scale
+      , self$time_column
+    )
+    return(new_obj)
+  }
   self$cal_time_steps = function(data, original_coercer = force) {
     column = data[[self$time_column]]
     check_valid_time_scales(self$time_scale)
@@ -63,12 +72,21 @@ mp_sim_bounds = function(sim_start, sim_end, time_scale, time_column = "time") {
 #' @seealso [mp_sim_bounds()]
 #' 
 #' @export
-mp_sim_offset = function(sim_start_offset, sim_end_offset, time_scale, time_column = "time") {
+mp_sim_offset = function(sim_start_offset, sim_end_offset, time_scale = "steps", time_column = "time") {
   self = Base()
   self$sim_start_offset = as.integer(sim_start_offset)
   self$sim_end_offset = as.integer(sim_end_offset)
   self$time_scale = time_scale
   self$time_column = time_column
+  self$extend = function(steps_to_extend) {
+    new_obj = mp_sim_offset(
+        self$sim_start_offset
+      , self$sim_end_offset + steps_to_extend
+      , self$time_scale
+      , self$time_column
+    )
+    return(new_obj)
+  }
   self$cal_time_steps = function(data, original_coercer = force) {
     column = data[[self$time_column]]
     check_valid_time_scales(self$time_scale)

R/mp_forecaster.R

@@ -72,7 +72,11 @@ mp_forecaster = function(calibrator, forecast_period_time_steps
   args$spec = spec
   if (!is.null(data)) args$data = data
   if (!is.null(outputs)) args$outputs = outputs
-  args$time = cal$time_steps_obj$extended_time_arg(forecast_period_time_steps)
+  if (is.null(args$time)) {
+    args$time = calibrator$time_steps_obj$extended_time_arg(forecast_period_time_steps)
+  } else {
+    args$time = args$time$extend(forecast_period_time_steps)
+  }
   do.call(mp_tmb_calibrator, args)
 }
 

R/mp_tmb_calibrator.R

@@ -446,37 +446,6 @@ TMBCalDataStruc = function(data, time) {
     FALSE
   }
 
-  # self$time_steps = time$bound_steps()[2L]
-  # data$time_ids = time$time_ids(data$time)
-  # self$data_time_ids = data$time_ids
-  # self$data_time_steps = max(data$time_ids)
-
-  # if (nrow(data) == 0L) {
-  #   time = Steps(1, 1)
-  # } else {
-  #   if (is.null(time)) {
-  #     if (infer_time_step(data$time)) {
-  #       data$time = as.integer(data$time)
-  #       time = Steps(min(data$time), max(data$time))
-  #     } else {
-  #       ## TODO: I'm guessing this could fail cryptically
-  #       time = Daily(min(data$time), max(data$time), checker = NoError)
-  #     }
-  #   }
-  #   else {
-  #     time = assert_cls(time, "CalTime", match.call(), "?mp_cal_time")
-  #     time$update_data_bounds(data)
-  #   }
-  # }
-  # self$time_steps = time$bound_steps()[2L]
-  # data$time_ids = time$time_ids(data$time)
-  # self$data_time_ids = data$time_ids
-  # if (nrow(data) == 0L) {
-  #   self$data_time_steps = 1L
-  # } else {
-  #   self$data_time_steps = max(data$time_ids)
-  # }
-
   data = rename_synonyms(data
     , time = c(
         "time", "Time", "ID", "time_id", "id", "date", "Date"
@@ -502,7 +471,9 @@ TMBCalDataStruc = function(data, time) {
     original_coercer = force
   }
   if (nrow(data) == 0L) {
-    time = mp_sim_bounds(1L, 1L, "steps")
+    if (is.null(time)) {
+      time = mp_sim_bounds(1L, 1L, "steps")
+    }
   } else {
     if (is.null(time)) {
       if (infer_time_step(data$time)) {
@@ -590,9 +561,6 @@ CalTimeStepsAbstract = function() {
   }
   self$sim_vec = function() seq(from = self$sim_1st(), by = 1L, len = self$sim_len())
   self$dat_vec = function() seq(from = self$dat_1st(), by = 1L, len = self$dat_len())
-  self$extended_time_arg = function(extension) {
-    mp_sim_offset(0, as.integer(extension), "steps")
-  }
   return_object(self, "CalTimeStepsAbstract")
 }
 CalTimeStepsInt = function(ext_sim_1st, ext_sim_end, ext_dat_1st, ext_dat_end, original_coercer = force) {
@@ -611,6 +579,9 @@ CalTimeStepsInt = function(ext_sim_1st, ext_sim_end, ext_dat_1st, ext_dat_end, o
     self$original_coercer(external)
   }
   self$external_to_internal = function(external) external - self$ext_sim_1st + self$sim_1st()
+  self$extended_time_arg = function(extension) {
+    mp_sim_offset(0, as.integer(extension), "steps")
+  }
   return_object(self, "CalTimeStepsInt")
 }
 if (FALSE) {

R/tmb_model.R

@@ -656,16 +656,16 @@ value_column_calibrator_util = function(baseline, simulator) {
     , default = "default"
     , optimized = "current"
   )
-  opt_attempted = simulator$optimization_history$opt_attempted()
-  if ((value_column_name == "current") & !opt_attempted) {
-    mp_wrap(
-        "The model object has not been optimized, and so the default"
-      , "(non-optimized) parameter set will be used as the baseline."
-      , "Please either explicitly choose"
-      , "to use the default set of parameters as the baseline, or optimize"
-      , "the model object using mp_optimize(model, ...)."
-    ) |> warning()
-  }
+  # opt_attempted = simulator$optimization_history$opt_attempted()
+  # if ((value_column_name == "current") & !opt_attempted) {
+  #   mp_wrap(
+  #       "The model object has not been optimized, and so the default"
+  #     , "(non-optimized) parameter set will be used as the baseline."
+  #     , "Please either explicitly choose"
+  #     , "to use the default set of parameters as the baseline, or optimize"
+  #     , "the model object using mp_optimize(model, ...)."
+  #   ) |> warning()
+  # }
   return(value_column_name)
 }
 
@@ -689,12 +689,14 @@ mp_trajectory_par.TMBCalibrator = function(model, parameter_updates = list()
     , baseline = c("recommended", "default", "optimized")
   ) {
   baseline = match.arg(baseline)
-  model = model$simulator
-  value_column_name = value_column_calibrator_util(baseline, model)
-  trajectory_par_util(model
+  simulator = model$simulator
+  value_column_name = value_column_calibrator_util(baseline, simulator)
+  traj = trajectory_par_util(simulator
     , parameter_updates, value_column_name
     , include_initial, include_final
   )
+  traj$time = model$time_steps_obj$internal_to_external(traj$time)
+  return(traj)
 }
 
 #' @param conf.int Should confidence intervals be produced?

man/mp_sim_bounds.Rd

@@ -122,7 +122,7 @@ sf_sir = mp_tmb_insert(sf_sir
     
     ## at the end (i.e. Infinity) of the expressions evaluated
     ## 'during' each iteration of the simulation loop ...
-  , at = Inf  
+  , at = Inf
   , phase = "during"
   
     ## add a new default value for the reporting probability