function to return all dynamic variables

Author: stevencarlislewalker

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: macpan2
 Title: Fast and Flexible Compartmental Modelling
-Version: 3.4.0
+Version: 3.5.0
 Authors@R: c(
   person("Steve Walker", email="[email protected]", role=c("cre", "aut")),
   person("Weiguang Guan", role="aut"),

NAMESPACE

@@ -241,6 +241,7 @@ export(mp_discrete_stoch)
 export(mp_dot_layout)
 export(mp_dynamic_model)
 export(mp_dynamic_simulator)
+export(mp_dynamic_vars)
 export(mp_effects_descr)
 export(mp_euler)
 export(mp_euler_multinomial)
@@ -290,6 +291,7 @@ export(mp_opt_attempted)
 export(mp_optimize)
 export(mp_optimized_spec)
 export(mp_optimizer_output)
+export(mp_other_dynamic_vars)
 export(mp_outflow)
 export(mp_par)
 export(mp_parameterization)

R/flow_frame.R

@@ -159,9 +159,21 @@ mp_state_dependence_frame = function(spec) {
   )
 }
 
-#' State and Flow Variable Names
+#' Dynamic Variable Names
 #' 
-#' Get the state and/or flow variables in a model specification.
+#' Get the state, flow, and other dynamic variables in a model specification.
+#' Dynamic variables are any variable that is updated every time step. 
+#' State and flow variables are special dynamic variables involved in 
+#' compartmental models that have been explicitly represented using functions 
+#' like \code{\link{mp_per_capita_flow}} that define flows among compartments
+#' (i.e., states).
+#' 
+#' State and flow variables will be identical regardless of the state update 
+#' method (e.g., \code{\link{mp_rk4}}), but other dynamic variables might
+#' appear for one particular state update method that does not appear for 
+#' another. For example, the first Runge Kutta step for a state in a model 
+#' with an \code{\link{mp_rk4}} updater, will not appear with an
+#' \code{\link{mp_euler}} updater.
 #' 
 #' @param spec Model specification (\code{\link{mp_tmb_model_spec}}).
 #' @param topological_sort Should the states and flows be 
@@ -175,9 +187,7 @@ mp_state_dependence_frame = function(spec) {
 #' @param trans Add a prefix to the names for indicating if a transformed
 #' version of the variables is preferred.
 #' 
-#' @return Character vector of names of all state and/or flow variables that 
-#' have been explicitly represented in the model using functions like
-#' \code{\link{mp_per_capita_flow}}.
+#' @return Character vector of names of all requested variables.
 #' 
 #' @examples
 #' si = mp_tmb_library("starter_models", "si", package = "macpan2")
@@ -223,6 +233,20 @@ mp_state_flow_vars = function(spec, topological_sort = FALSE, loops = "^$", tran
   )
 }
 
+#' @describeIn mp_vars All variables that are updated once per time-step.
+#' @export
+mp_dynamic_vars = function(spec) spec$all_dynamic_vars()
+
+#' @describeIn mp_vars All variables that are updated once per time-step,
+#' excluding those that are state and flow variables.
+#' @export
+mp_other_dynamic_vars = function(spec) {
+  setdiff(
+      mp_dynamic_vars(spec)
+    , mp_state_flow_vars(spec)
+  )
+}
+
 #' Data Frame Describing Each Change to Each State Variable
 #' 
 #' Get a data frame with one row for each change made to each state variable 

R/mp_tmb_model_spec.R

@@ -44,6 +44,7 @@ TMBModelSpec = function(
       , self$update_method$after()
     )
   }
+  self$expr_list_during = function() ExprList(self$update_method$during())
 
   self$all_derived_vars = function() {
     self$expr_list()$all_derived_vars()
@@ -60,6 +61,9 @@ TMBModelSpec = function(
   self$all_rhs_vars = function() {
     self$expr_list()$all_formula_vars("right")
   }
+  self$all_dynamic_vars = function() {
+    self$expr_list_during()$all_formula_vars("left")
+  }
   self$all_default_mats = function() {
     setdiff(
         self$all_default_vars()

man/mp_vars.Rd

@@ -0,0 +1,24 @@
+test_that("dynamic variables interact properly with the state updater", {
+  spec = test_cache_read("SPEC-macpan_base.rds")
+  euler_dyn_vars = spec |> mp_dynamic_vars()
+  euler_state_flow_vars = spec |> mp_state_flow_vars()
+  expect_in(euler_dyn_vars
+    , spec |> mp_rk4() |> mp_dynamic_vars()
+  )
+  expect_setequal(euler_dyn_vars
+    , spec |> mp_hazard() |> mp_dynamic_vars()
+  )
+  expect_setequal(euler_dyn_vars
+    , spec |> mp_discrete_stoch() |> mp_dynamic_vars()
+  )
+  expect_setequal(euler_state_flow_vars
+    , spec |> mp_rk4() |> mp_state_flow_vars()
+  )
+  expect_setequal(euler_state_flow_vars
+    , spec |> mp_hazard() |> mp_state_flow_vars()
+  )
+  expect_setequal(euler_state_flow_vars
+    , spec |> mp_discrete_stoch() |> mp_state_flow_vars()
+  )
+  
+})