docs and fix #133

NAMESPACE

@@ -4,6 +4,7 @@ S3method(Index,Index)
 S3method(Index,Partition)
 S3method(Index,data.frame)
 S3method(Vector,Index)
+S3method(Vector,Vector)
 S3method(Vector,data.frame)
 S3method(Vector,numeric)
 S3method(as.data.frame,Index)

R/index_to_tmb.R

@@ -1,3 +1,13 @@
+#' TMB Simulator from Dynamic Model
+#'
+#' @param dynamic_model Object product by \code{\link{dynamic_model}}.
+#' @param vectors Named list of named vectors as initial values for the
+#' simulations that are referenced in the expression list in the dynamic model.
+#' @param unstruc_mats = Named list of objects that can be coerced to
+#' numerical matrices that are used in the expression list of the
+#' dynamic model.
+#' @inheritParams TMBModel
+#'
 #' @importFrom oor method_apply
 #' @export
 mp_tmb_simulator = function(dynamic_model
@@ -46,6 +56,12 @@ mp_tmb_simulator.DynamicModel = function(dynamic_model
     indexed_mats = dynamic_model$init_vecs
     mats_to_save = names(indexed_mats)
   } else {
+    for (v in names(vectors)) {
+      vectors[[v]] = Vector(
+        vectors[[v]],
+        dynamic_model$init_vecs[[v]]$index
+      )
+    }
     indexed_mats = lapply(vectors, as.matrix)
   }
   if (is.null(unstruc_mats)) {

R/model_def_run.R

@@ -111,6 +111,10 @@ DynamicModel = function(expr_list = ExprList(), ledgers = list(), init_vecs = li
 }
 
 
+#' Dynamic Model
+#'
+#'
+#'
 #' @export
 mp_dynamic_model = DynamicModel
 

R/vector.R

@@ -58,13 +58,19 @@ Vector.numeric = function(x, index, ...) {
   do.call(v$set_numbers, args)
 }
 
+#' @export
+Vector.Vector = function(x, index, ...) {
+  Vector(x$numbers(), index, ...)
+}
+
 #' @export
 Vector.Index = function(x, ...) {
   self = Base()
   self$index = x
   self$.numbers = zero_vector(self$index$labels())
   self$numbers = function(...) {
     l = list(...)
+    ## check if all numbers
     if (length(l) == 0L) return(self$.numbers)
     i = mp_subset(self$index, ...)$labels()
     self$.numbers[i]
@@ -131,15 +137,17 @@ print.Vector = function(x, ...) print(x$numbers())
 names.Vector = function(x) x$numbers() |> names()
 
 #' @export
-as.matrix.Vector = function(x, ...) x$numbers() |> as.matrix()
+as.matrix.Vector = function(x, ...) {
+  x$numbers() |> as.matrix()
+}
 
 zero_vector = function(labels) setNames(rep(0, length(labels)), labels)
 
 #' Stub
-#' 
+#'
 #' This documentation was originally in [mp_index()] and should be cleaned up
 #' See issue #131
-#' 
+#'
 #' #' These labels can be used to create 'multidimensional' names for the elements
 #' of vectors. Here is the above example expressed in vector form.
 #' ```{r, echo = FALSE}
@@ -161,7 +169,7 @@ zero_vector = function(labels) setNames(rep(0, length(labels)), labels)
 #' ```{r, echo = FALSE}
 #' mp_vector(symp)$set_numbers(Epi = c(S = 1000))$set_numbers(Epi = c(I = 1), Symptoms = "severe")
 #' ```
-#' 
+#'
 #' @examples
 #' state = mp_index(
 #'   Epi = c("S", "I", "S", "I"),
@@ -173,7 +181,7 @@ zero_vector = function(labels) setNames(rep(0, length(labels)), labels)
 #'   |> mp_set_numbers(Epi = c(I = 1), Age = "old")
 #' )
 #' print(state_vector)
-#' 
+#'
 #' @export
 mp_vector = function(x, ...) UseMethod("mp_vector")