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new model definitions! with sir example
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,120 @@ | ||
| FormulaData = function(frame, reference_index_list, labelling_names_list) { | ||
| FormulaData = function(...) { | ||
| self = Base() | ||
| self$frame = frame | ||
| self$reference_index_list = reference_index_list | ||
| self$labelling_names_list = labelling_names_list | ||
| self$link_list = list(...) | ||
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|
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| labelling_names_list = (self$link_list | ||
| |> lapply(getElement, "labelling_names_list") | ||
| |> unname() | ||
| |> unique() | ||
| ) | ||
| stopifnot(length(labelling_names_list) == 1L) | ||
| self$labelling_names_list = labelling_names_list[[1L]] | ||
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| reference_index_list = (self$link_list | ||
| |> lapply(getElement, "reference_index_list") | ||
| |> unname() | ||
| |> unique() | ||
| ) | ||
| stopifnot(length(reference_index_list) == 1L) | ||
| self$reference_index_list = reference_index_list[[1L]] | ||
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| table_names = (self$link_list | ||
| |> method_apply("table_names") | ||
| |> unname() | ||
| |> unique() | ||
| ) | ||
| stopifnot(length(table_names) == 1L) | ||
| self$table_names = table_names[[1L]] | ||
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| self$labels_frame = function() { | ||
| (self$link_list | ||
| |> method_apply("labels_frame") | ||
| |> bind_rows() | ||
| ) | ||
| } | ||
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| self$positions_frame = function(zero_based = FALSE) { | ||
| positions_list = list() | ||
| for (i in seq_along(self$link_list)) { | ||
| positions_list[[i]] = list() | ||
| for (d in self$table_names) { | ||
| positions_list[[i]][[d]] = self$link_list[[i]]$positions_for[[d]](zero_based) | ||
| } | ||
| positions_list[[i]] = as.data.frame(positions_list[[i]]) | ||
| } | ||
| bind_rows(positions_list) | ||
| } | ||
|
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||
| return_object(self, "FormulaData") | ||
| } | ||
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| #' #' @export | ||
| #' print.FormulaData = function(x, ...) { | ||
| #' print(x$frame, row.names = FALSE) | ||
| #' } | ||
|
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||
|
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||
| #' @export | ||
| print.FormulaData = function(x, ...) { | ||
| print(x$frame, row.names = FALSE) | ||
| mp_formula_data = function(...) FormulaData(...) | ||
|
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||
| #' Indexed Expressions | ||
| #' | ||
| #' @param ... Formula objects that reference the columns in the | ||
| #' \code{index_data}, the vectors in \code{vector_list} and the matrices | ||
| #' in \code{unstructured_matrix_list}. | ||
| #' @param index_data An object produced using \code{\link{mp_formula_data}}. | ||
| #' @param vector_list Named list of objected produced using | ||
| #' \code{\link{mp_vector}}. | ||
| #' @param unstructured_matrix_list Named list of objects that can be coerced | ||
| #' to a matrix. | ||
| #' | ||
| #' @export | ||
| IndexedExpressions = function(... | ||
| , index_data | ||
| , vector_list = list() | ||
| , unstructured_matrix_list = list() | ||
| ) { | ||
| self = Base() | ||
| self$formulas = list(...) | ||
| self$index_data = index_data | ||
| self$vector_list = vector_list | ||
| self$unstructured_matrix_list = unstructured_matrix_list | ||
| self$int_vecs = function(zero_based = FALSE) { | ||
| self$index_data$positions_frame(zero_based) |> as.list() | ||
| } | ||
| self$mats_list = function() { | ||
| all_vars = (self$formulas | ||
| |> lapply(macpan2:::formula_components) | ||
| |> lapply(getElement, "variables") | ||
| |> unlist(use.names = FALSE, recursive = FALSE) | ||
| |> unique() | ||
| ) | ||
| derived = setdiff(all_vars, c( | ||
| names(self$vector_list), | ||
| self$index_data$table_names, | ||
| names(self$unstructured_matrix_list) | ||
| )) | ||
| derived = (empty_matrix | ||
| |> list() | ||
| |> rep(length(derived)) | ||
| |> setNames(derived) | ||
| ) | ||
| vectors = method_apply(self$vector_list, "numbers") | ||
| unstruc = self$unstructured_matrix_list | ||
| c(vectors, unstruc, derived) | ||
| } | ||
| self$simulate = function(time_steps = 1L) { | ||
| simple_sims( | ||
| self$formulas, | ||
| time_steps, | ||
| self$int_vecs(zero_based = TRUE), | ||
| self$mats_list() | ||
| ) | ||
| } | ||
| return_object(self, "IndexedExpressions") | ||
| } | ||
|
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||
|
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||
| #' @export | ||
| mp_indexed_exprs = IndexedExpressions | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| #' @export | ||
| mp_tmb_simulator = function(expr_list = ExprList() | ||
| , index_data = list() | ||
| , indexed_vecs = list() | ||
| , unstruc_mats = list() | ||
| , time_steps = 0L | ||
| , mats_to_save = names(indexed_vecs) | ||
| , mats_to_return = names(indexed_vecs) | ||
| , ... | ||
| ) { | ||
| int_vecs = (index_data | ||
| |> method_apply("positions_frame", zero_based = TRUE) | ||
| |> lapply(as.list) | ||
| |> unname() | ||
| |> unlist(recursive = FALSE) | ||
| ) | ||
| indexed_mats = lapply(indexed_vecs, as.matrix) | ||
|
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| all_vars = expr_list$all_formula_vars() | ||
|
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| derived_nms = setdiff(all_vars, c( | ||
| names(int_vecs), names(indexed_mats), names(unstruc_mats) | ||
| )) | ||
|
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| derived_mats = (empty_matrix | ||
| |> list() | ||
| |> rep(length(derived_nms)) | ||
| |> setNames(derived_nms) | ||
| ) | ||
|
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| mats = c(indexed_mats, unstruc_mats, derived_mats) | ||
| mats_list_options = list( | ||
| .mats_to_save = mats_to_save, | ||
| .mats_to_return = mats_to_return | ||
| ) | ||
| engine_methods = EngineMethods(int_vecs = do.call(IntVecs, int_vecs)) | ||
| tmb_model = TMBModel( | ||
| init_mats = do.call(MatsList, c(mats, mats_list_options)) | ||
| , expr_list = expr_list | ||
| , engine_methods = engine_methods | ||
| , time_steps = Time(time_steps) | ||
| , ... | ||
| ) | ||
| tmb_model$simulator() | ||
| } |
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