definition and windows compiling

.github/workflows/R-CMD-check.yaml

@@ -52,3 +52,5 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual", "--no-build-vignettes")'
+          error_on: '"error"'

Makefile

@@ -114,15 +114,15 @@ doc-update: R/*.R misc/dev/dev.cpp
 
 pkg-build:: ../macpan2_$(VERSION).tar.gz
 ../macpan2_$(VERSION).tar.gz: DESCRIPTION man/*.Rd R/*.R src/*.cpp tests/testthat/test-*.R tests/testthat.R inst/starter_models/**/*.csv inst/starter_models/**/*.json
-	R CMD build --no-build-vignettes .
+	cd .. && R CMD build --no-build-vignettes macpan2
 
 
 pkg-check: ../macpan2_$(VERSION).tar.gz
-	R CMD check ../macpan2_$(VERSION).tar.gz
+	cd .. && R CMD check macpan2_$(VERSION).tar.gz
 
 
 pkg-install: ../macpan2_$(VERSION).tar.gz
-	R CMD INSTALL --no-multiarch --install-tests ../macpan2_$(VERSION).tar.gz
+	cd .. && R CMD INSTALL --no-multiarch --install-tests macpan2_$(VERSION).tar.gz
 
 
 compile-dev: misc/dev/dev.cpp

R/formula_data.R

@@ -1,8 +1,8 @@
-FormulaData = function(frame, reference_index_list) {
+FormulaData = function(frame, reference_index_list, labelling_names_list) {
   self = Base()
   self$frame = frame
   self$reference_index_list = reference_index_list
-
+  self$labelling_names_list = labelling_names_list
   return_object(self, "FormulaData")
 }
 

R/link.R

@@ -18,14 +18,15 @@
 #' ```
 #'
 #' @export
-Link = function(frame, column_map, reference_index_list) {
+Link = function(frame, column_map, reference_index_list, labelling_names_list) {
   self = Base()
   self$frame = frame
   self$column_map = column_map
   self$reference_index_list = reference_index_list
-  self$labelling_names_list = function() {
-    lapply(self$reference_index_list, getElement, "labelling_names")
-  }
+  self$labelling_names_list = labelling_names_list
+  # function() {
+  #   lapply(self$reference_index_list, getElement, "labelling_names")
+  # }
   self$table_names = function() names(self$column_map)
   self$labels_for = list()
   self$labels_frame = function() {
@@ -65,6 +66,7 @@ Link = function(frame, column_map, reference_index_list) {
     Link(self$frame[i, , drop = FALSE]
       , column_map = self$column_map
       , reference_index_list = self$reference_index_list
+      , labelling_names_list = self$labelling_names_list
     )
   }
   self$partition = self$partition_for[[1L]]()  ## hack! should probably have a method and then change the partition field in Index to a method as well
@@ -102,10 +104,10 @@ FrameGetter = function(link, dimension_name) {
   self$get_partition = function() self$get_frame() |> Partition()
   self$get_index = function() Index(
     self$get_partition(),
-    self$link$labelling_names_list()[[self$dimension_name]]
+    self$link$labelling_names_list[[self$dimension_name]]
   )
   self$get_labels = function() {
-    i = self$link$labelling_names_list()[[self$dimension_name]]
+    i = self$link$labelling_names_list[[self$dimension_name]]
     f = self$get_frame()[, i, drop = FALSE]
     l = as.list(f)
     paste_args = c(l, sep = ".")
@@ -125,7 +127,7 @@ initial_reference_index_list = function(index, dimension_name) {
   setNames(list(index), dimension_name)
 }
 
-## TODO XXX
+
 initial_labelling_names_list = function(labelling_names, dimension_name) {
   setNames(
     list(labelling_names),
@@ -205,14 +207,16 @@ merge_util = function(x, y, by.x, by.y) {
 
   z_column_map = c(x_cmap, y_cmap)
   z_reference_index_list = c(x$reference_index_list, y$reference_index_list)
+  z_lab_names_list = c(x$labelling_names_list, y$labelling_names_list)
 
   ## ----
   ## wrap up the result with provenance-preserving column map
   ## ----
   Link(
     z,
     z_column_map,
-    z_reference_index_list
+    z_reference_index_list,
+    z_lab_names_list
   )
 }
 
@@ -230,10 +234,11 @@ filter_by_list = function(x_orig, y_orig, by_list) {
 }
 
 #' @export
-init_merge = function(frame, dimension_name, reference_index) {
+init_merge = function(frame, dimension_name, reference_index, labelling_names) {
   Link(frame
     , initial_column_map(names(frame), dimension_name)
     , initial_reference_index_list(reference_index, dimension_name)
+    , initial_labelling_names_list(labelling_names, dimension_name)
   )
 }
 
@@ -288,7 +293,7 @@ explicit_provenance = function(x, col_nm) {
   )
 
   f = x$frame
-  l = x$labelling_names_list()
+  l = x$labelling_names_list
 
   orig_col = f[[col_nm]]
   for (tab_nm in tabs_to_fix) {
@@ -297,6 +302,7 @@ explicit_provenance = function(x, col_nm) {
     m[[tab_nm]][[col_nm]] = new_col_nm
   }
   f[[col_nm]] = NULL
+  ## TODO: update with four-arg form of Link
   Link(f, m, l)
 }
 
@@ -370,7 +376,7 @@ print.summary.Link = function(x, ...) {
 names.Link = function(x) names(x$frame)
 
 #' @export
-labelling_names.Link = function(x) x$labelling_names_list()
+labelling_names.Link = function(x) x$labelling_names_list
 
 
 link_format_picker = function(x

R/mp.R

@@ -144,7 +144,7 @@ mp_union.Link = function(...) {
     ) |> stop()
   }
   ## TODO: should really be checking for reference_index_list
-  labelling_names_list = method_apply(l, "labelling_names_list") |> unique()
+  labelling_names_list = lapply(l, getElement, "labelling_names_list") |> unique()
   if (length(labelling_names_list) != 1L) {
     msg_colon(
       msg(
@@ -157,7 +157,7 @@ mp_union.Link = function(...) {
     ) |> stop()
   }
   frame = mp_rbind(...)
-  FormulaData(frame, l[[1L]]$reference_index_list)
+  FormulaData(frame, l[[1L]]$reference_index_list, l[[1L]]$labelling_names_list)
 }
 
 #' @export
@@ -194,7 +194,7 @@ mp_choose = function(x, subset_name, ...) {
       p = p$filter(vals, .wrt = cc)
     }
   }
-  init_merge(p$frame(), subset_name, x$reference_index())
+  init_merge(p$frame(), subset_name, x$reference_index(), x$labelling_names)
 }
 
 #' @export
@@ -205,7 +205,7 @@ mp_choose_out = function(x, subset_name, ...) {
     vals = l[[cc]]
     p = p$filter_out(vals, .wrt = cc)
   }
-  init_merge(p$frame(), subset_name, x$labelling_names)
+  init_merge(p$frame(), subset_name, x$reference_index(), x$labelling_names)
 }
 
 #' @export
@@ -375,10 +375,10 @@ mp_rename = function(x, ...) {
 }
 
 #' @export
-mp_select = function(basis, grouping_dimension) {
-  frame = basis$partition$select(to_names(grouping_dimension))$frame()
-  nms = names(frame)[names(frame) %in% basis$labelling_names]
-  frame |> Index(labelling_names = nms, basis$partition)
+mp_select = function(index, grouping_dimension) {
+  frame = index$partition$select(to_names(grouping_dimension))$frame()
+  nms = names(frame)[names(frame) %in% index$labelling_names]
+  frame |> Index(labelling_names = nms, index)
 }
 
 #' @export

misc/experiments/refactorcpp.R

@@ -43,15 +43,19 @@ trans_rates = (trans_rates_sir
   |> mp_cartesian(contact)
 )
 
-mp_join(
+xx = mp_join(
   alive = mp_subset(state, Vital = "alive"),
   N = mp_select(state, "Loc.Age"),
   alive.N = "Loc.Age"
 )
 
-mp_choose(mp_select(state, "Loc.Age"), "N")
 
 
+mp_labels
+xx$reference_index_list$N$labelling_names
+yy = mp_formula_data(xx)
+yy$reference_index_list
+
 yy = Vector(state)
 yy$numbers()
 yy$set_numbers(Loc = c(cal = 1000, ham = 2000, que = 3000), Epi = "S")
@@ -118,8 +122,8 @@ trans_decomp = mp_decompose(
   , infectivity = "Loc"
   , susceptibility = "AgeInfection"
 )
-trans_decomp$linked_indices
 
+trans_decomp
 trans_decomp$formula
 trans_decomp$input_formula
 macpan2:::update_formula(g ~ y * x * z, g ~ friend)

src/macpan2.cpp

@@ -470,7 +470,6 @@ class ArgList {
             int j = m.rows();
             if (j == 1) {
               std::vector<int> v = get_as_int_vec(i);
-              // std::cout << "HI" << v[0] << std::endl;
               return v[0];
             }
             return j;