fix #350

Author: stevencarlislewalker

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: macpan2
 Title: Fast and Flexible Compartmental Modelling
-Version: 3.2.2
+Version: 3.3.0
 Authors@R: c(
   person("Steve Walker", email="swalk@mcmaster.ca", role=c("cre", "aut")),
   person("Weiguang Guan", role="aut"),

R/fit_methods.R

@@ -113,7 +113,7 @@ mp_tmb_coef.TMBSimulator = function(model, back_transform = TRUE, ...) {
     }
     tab = bind_rows(tab)
   }
-  tab
+  rm_no_info_coef_cols(tab)
 }
 
 #' @export

R/formula_list_generators.R

@@ -1157,4 +1157,8 @@ to_change_component.formula = function(x) Formula(x)
 mp_reduce = function(model) UseMethod("mp_reduce")
 
 #' @export
-mp_reduce.TMBModelSpec = function(model) model$expand()
+mp_reduce.TMBModelSpec = function(model) {
+  msg = 
+  warning("mp_reduce() is deprecated. Please use mp_expand() instead.")
+  model$expand()
+}

R/lists.R

@@ -93,22 +93,55 @@ melt_default_matrix_list = function(x, zeros_are_blank = TRUE, simplify_as_scala
     |> lapply(melt_matrix, zeros_are_blank)
     |> bind_rows(.id = "matrix")
   )
-  if (simplify_as_scalars) {
-    rm_rs = all(f$row == "")
-    rm_cs = all(f$col == "")
-    if (rm_rs) f$row = NULL
-    if (rm_cs) f$col = NULL
-    if (rm_rs & rm_cs) {
-      nms = colnames(f)
-      mat_col = nms == "matrix"
-      if (any(mat_col)) names(f)[mat_col] = "quantity"
-    }
-  }
+  if (simplify_as_scalars) f = rm_no_info_traj_cols(f)
 
   rownames(f) = NULL
   f
 }
 
+rm_no_info_traj_cols = function(x
+    , matrix_col_name = "quantity"
+    , collapse_traj = getOption("macpan2_collapse_traj")
+  ) {
+  
+  if (!collapse_traj) return(x)
+  
+  ## check if time is zero-info too? harder to know what
+  ## the implied value should be. argument for developers
+  ## to control context dependence of this implied value?
+  
+  urs = unique(x$row)
+  ucs = unique(x$col)
+  rm_rs = identical(urs, "") | identical(as.integer(urs), 0L)
+  rm_cs = identical(ucs, "") | identical(as.integer(ucs), 0L)
+  if (rm_rs) x$row = NULL
+  if (rm_cs) x$col = NULL
+  if (rm_rs & rm_cs) {
+    nms = colnames(x)
+    mat_col = nms == "matrix"
+    if (any(mat_col)) names(x)[mat_col] = matrix_col_name
+  }
+  return(x)
+}
+
+rm_no_info_coef_cols = function(x
+    , matrix_col_name = "par"
+    , collapse_coef = getOption("macpan2_collapse_coef")
+  ) {
+  if (!collapse_coef) return(x)
+  x = rm_no_info_traj_cols(x)
+  x$term = NULL
+  if (nrow(x) == 1L) {
+    if (x$type == "fixed") x$type = NULL
+    return(x)
+  }
+  cols_to_keep = vapply(x
+    , \(col) is.numeric(col) | (length(unique(col)) > 1L)
+    , logical(1L)
+  )
+  return(x[ , cols_to_keep, drop = FALSE])
+}
+
 melt_list_of_char_vecs = function(x) {
   n = vapply(x, length, integer(1L))
   list(

R/mp_tmb_calibrator.R

@@ -495,7 +495,9 @@ TMBCalDataStruc = function(data, time) {
       , "time_step", "timeStep", "TimeStep"
     )
     , matrix = c(
-        "matrix", "Matrix", "mat", "Mat", "variable", "var", "Variable", "Var"
+          "matrix", "Matrix", "mat", "Mat"
+        , "variable", "var", "Variable", "Var"
+        , "quantity", "Quantity"
     )
     , row = c("row", "Row")
     , col = c("col", "Col", "column", "Column")

R/tmb_model.R

@@ -549,7 +549,8 @@ mp_trajectory.TMBSimulator = function(model, include_initial = FALSE) {
   macro = getOption("macpan2_traj_tmb_macro") |> as.character()
   if (length(macro) > 1L) macro = macro[[1L]]
   if (length(macro) < 1L) macro = "simulate"
-  model[[macro]](.phases = phases) |> reset_rownames()
+  traj = model[[macro]](.phases = phases) |> reset_rownames()
+  rm_no_info_traj_cols(traj, "matrix")
 }
 
 #' @export
@@ -597,7 +598,8 @@ trajectory_par_util = function(simulator
   ) {
   phases = trajectory_phases_util(include_initial, include_final)
   vector = trajectory_vec_util(simulator, parameter_updates, value_column_name)
-  simulator$simulate(vector, .phases = phases)
+  traj = simulator$simulate(vector, .phases = phases)
+  rm_no_info_traj_cols(traj, "matrix")
 }
 
 trajectory_rep_util = function(n, simulator
@@ -764,7 +766,7 @@ mp_trajectory_sd.TMBSimulator = function(model
     vars = intersect(c("value", "conf.low", "conf.high"), names(r))
     r = backtrans(r, vars, "matrix", "sd", "value")
   }
-  r
+  rm_no_info_traj_cols(r, "matrix")
 } 
 
 #' @export
@@ -780,7 +782,7 @@ mp_trajectory_sd.TMBCalibrator = function(model
     , back_transform
   )
   traj$time = model$time_steps_obj$internal_to_external(traj$time)
-  return(traj)
+  rm_no_info_traj_cols(traj, "matrix")
 }
 
 #' @export
@@ -790,7 +792,7 @@ mp_trajectory_ensemble.TMBSimulator = function(model
   ) {
   best_pars = get_last_best_par(model$ad_fun())
   traj = model$report_ensemble(best_pars, .n = n, .probs = probs)
-  return(traj)
+  rm_no_info_traj_cols(traj, "matrix")
 }
 
 #' @export
@@ -876,7 +878,7 @@ mp_trajectory_sim.TMBSimulator = function(model
     , n
     , probs = c(0.025, 0.25, 0.5, 0.75, 0.975)
   ) {
-  r = model$simulate()
+  r = model$simulate() |> rm_no_info_traj_cols("matrix")
   r = r[, names(r) != "value", drop = FALSE]
   rr = (n
     |> replicate(model$simulate_values()) 

R/zzz.R

@@ -10,6 +10,8 @@
   options(
       macpan2_dll = "macpan2"
     , macpan2_verbose = FALSE
+    , macpan2_collapse_traj = FALSE
+    , macpan2_collapse_coef = FALSE
     , macpan2_default_loss = c("clamped_poisson", "poisson", "sum_of_squares", "neg_bin")
     , macpan2_tmb_type = NULL
     , macpan2_tmb_check = TRUE

man/figures/sir-ggplot-example-1.png

@@ -23,6 +23,8 @@ knitr::opts_chunk$set(
 ## Potentially Useful
 
 * `macpan2_verbose = FALSE` : Should the [TMB](https://github.com/kaskr/adcomp) computational engine used by `macpan2` be verbose or not (default). In particular, the `silent` argument of `TMB::MakeADFun` gets `!getOption("macpan2_verbose")`.
+* `macpan2_collapse_traj = FALSE` : Should `row` and `col` columns in data frames returned by `mp_trajectory_*()` functions be removed if they provide no information (e.g., if all variables in the trajectory are scalars).
+* `macpan2_collapse_coef = FALSE` : Should `row` and `col` columns in data frames returned by `mp_*_coef()` functions be removed if they provide no information (e.g., if all variables in the trajectory are scalars).
 * `macpan2_session_name = "default"` and `macpan2_log_dir = tools::R_user_dir("macpan2")` : Where to put log files generated by the engine. By default, the path to log files will be `{macpan2_log_dir}/.macpan2/{macpan2_session_name}/log.txt`. If you want to get access to the log file you should set the value of `macpan2_log_dir`. If you want to set `macpan2_log_dir` to the working directory at the time the model is created, you should set `macpan2_log_dir = ""`.
 * `macpan2_tol_hazard_div = 1e-8` : Used by the `mp_hazard()` function to generate an expression that calls the `proportions()` engine function. This option becomes the third tolerance argument to `proportions()`.
 * `macpan2_tol_singular_cov = `1e-6` : Used to determine if estimated

vignettes/options.Rmd

@@ -111,6 +111,8 @@ The simulation results are output as a data frame with the following columns:
 - `row`, `col`: Placeholders for variable components in more complicated structured models (not covered in this article, but useful for example when S and I in different age groups or geographic locations are tracked separately).
 - `value`: The simulated value for a particular state and time step.
 
+(Note that the `row` and `col` placeholders can be completely omitted by using `option(macpan2_collapse_traj = TRUE)` near the start of your script that calls `mp_trajectory()`)
+
 ## Processing Results
 
 `macpan2` does not provide any data manipulation or plotting tools (although there are a few in `macpan2helpers`). The philosophy is to focus on the engine and modelling interface, but to provide outputs in formats that are easy to use with other data processing packages, like `ggplot2`, `dplyr`, and `tidyr`, all of which readily make use of data in long format.