refactor(D*Distribution): Removes TMB from names

Removes TMB from Distribution names and files to clean up the code and allow the downstream R interface to also remove these names. This is part of ensuring that the code is portable. If we change from TMB in the future we do not want to have to rename these things when a distribution is just a distribution, it does not have to come from TMB. Thank you @msupernaw for these changes.
NOAA-FIMS · Nov 25, 2024 · 7f72769 · 7f72769
1 parent 1c55ee1
commit 7f72769
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Showing 15 changed files with 82 additions and 82 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,9 @@
 export(AgeComp)
 export(BevertonHoltRecruitment)
 export(CreateTMBModel)
+export(DlnormDistribution)
+export(DmultinomDistribution)
+export(DnormDistribution)
 export(DoubleLogisticSelectivity)
 export(EWAAgrowth)
 export(FIMSFrame)
@@ -15,9 +18,6 @@ export(Parameter)
 export(ParameterVector)
 export(Population)
 export(SetFIMSFunctions)
-export(TMBDlnormDistribution)
-export(TMBDmultinomDistribution)
-export(TMBDnormDistribution)
 export(ToJSON)
 export(clear)
 export(clear_logs)

diff --git a/R/FIMS-package.R b/R/FIMS-package.R
@@ -21,12 +21,12 @@
 #' @export Index
 #' @export Population
 #' @export ParameterVector
-#' @export TMBDnormDistribution
+#' @export DnormDistribution
 #' @export LogisticMaturity
 #' @export LogisticSelectivity
 #' @export DoubleLogisticSelectivity
 #' @export EWAAgrowth
-#' @export TMBDlnormDistribution
-#' @export TMBDmultinomDistribution
+#' @export DlnormDistribution
+#' @export DmultinomDistribution
 ## usethis namespace: end
 NULL
diff --git a/R/create_default_parameters.R b/R/create_default_parameters.R
@@ -26,16 +26,16 @@
 #' fleet1 <- survey1 <- list(
 #'   selectivity = list(form = "LogisticSelectivity"),
 #'   data_distribution = c(
-#'     Index = "TMBDlnormDistribution",
-#'     AgeComp = "TMBDmultinomDistribution"
+#'     Index = "DlnormDistribution",
+#'     AgeComp = "DmultinomDistribution"
 #'   )
 #' )
 #' default_parameters <- fims_frame |>
 #'   create_default_parameters(
 #'     fleets = list(fleet1 = fleet1, survey1 = survey1),
 #'     recruitment = list(
 #'       form = "BevertonHoltRecruitment",
-#'       process_distribution = c(log_devs = "TMBDnormDistribution")
+#'       process_distribution = c(log_devs = "DnormDistribution")
 #'     ),
 #'     growth = list(form = "EWAAgrowth"),
 #'     maturity = list(form = "LogisticMaturity")
@@ -46,7 +46,7 @@ create_default_parameters <- function(
     fleets,
     recruitment = list(
       form = "BevertonHoltRecruitment",
-      process_distribution = c(log_devs = "TMBDnormDistribution")
+      process_distribution = c(log_devs = "DnormDistribution")
     ),
     growth = list(form = "EWAAgrowth"),
     maturity = list(form = "LogisticMaturity")) {
@@ -296,10 +296,10 @@ create_default_fleet <- function(fleets,
     (\(x) x$uncertainty)()
 
   index_distribution_default <- switch(index_distribution,
-    "TMBDnormDistribution" = create_default_TMBDnormDistribution(
+    "DnormDistribution" = create_default_DnormDistribution(
       value = index_uncertainty, input_type = "data", data = data
     ),
-    "TMBDlnormDistribution" = create_default_TMBDlnormDistribution(
+    "DlnormDistribution" = create_default_DlnormDistribution(
       value = index_uncertainty, input_type = "data", data = data
     )
   )
@@ -358,16 +358,16 @@ create_default_BevertonHoltRecruitment <- function(data) {
   return(default)
 }
 
-#' Create Default TMBDnormDistribution Parameters
+#' Create Default DnormDistribution Parameters
 #'
 #' @description
-#' Create default parameters for TMBDnormDistribution.
+#' Create default parameters for DnormDistribution.
 #' @param value Default value for `log_sd`.
 #' @param data An S4 object. FIMS input data.
 #' @param input_type A character. Specifies if input is data or process.
-#' @return A list of default parameters for TMBDnormDistribution.
+#' @return A list of default parameters for DnormDistribution.
 #' @noRd
-create_default_TMBDnormDistribution <- function(value = log(0.4), data, input_type = "data") {
+create_default_DnormDistribution <- function(value = log(0.4), data, input_type = "data") {
   # Check if input_type is valid
   valid_input_types <- c("data", "process")
   check_valid_input(input = input_type, valid_options = valid_input_types, arg_name = "input_type")
@@ -396,16 +396,16 @@ create_default_TMBDnormDistribution <- function(value = log(0.4), data, input_ty
   return(default)
 }
 
-#' Create Default TMBDlnormDistribution Parameters
+#' Create Default DlnormDistribution Parameters
 #'
 #' @description
-#' Create default parameters for TMBDlnormDistribution.
+#' Create default parameters for DlnormDistribution.
 #' @param value Default value for `log_sd`.
 #' @param data An S4 object. FIMS input data.
 #' @param input_type A character. Specifies if input is data or process.
-#' @return A list of default parameters for TMBDlnormDistribution.
+#' @return A list of default parameters for DlnormDistribution.
 #' @noRd
-create_default_TMBDlnormDistribution <- function(value = 0.1, data, input_type = "data") {
+create_default_DlnormDistribution <- function(value = 0.1, data, input_type = "data") {
   # Validate input value
   if (!is.numeric(value) || any(value <= 0, na.rm = TRUE)) {
     cli::cli_abort("The {.var value} argument must be positive numeric values.")
@@ -469,7 +469,7 @@ create_default_recruitment <- function(recruitment, data) {
   distribution_default <- NULL
   if (!is.null(distribution_input)) {
     distribution_default <- switch(distribution_input,
-      "TMBDnormDistribution" = create_default_TMBDnormDistribution(
+      "DnormDistribution" = create_default_DnormDistribution(
         value = 0.1,
         data = data,
         input_type = "process"

diff --git a/R/distribution_formulas.R b/R/distribution_formulas.R
@@ -166,7 +166,7 @@ initialize_data_distribution <- function(
   # Set up distribution based on `family` argument`
   if (family[["family"]] == "lognormal") {
     # create new Rcpp module
-    new_module <- new(TMBDlnormDistribution)
+    new_module <- new(DlnormDistribution)
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd <- new(
@@ -186,7 +186,7 @@ initialize_data_distribution <- function(
 
   if (family[["family"]] == "gaussian") {
     # create new Rcpp module
-    new_module <- new(TMBDnormDistribution)
+    new_module <- new(DnormDistribution)
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd$resize(length(sd$value))
@@ -206,7 +206,7 @@ initialize_data_distribution <- function(
 
   if (family[["family"]] == "multinomial") {
     #create new Rcpp module
-    new_module <- new(TMBDmultinomDistribution)
+    new_module <- new(DmultinomDistribution)
   }
 
   # setup link to observed data
@@ -267,7 +267,7 @@ initialize_process_distribution <- function(module,
   # Set up distribution based on `family` argument`
   if (family[["family"]] == "lognormal") {
     # create new Rcpp module
-    new_module <- new(TMBDlnormDistribution)
+    new_module <- new(DlnormDistribution)
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd <- new(
@@ -287,7 +287,7 @@ initialize_process_distribution <- function(module,
 
   if (family[["family"]] == "gaussian") {
     # create new Rcpp module
-    new_module <- new(TMBDnormDistribution)
+    new_module <- new(DnormDistribution)
 
     # populate logged standard deviation parameter with log of input
     new_module$log_sd$resize(length(sd$value))

diff --git a/inst/include/interface/rcpp/rcpp_interface.hpp b/inst/include/interface/rcpp/rcpp_interface.hpp
@@ -20,7 +20,7 @@
 #include "rcpp_objects/rcpp_population.hpp"
 #include "rcpp_objects/rcpp_recruitment.hpp"
 #include "rcpp_objects/rcpp_selectivity.hpp"
-#include "rcpp_objects/rcpp_tmb_distribution.hpp"
+#include "rcpp_objects/rcpp_distribution.hpp"
 
 
 SEXP FIMS_objective_function;
@@ -429,7 +429,7 @@ void clear() {
   DoubleLogisticSelectivityInterface::id_g = 1;
   DoubleLogisticSelectivityInterface::live_objects.clear();
 
-  // rcpp_tmb_distribution.hpp
+  // rcpp_distribution.hpp
   DistributionsInterfaceBase::id_g = 1;
   DistributionsInterfaceBase::live_objects.clear();
 
@@ -724,7 +724,7 @@ RCPP_MODULE(fims) {
       .method("get_id", &EWAAGrowthInterface::get_id)
       .method("evaluate", &EWAAGrowthInterface::evaluate);
 
-  Rcpp::class_<DnormDistributionsInterface>("TMBDnormDistribution")
+  Rcpp::class_<DnormDistributionsInterface>("DnormDistribution")
       .constructor()
       .method("get_id", &DnormDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
       .method("evaluate", &DnormDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")
@@ -734,7 +734,7 @@ RCPP_MODULE(fims) {
       .field("expected_values", &DnormDistributionsInterface::expected_values, "Mean of the distribution.")
       .field("log_sd", &DnormDistributionsInterface::log_sd, "The natural log of the standard deviation.");
 
-  Rcpp::class_<DlnormDistributionsInterface>("TMBDlnormDistribution")
+  Rcpp::class_<DlnormDistributionsInterface>("DlnormDistribution")
       .constructor()
       .method("get_id", &DlnormDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
       .method("evaluate", &DlnormDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")
@@ -744,7 +744,7 @@ RCPP_MODULE(fims) {
       .field("expected_values", &DlnormDistributionsInterface::expected_values, "Mean of the distribution on the log scale.")
       .field("log_sd", &DlnormDistributionsInterface::log_sd, "The natural log of the standard deviation of the distribution on the log scale.");
 
-  Rcpp::class_<DmultinomDistributionsInterface>("TMBDmultinomDistribution")
+  Rcpp::class_<DmultinomDistributionsInterface>("DmultinomDistribution")
       .constructor()
       .method("get_id", &DmultinomDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
       .method("evaluate", &DmultinomDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")

diff --git a/...pp/rcpp_objects/rcpp_tmb_distribution.hpp → ...e/rcpp/rcpp_objects/rcpp_distribution.hpp b/...pp/rcpp_objects/rcpp_tmb_distribution.hpp → ...e/rcpp/rcpp_objects/rcpp_distribution.hpp
@@ -6,8 +6,8 @@
  * source folder for reuse information.
  *
  */
-#ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_TMB_DISTRIBUTION_HPP
-#define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_TMB_DISTRIBUTION_HPP
+#ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_DISTRIBUTION_HPP
+#define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_DISTRIBUTION_HPP
 
 #include "../../../distributions/distributions.hpp"
 #include "../../interface.hpp"
@@ -83,7 +83,7 @@ std::map<uint32_t,
 /**
  * @brief Rcpp interface for Dnorm as an S4 object. To instantiate
  * from R:
- * dnorm_ <- new(TMBDnormDistribution)
+ * dnorm_ <- new(DnormDistribution)
  *
  */
 class DnormDistributionsInterface : public DistributionsInterfaceBase {
@@ -280,7 +280,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
 /**
  * @brief Rcpp interface for Dlnorm as an S4 object. To instantiate
  * from R:
- * dlnorm_ <- new(TMBDlnormDistribution)
+ * dlnorm_ <- new(DlnormDistribution)
  *
  */
 class DlnormDistributionsInterface : public DistributionsInterfaceBase {
@@ -484,7 +484,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
 /**
  * @brief Rcpp interface for Dmultinom as an S4 object. To instantiate
  * from R:
- * dmultinom_ <- new(TMBDmultinomDistribution)
+ * dmultinom_ <- new(DmultinomDistribution)
  *
  */
 // template <typename Type>

diff --git a/man/create_default_parameters.Rd b/man/create_default_parameters.Rd
diff --git a/tests/testthat/helper-integration-tests-setup.R b/tests/testthat/helper-integration-tests-setup.R
@@ -94,7 +94,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
   fishing_fleet$SetObservedAgeCompData(fishing_fleet_age_comp$get_id())
 
   # Set up fishery index data using the lognormal
-  fishing_fleet_index_distribution <- methods::new(TMBDlnormDistribution)
+  fishing_fleet_index_distribution <- methods::new(DlnormDistribution)
   # lognormal observation error transformed on the log scale
   fishing_fleet_index_distribution$log_sd$resize(om_input$nyr)
   for (y in 1:om_input$nyr) {
@@ -106,7 +106,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
   fishing_fleet_index_distribution$set_distribution_links("data", fishing_fleet$log_expected_index$get_id())
 
   # Set up fishery age composition data using the multinomial
-  fishing_fleet_agecomp_distribution <- methods::new(TMBDmultinomDistribution)
+  fishing_fleet_agecomp_distribution <- methods::new(DmultinomDistribution)
   fishing_fleet_agecomp_distribution$set_observed_data(fishing_fleet$GetObservedAgeCompDataID())
   fishing_fleet_agecomp_distribution$set_distribution_links("data", fishing_fleet$proportion_catch_numbers_at_age$get_id())
 
@@ -141,7 +141,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
   survey_fleet$SetObservedAgeCompData(survey_fleet_age_comp$get_id())
 
   # Set up survey index data using the lognormal
-  survey_fleet_index_distribution <- methods::new(TMBDlnormDistribution)
+  survey_fleet_index_distribution <- methods::new(DlnormDistribution)
   # lognormal observation error transformed on the log scale
   # sd = sqrt(log(cv^2 + 1)), sd is log transformed
   survey_fleet_index_distribution$log_sd$resize(om_input$nyr)
@@ -155,7 +155,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
 
   # Age composition data
 
-  survey_fleet_agecomp_distribution <- methods::new(TMBDmultinomDistribution)
+  survey_fleet_agecomp_distribution <- methods::new(DmultinomDistribution)
   survey_fleet_agecomp_distribution$set_observed_data(survey_fleet$GetObservedAgeCompDataID())
   survey_fleet_agecomp_distribution$set_distribution_links("data", survey_fleet$proportion_catch_numbers_at_age$get_id())
 
@@ -186,7 +186,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
   for (y in 1:(om_input$nyr - 1)) {
     recruitment$log_devs[y]$value <- om_input$logR.resid[y + 1]
   }
-  recruitment_distribution <- new(TMBDnormDistribution)
+  recruitment_distribution <- new(DnormDistribution)
   # set up logR_sd using the normal log_sd parameter
   # logR_sd is NOT logged. It needs to enter the model logged b/c the exp() is
   # taken before the likelihood calculation
@@ -449,15 +449,15 @@ setup_and_run_FIMS_with_wrappers <- function(iter_id,
     fleet1 = list(
       selectivity = list(form = "LogisticSelectivity"),
       data_distribution = c(
-        Index = "TMBDlnormDistribution",
-        AgeComp = "TMBDmultinomDistribution"
+        Index = "DlnormDistribution",
+        AgeComp = "DmultinomDistribution"
       )
     ),
     survey1 = list(
       selectivity = list(form = "LogisticSelectivity"),
       data_distribution = c(
-        Index = "TMBDlnormDistribution",
-        AgeComp = "TMBDmultinomDistribution"
+        Index = "DlnormDistribution",
+        AgeComp = "DmultinomDistribution"
       )
     )
   )
@@ -467,7 +467,7 @@ setup_and_run_FIMS_with_wrappers <- function(iter_id,
       fleets = fleets,
       recruitment = list(
         form = "BevertonHoltRecruitment",
-        process_distribution = c(log_devs = "TMBDnormDistribution")
+        process_distribution = c(log_devs = "DnormDistribution")
       ),
       growth = list(form = "EWAAgrowth"),
       maturity = list(form = "LogisticMaturity")
@@ -489,7 +489,7 @@ setup_and_run_FIMS_with_wrappers <- function(iter_id,
       BevertonHoltRecruitment.log_rzero.value = log(om_input$R0),
       BevertonHoltRecruitment.log_devs.value = om_input$logR.resid[-1],
       BevertonHoltRecruitment.log_devs.estimated = FALSE,
-      TMBDnormDistribution.log_sd.value = om_input$logR_sd
+      DnormDistribution.log_sd.value = om_input$logR_sd
     ),
     maturity = list(
       LogisticMaturity.inflection_point.value = om_input$A50.mat,

diff --git a/tests/testthat/test-create_default_parameters.R b/tests/testthat/test-create_default_parameters.R
@@ -4,8 +4,8 @@ data <- FIMSFrame(data_mile1)
 fleet1 <- survey1 <- list(
   selectivity = list(form = "LogisticSelectivity"),
   data_distribution = c(
-    Index = "TMBDlnormDistribution",
-    AgeComp = "TMBDmultinomDistribution"
+    Index = "DlnormDistribution",
+    AgeComp = "DmultinomDistribution"
   )
 )
 
@@ -31,8 +31,8 @@ test_that("create_default_parameters detects missing fleet names", {
   invalid_fleet <- list(
     selectivity = list(form = "LogisticSelectivity"),
     data_distribution = c(
-      Index = "TMBDlnormDistribution",
-      AgeComp = "TMBDmultinomDistribution"
+      Index = "DlnormDistribution",
+      AgeComp = "DmultinomDistribution"
     )
   )