refactor distribution names

NOAA-FIMS · Nov 17, 2024 · 8b0dbda · 8b0dbda
1 parent 325e436
commit 8b0dbda
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Showing 6 changed files with 168 additions and 168 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -15,9 +15,9 @@ export(Parameter)
 export(ParameterVector)
 export(Population)
 export(SetFIMSFunctions)
-export(TMBDlnormDistribution)
-export(TMBDmultinomDistribution)
-export(TMBDnormDistribution)
+export(DlnormDistribution)
+export(DmultinomDistribution)
+export(DnormDistribution)
 export(ToJSON)
 export(clear)
 export(clear_logs)

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_distributions.hpp"
 
 
 SEXP FIMS_objective_function;
@@ -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 → .../rcpp/rcpp_objects/rcpp_distributions.hpp b/...pp/rcpp_objects/rcpp_tmb_distribution.hpp → .../rcpp/rcpp_objects/rcpp_distributions.hpp
diff --git a/tests/testthat/test-fims-wrappers.R b/tests/testthat/test-fims-wrappers.R
@@ -3,15 +3,15 @@
 #   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"
 #     )
 #   )
 # )
@@ -24,7 +24,7 @@
 #     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")

diff --git a/tests/testthat/test-integration-fims-estimation-with-wrappers.R b/tests/testthat/test-integration-fims-estimation-with-wrappers.R
@@ -4,15 +4,15 @@ fleets <- list(
   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"
     )
   )
 )
@@ -25,7 +25,7 @@ default_parameters <- data_mile1 |>
     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")
@@ -44,7 +44,7 @@ modified_parameters <- list(
     BevertonHoltRecruitment.log_rzero.value = log(om_input_list[[1]]$R0),
     BevertonHoltRecruitment.log_devs.value = om_input_list[[1]]$logR.resid[-1],
     BevertonHoltRecruitment.log_devs.estimated = FALSE,
-    TMBDnormDistribution.log_sd.value = om_input_list[[1]]$logR_sd
+    DnormDistribution.log_sd.value = om_input_list[[1]]$logR_sd
   ),
   maturity = list(
     LogisticMaturity.inflection_point.value = om_input_list[[1]]$A50.mat,