diff --git a/NAMESPACE b/NAMESPACE index b58292af..af7dad6e 100644 --- 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 index a30628a0..8f1da4e1 100644 --- 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 index e33ba789..f0164917 100644 --- a/R/create_default_parameters.R +++ b/R/create_default_parameters.R @@ -26,8 +26,8 @@ #' fleet1 <- survey1 <- list( #' selectivity = list(form = "LogisticSelectivity"), #' data_distribution = c( -#' Index = "TMBDlnormDistribution", -#' AgeComp = "TMBDmultinomDistribution" +#' Index = "DlnormDistribution", +#' AgeComp = "DmultinomDistribution" #' ) #' ) #' default_parameters <- fims_frame |> @@ -35,7 +35,7 @@ #' 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 index b3eb28b2..18a0f2d5 100644 --- 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 index df215249..eabd3848 100644 --- 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_("TMBDnormDistribution") + Rcpp::class_("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_("TMBDlnormDistribution") + Rcpp::class_("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_("TMBDmultinomDistribution") + Rcpp::class_("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/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_distribution.hpp similarity index 98% rename from inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp rename to inst/include/interface/rcpp/rcpp_objects/rcpp_distribution.hpp index cf5af08e..0fcb4faa 100644 --- a/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp +++ b/inst/include/interface/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 diff --git a/man/create_default_parameters.Rd b/man/create_default_parameters.Rd index fe6e9d95..dfaab6ac 100644 --- a/man/create_default_parameters.Rd +++ b/man/create_default_parameters.Rd @@ -9,7 +9,7 @@ create_default_parameters( data, fleets, recruitment = list(form = "BevertonHoltRecruitment", process_distribution = c(log_devs - = "TMBDnormDistribution")), + = "DnormDistribution")), growth = list(form = "EWAAgrowth"), maturity = list(form = "LogisticMaturity") ) @@ -66,8 +66,8 @@ fims_frame <- FIMSFrame(data_mile1) fleet1 <- survey1 <- list( selectivity = list(form = "LogisticSelectivity"), data_distribution = c( - Index = "TMBDlnormDistribution", - AgeComp = "TMBDmultinomDistribution" + Index = "DlnormDistribution", + AgeComp = "DmultinomDistribution" ) ) default_parameters <- fims_frame |> @@ -75,7 +75,7 @@ default_parameters <- fims_frame |> 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") diff --git a/tests/testthat/helper-integration-tests-setup.R b/tests/testthat/helper-integration-tests-setup.R index 2d8e2331..614f8541 100644 --- 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 index 948979a1..a3c2fc03 100644 --- 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" ) ) diff --git a/tests/testthat/test-fims-wrappers.R b/tests/testthat/test-fims-wrappers.R index 7c1fa658..ea77483c 100644 --- 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-initialize_modules.R b/tests/testthat/test-initialize_modules.R index bbd1be6f..a25a704d 100644 --- a/tests/testthat/test-initialize_modules.R +++ b/tests/testthat/test-initialize_modules.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" ) ) diff --git a/tests/testthat/test-integration-fims-estimation-with-wrappers.R b/tests/testthat/test-integration-fims-estimation-with-wrappers.R index a46f9cbd..a33b59f5 100644 --- 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]]$A50.mat, diff --git a/tests/testthat/test-rcpp-tmb-distributions.R b/tests/testthat/test-rcpp-distributions.R similarity index 90% rename from tests/testthat/test-rcpp-tmb-distributions.R rename to tests/testthat/test-rcpp-distributions.R index 3b7758fe..8e501520 100644 --- a/tests/testthat/test-rcpp-tmb-distributions.R +++ b/tests/testthat/test-rcpp-distributions.R @@ -10,7 +10,7 @@ test_that("normal_lpdf", { y <- stats::rnorm(1) # create a fims Rcpp object # initialize the Dnorm module - dnorm_ <- new(TMBDnormDistribution) + dnorm_ <- new(DnormDistribution) # populate class members dnorm_$x <- new(ParameterVector, y, 1) dnorm_$expected_values <- new(ParameterVector, 0, 1) @@ -25,7 +25,7 @@ test_that("normal_lpdf", { y <- stats::rnorm(10) # create a fims Rcpp object # initialize the Dnorm module - dnorm_ <- new(TMBDnormDistribution) + dnorm_ <- new(DnormDistribution) # populate class members dnorm_$x <- new(ParameterVector, y, 10) dnorm_$expected_values <- new(ParameterVector, 0, 1) @@ -40,7 +40,7 @@ test_that("normal_lpdf", { y <- stats::rnorm(10) # create a fims Rcpp object # initialize the Dnorm module - dnorm_ <- new(TMBDnormDistribution) + dnorm_ <- new(DnormDistribution) # populate class members dnorm_$x <- new(ParameterVector, y, 10) dnorm_$expected_values <- new(ParameterVector, rep(0, 10), 10) @@ -54,7 +54,7 @@ test_that("normal_lpdf", { # y <- stats::rnorm(10) # # create a fims Rcpp object # # initialize the Dnorm module - # dnorm_ <- new(TMBDnormDistribution) + # dnorm_ <- new(DnormDistribution) # # populate class members # dnorm_$x <- new(FIMS:::ParameterVector, y, 10) # dnorm_$expected_values <- new(FIMS:::ParameterVector, 0, 11) @@ -74,7 +74,7 @@ test_that("lognormal_lpdf", { # create a fims Rcpp object # initialize the Dlnorm module - dlnorm_ <- new(TMBDlnormDistribution) + dlnorm_ <- new(DlnormDistribution) # populate class members dlnorm_$x <- new(ParameterVector, y, 1) dlnorm_$expected_values <- new(ParameterVector, 0, 1) @@ -89,7 +89,7 @@ test_that("lognormal_lpdf", { # create a fims Rcpp object # initialize the Dlnorm module - dlnorm_ <- new(TMBDlnormDistribution) + dlnorm_ <- new(DlnormDistribution) # populate class members dlnorm_$x <- new(ParameterVector, y, 10) dlnorm_$expected_values <- new(ParameterVector, 0, 1) @@ -105,7 +105,7 @@ test_that("lognormal_lpdf", { # create a fims Rcpp object # initialize the Dlnorm module - dlnorm_ <- new(TMBDlnormDistribution) + dlnorm_ <- new(DlnormDistribution) # populate class members dlnorm_$x <- new(ParameterVector, y, 10) dlnorm_$expected_values <- new(ParameterVector, rep(0, 10), 10) @@ -120,7 +120,7 @@ test_that("lognormal_lpdf", { # # # create a fims Rcpp object # # initialize the Dlnorm module - # dlnorm_ <- new(TMBDlnormDistribution) + # dlnorm_ <- new(DlnormDistribution) # # populate class members # dlnorm_$x <- new(ParameterVector, y, 10) # dlnorm_$expected_values <- new(ParameterVector, 0, 11) @@ -135,7 +135,7 @@ test_that("multinomial_lpdf", { x <- t(stats::rmultinom(1, 100, p)) # create a fims Rcpp object # initialize the Dmultinom module - dmultinom_ <- new(TMBDmultinomDistribution) + dmultinom_ <- new(DmultinomDistribution) # populate class members dmultinom_$expected_values <- new(ParameterVector, p, 10) dmultinom_$dims <- c(1, 10) diff --git a/tests/testthat/test-update_parameters.R b/tests/testthat/test-update_parameters.R index 060ef5ed..9e04b34a 100644 --- a/tests/testthat/test-update_parameters.R +++ b/tests/testthat/test-update_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" ) ) diff --git a/vignettes/fims-demo.Rmd b/vignettes/fims-demo.Rmd index e2097e70..5dae4b4b 100644 --- a/vignettes/fims-demo.Rmd +++ b/vignettes/fims-demo.Rmd @@ -62,8 +62,8 @@ Here, we define specifications for fleets, recruitment, growth, and maturity mod fleet1 <- survey1 <- list( selectivity = list(form = "LogisticSelectivity"), data_distribution = c( - Index = "TMBDlnormDistribution", - AgeComp = "TMBDmultinomDistribution" + Index = "DlnormDistribution", + AgeComp = "DmultinomDistribution" ) ) @@ -73,7 +73,7 @@ default_parameters <- fims_frame |> 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")