New 464 load module

NAMESPACE

@@ -1,9 +1,27 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(AgeComp)
+export(BevertonHoltRecruitment)
+export(CreateTMBModel)
+export(DoubleLogisticSelectivity)
+export(EWAAgrowth)
 export(FIMSFrame)
 export(FIMSFrameAge)
+export(Fleet)
+export(Index)
+export(LogisticMaturity)
+export(LogisticSelectivity)
+export(Parameter)
+export(Population)
+export(TMBDlnormDistribution)
+export(TMBDmultinomDistribution)
+export(TMBDnormDistribution)
+export(clear)
+export(clear_logs)
 export(create_fims_rcpp_interface)
+export(get_fixed)
+export(get_random)
 export(m_agecomp)
 export(m_index)
 export(m_landings)

R/FIMS-package.R

@@ -6,5 +6,23 @@
 #' @import methods
 #' @importFrom ggplot2 .data
 #' @importFrom usethis use_template ui_stop
+#' @export CreateTMBModel
+#' @export get_fixed
+#' @export get_random
+#' @export clear
+#' @export clear_logs
+#' @export Parameter
+#' @export BevertonHoltRecruitment
+#' @export Fleet
+#' @export AgeComp
+#' @export Index
+#' @export Population
+#' @export TMBDnormDistribution
+#' @export LogisticMaturity
+#' @export LogisticSelectivity
+#' @export DoubleLogisticSelectivity
+#' @export EWAAgrowth
+#' @export TMBDlnormDistribution
+#' @export TMBDmultinomDistribution
 ## usethis namespace: end
 NULL

R/zzz.R

@@ -1,3 +1,5 @@
+Rcpp::loadModule(module = "fims", what = TRUE)
+
 .onUnload <- function(libpath) {
   library.dynam.unload("FIMS", libpath)
 }

inst/include/interface/interface.hpp

@@ -20,7 +20,6 @@
 // use isnan macro in math.h instead of TMB's isnan for fixing the r-cmd-check
 // issue
 #include <math.h>
-//#define TMB_LIB_INIT R_init_FIMS
 #include <TMB.hpp>
 
 // define REPORT, ADREPORT, and SIMULATE

inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp

@@ -14,7 +14,7 @@
 /**
  * @brief Rcpp interface for Data as an S4 object. To instantiate
  * from R:
- * fleet <- new(fims$Data)
+ * fleet <- new(Data)
  *
  */
 class DataInterfaceBase : public FIMSRcppInterfaceBase {
@@ -56,7 +56,7 @@ std::map<uint32_t, DataInterfaceBase*> DataInterfaceBase::live_objects;
 /**
  * @brief Rcpp interface for age comp data as an S4 object. To instantiate
  * from R:
- * acomp <- new(fims$AgeComp)
+ * acomp <- new(AgeComp)
  */
 class AgeCompDataInterface : public DataInterfaceBase {
  public:
@@ -123,7 +123,7 @@ class AgeCompDataInterface : public DataInterfaceBase {
 /**
  * @brief Rcpp interface for data as an S4 object. To instantiate
  * from R:
- * fleet <- new(fims$Index)
+ * fleet <- new(Index)
  */
 class IndexDataInterface : public DataInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp

@@ -47,7 +47,7 @@ std::map<uint32_t, FleetInterfaceBase*> FleetInterfaceBase::live_objects;
 /**
  * @brief Rcpp interface for Fleet as an S4 object. To instantiate
  * from R:
- * fleet <- new(fims$Fleet)
+ * fleet <- new(Fleet)
  *
  */
 class FleetInterface : public FleetInterfaceBase {

inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp

@@ -53,7 +53,7 @@ std::map<uint32_t, GrowthInterfaceBase*> GrowthInterfaceBase::live_objects;
 /**
  * @brief Rcpp interface for EWAAgrowth as an S4 object. To instantiate
  * from R:
- * ewaa <- new(fims$EWAAgrowth)
+ * ewaa <- new(EWAAgrowth)
  *
  */
 class EWAAGrowthInterface : public GrowthInterfaceBase {

inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp

@@ -56,7 +56,7 @@ std::map<uint32_t, MaturityInterfaceBase*> MaturityInterfaceBase::live_objects;
 
 /**
  * @brief Rcpp interface for logistic maturity as an S4 object. To
- * instantiate from R: logistic_maturity <- new(fims$logistic_maturity)
+ * instantiate from R: logistic_maturity <- new(logistic_maturity)
  */
 class LogisticMaturityInterface : public MaturityInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp

@@ -49,7 +49,7 @@ std::map<uint32_t, PopulationInterfaceBase*>
 /**
  * @brief Rcpp interface for a new Population. To instantiate
  * from R:
- * population <- new(fims$population)
+ * population <- new(population)
  */
 class PopulationInterface : public PopulationInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp

@@ -65,7 +65,7 @@ std::map<uint32_t, RecruitmentInterfaceBase*>
 /**
  * @brief Rcpp interface for Beverton-Holt as an S4 object. To instantiate
  * from R:
- * beverton_holt <- new(fims$beverton_holt)
+ * beverton_holt <- new(beverton_holt)
  */
 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp

@@ -56,7 +56,7 @@ std::map<uint32_t, SelectivityInterfaceBase*>
 
 /**
  * @brief Rcpp interface for logistic selectivity as an S4 object. To
- * instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
+ * instantiate from R: logistic_selectivity <- new(logistic_selectivity)
  */
 class LogisticSelectivityInterface : public SelectivityInterfaceBase {
  public:
@@ -133,7 +133,7 @@ class LogisticSelectivityInterface : public SelectivityInterfaceBase {
 
 /**
  * @brief Rcpp interface for logistic selectivity as an S4 object. To
- * instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
+ * instantiate from R: logistic_selectivity <- new(logistic_selectivity)
  */
 class DoubleLogisticSelectivityInterface : public SelectivityInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp

@@ -58,7 +58,7 @@ std::map<uint32_t,
 /**
  * @brief Rcpp interface for Dnorm as an S4 object. To instantiate
  * from R:
- * dnorm_ <- new(fims$TMBDnormDistribution)
+ * dnorm_ <- new(TMBDnormDistribution)
  *
  */
 class DnormDistributionsInterface : public DistributionsInterfaceBase {
@@ -128,7 +128,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
 /**
  * @brief Rcpp interface for Dlnorm as an S4 object. To instantiate
  * from R:
- * dlnorm_ <- new(fims$TMBDlnormDistribution)
+ * dlnorm_ <- new(TMBDlnormDistribution)
  *
  */
 class DlnormDistributionsInterface : public DistributionsInterfaceBase {
@@ -200,7 +200,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
 /**
  * @brief Rcpp interface for Dmultinom as an S4 object. To instantiate
  * from R:
- * dmultinom_ <- new(fims$TMBDmultinomDistribution)
+ * dmultinom_ <- new(TMBDmultinomDistribution)
  *
  */
 // template <typename Type>

tests/testthat/test-data-object.R

@@ -23,32 +23,30 @@ fleet_names_index <- dplyr::filter(
 nindex <- length(fleet_names_index)
 
 test_that("Can add index data to model", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
 
   indexdat <- vector(mode = "list", length = nindex)
   names(indexdat) <- fleet_names_index
 
   for (index_i in 1:nindex) {
-    index <- fims$Index
+    index <- Index
     indexdat[[fleet_names_index[index_i]]] <- new(index, nyears)
     expect_silent(indexdat[[fleet_names_index[index_i]]] <-
       m_index(age_frame, fleet_names_index[index_i]))
   }
 
-  fims$clear()
+  clear()
 })
 
 test_that("Can add agecomp data to model", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
 
   agecompdat <- vector(mode = "list", length = nagecomp)
   names(agecompdat) <- fleet_names_agecomp
 
   for (fleet_f in 1:nagecomp) {
-    agecompdat[[fleet_names_agecomp[fleet_f]]] <- new(fims$AgeComp, nyears, nages)
+    agecompdat[[fleet_names_agecomp[fleet_f]]] <- new(AgeComp, nyears, nages)
     expect_silent(agecompdat[[fleet_names_agecomp[fleet_f]]]$age_comp_data <-
       m_agecomp(age_frame, fleet_names_agecomp[fleet_f]))
   }
 
-  fims$clear()
+  clear()
 })

tests/testthat/test-ewaa.r

@@ -1,14 +1,13 @@
 data(package = "FIMS")
 
 test_that("ewaa data can be added to model", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
-  ewaa_growth <- new(fims$EWAAgrowth)
+  ewaa_growth <- new(EWAAgrowth)
   age_frame <- FIMSFrameAge(data_mile1)
   ewaa_growth$ages <- m_ages(age_frame)
   ewaa_growth$weights <- m_weightatage(age_frame)
   expect_equal(ewaa_growth$evaluate(1), 0.00053065552)
 
-  ewaa_growth2 <- new(fims$EWAAgrowth)
+  ewaa_growth2 <- new(EWAAgrowth)
   ewaa_growth2$ages <- c(ewaa_growth$ages, 12)
   ewaa_growth2$weights <- m_weightatage(age_frame)
   expect_error(
@@ -17,5 +16,5 @@ test_that("ewaa data can be added to model", {
     ignore.case = FALSE
   )
 
-  fims$clear()
+  clear()
 })

tests/testthat/test-fims-rcpp.R

@@ -1,10 +1,9 @@
 test_that("Rcpp interface works for modules", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
 
-  expect_no_error(parameter <- new(fims$Parameter, .1))
-  expect_no_error(beverton_holt <- new(fims$BevertonHoltRecruitment))
-  expect_no_error(logistic_selectivity <- new(fims$LogisticSelectivity))
-  expect_no_error(ewaa_growth <- new(fims$EWAAgrowth))
+  expect_no_error(parameter <- new(Parameter, .1))
+  expect_no_error(beverton_holt <- new(BevertonHoltRecruitment))
+  expect_no_error(logistic_selectivity <- new(LogisticSelectivity))
+  expect_no_error(ewaa_growth <- new(EWAAgrowth))
   logistic_selectivity$slope$value <- .7
   logistic_selectivity$inflection_point$value <- 5.0
 
@@ -18,5 +17,5 @@ test_that("Rcpp interface works for modules", {
   expect_equal(ewaa_growth$get_id(), 1)
   expect_equal(beverton_holt$get_id(), 1)
 
-  fims$clear()
+  clear()
 })

tests/testthat/test-fleet-interface.R

@@ -1,18 +1,17 @@
 test_that("Fleet: selectivity IDs can be added to the
 fleet module", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
 
   # Create selectivity for fleet 1
-  selectivity_fleet1 <- new(fims$LogisticSelectivity)
+  selectivity_fleet1 <- new(LogisticSelectivity)
   expect_equal((selectivity_fleet1$get_id()), 1)
 
   # Create selectivity for fleet 2
-  selectivity_fleet2 <- new(fims$LogisticSelectivity)
+  selectivity_fleet2 <- new(LogisticSelectivity)
   expect_equal((selectivity_fleet2$get_id()), 2)
 
   # Add selectivity to fleet
-  fleet1 <- new(fims$Fleet)
-  fleet2 <- new(fims$Fleet)
+  fleet1 <- new(Fleet)
+  fleet2 <- new(Fleet)
 
   # Expect code produces no output, error, message, or warnings
   expect_silent(fleet1$SetSelectivity(selectivity_fleet1$get_id()))
@@ -21,42 +20,38 @@ fleet module", {
   # Expect code produces error when ID of selectivity is a character string
   expect_error(fleet1$SetSelectivity("id"))
 
-  fims$clear()
+  clear()
 })
 
 
 test_that("Fleet: SetAgeCompLikelihood works", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
-  fleet <- new(fims$Fleet)
+  fleet <- new(Fleet)
 
   expect_silent(fleet$SetAgeCompLikelihood(1))
 
-  fims$clear()
+  clear()
 })
 
 test_that("Fleet: SetIndexLikelihood works", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
-  fleet <- new(fims$Fleet)
+  fleet <- new(Fleet)
 
   expect_silent(fleet$SetIndexLikelihood(1))
 
-  fims$clear()
+  clear()
 })
 
 test_that("Fleet: SetObservedAgeCompData works", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
-  fleet <- new(fims$Fleet)
+  fleet <- new(Fleet)
 
   expect_silent(fleet$SetObservedAgeCompData(1))
 
-  fims$clear()
+  clear()
 })
 
 test_that("Fleet: SetObservedIndexData works", {
-  fims <- Rcpp::Module("fims", PACKAGE = "FIMS")
-  fleet <- new(fims$Fleet)
+  fleet <- new(Fleet)
 
   expect_silent(fleet$SetObservedIndexData(1))
 
-  fims$clear()
+  clear()
 })