make FIMS run without age composition data

* add if statement in functions from R/initialize_modules.R to create a FIMS model without age comp data
* add an R test to run a FIMS model without age comp data

R/initialize_modules.R

@@ -408,12 +408,6 @@ initialize_selectivity <- function(parameters, data, fleet_name) {
 #' The initialized fleet module as an object.
 #' @noRd
 initialize_fleet <- function(parameters, data, fleet_name, linked_ids) {
-  if (any(is.na(linked_ids[c("selectivity", "index", "age_comp")]))) {
-    cli::cli_abort(c(
-      "{.var linked_ids} for {fleet_name} must include 'selectivity', 'index',
-      and 'age_comp' IDs."
-    ))
-  }
 
   module <- initialize_module(
     parameters = parameters,
@@ -423,12 +417,17 @@ initialize_fleet <- function(parameters, data, fleet_name, linked_ids) {
 
   module$SetSelectivity(linked_ids["selectivity"])
   module$SetObservedIndexData(linked_ids["index"])
-  module$SetObservedAgeCompData(linked_ids["age_comp"])
 
   fleet_types <- get_data(data) |>
       dplyr::filter(name == fleet_name) |>
       dplyr::pull(type) |>
       unique()
+
+  if ("age" %in% fleet_types &
+      "AgeComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_name]][["data_distribution"]])) {
+    module$SetObservedAgeCompData(linked_ids["age_comp"])
+  }
+
   if ("length" %in% fleet_types &
       "LengthComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_name]][["data_distribution"]])) {
     module$SetObservedLengthCompData(linked_ids["length_comp"])
@@ -616,14 +615,8 @@ initialize_fims <- function(parameters, data) {
       fleet_name = fleet_names[i]
     )
 
-    fleet_age_comp[[i]] <- initialize_age_comp(
-      data = data,
-      fleet_name = fleet_names[i]
-    )
-
     fleet_module_ids <- c(
       index = fleet_index[[i]]$get_id(),
-      age_comp = fleet_age_comp[[i]]$get_id(),
       selectivity = fleet_selectivity[[i]]$get_id()
     )
 
@@ -632,6 +625,19 @@ initialize_fims <- function(parameters, data) {
       dplyr::pull(type) |>
       unique()
 
+    if ("age" %in% fleet_types &
+        "AgeComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_names[i]]][["data_distribution"]])) {
+      fleet_age_comp[[i]] <- initialize_age_comp(
+        data = data,
+        fleet_name = fleet_names[i]
+      )
+
+      fleet_module_ids <- c(
+        fleet_module_ids,
+        c(age_comp = fleet_age_comp[[i]]$get_id())
+      )
+    }
+
     if ("length" %in% fleet_types &
         "LengthComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_names[i]]][["data_distribution"]])) {
       fleet_length_comp[[i]] <- initialize_length_comp(
@@ -683,11 +689,14 @@ initialize_fims <- function(parameters, data) {
       data_type = "index"
     )
 
-    fleet_agecomp_distribution[[i]] <- initialize_data_distribution(
-      module = fleet[[i]],
-      family = multinomial(link = "logit"),
-      data_type = "agecomp"
-    )
+    if ("age" %in% fleet_types &
+       "AgeComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_names[i]]][["data_distribution"]])) {
+     fleet_agecomp_distribution[[i]] <- initialize_data_distribution(
+       module = fleet[[i]],
+       family = multinomial(link = "logit"),
+       data_type = "agecomp"
+     )
+   }
 
     if ("length" %in% fleet_types &
         "LengthComp" %in% names(parameters[["modules"]][["fleets"]][[fleet_names[i]]][["data_distribution"]])) {

tests/testthat/test-integration-fims-estimation-with-wrappers.R

@@ -231,7 +231,7 @@ test_that("estimation test of fims using wrapper functions", {
   )
 })
 
-test_that("estimation test with length comp using wrappers",{
+test_that("estimation test with age and length comp using wrappers",{
   # Load operating model data for the current iteration
   iter_id <- 1
   om_input <- om_input_list[[iter_id]]
@@ -322,3 +322,95 @@ test_that("estimation test with length comp using wrappers",{
     use_fimsfit = TRUE
   )
 })
+
+test_that("estimation test with length comp using wrappers",{
+  # Load operating model data for the current iteration
+  iter_id <- 1
+  om_input <- om_input_list[[iter_id]]
+  om_output <- om_output_list[[iter_id]]
+  em_input <- em_input_list[[iter_id]]
+
+  fims_data <- data1 |>
+    dplyr::filter(type != "age") |>
+    FIMS::FIMSFrame()
+
+  # Clear any previous FIMS settings
+  clear()
+
+  fleets <- list(
+    fleet1 = list(
+      selectivity = list(form = "LogisticSelectivity"),
+      data_distribution = c(
+        Index = "DlnormDistribution",
+        LengthComp = "DmultinomDistribution"
+      )
+    ),
+    survey1 = list(
+      selectivity = list(form = "LogisticSelectivity"),
+      data_distribution = c(
+        Index = "DlnormDistribution",
+        LengthComp = "DmultinomDistribution"
+      )
+    )
+  )
+
+  lengthcomp_parameters <- fims_data |>
+    create_default_parameters(
+      fleets = fleets,
+      recruitment = list(
+        form = "BevertonHoltRecruitment",
+        process_distribution = c(log_devs = "DnormDistribution")
+      ),
+      growth = list(form = "EWAAgrowth"),
+      maturity = list(form = "LogisticMaturity")
+    )
+
+  modified_parameters <- list(
+    fleet1 = list(
+      Fleet.log_Fmort.value = log(om_output_list[[1]]$f)
+    ),
+    survey1 = list(
+      LogisticSelectivity.inflection_point.value = 1.5,
+      LogisticSelectivity.slope.value = 2,
+      Fleet.log_q.value = log(om_output_list[[1]]$survey_q$survey1)
+    ),
+    recruitment = list(
+      BevertonHoltRecruitment.log_rzero.value = log(om_input_list[[1]]$R0),
+      BevertonHoltRecruitment.log_devs.value = om_input_list[[1]]$logR.resid[-1],
+      BevertonHoltRecruitment.log_devs.estimated = FALSE,
+      DnormDistribution.log_sd.value = om_input_list[[1]]$logR_sd
+    ),
+    maturity = list(
+      LogisticMaturity.inflection_point.value = om_input_list[[1]]$A50.mat,
+      LogisticMaturity.inflection_point.estimated = FALSE,
+      LogisticMaturity.slope.value = om_input_list[[1]]$slope.mat,
+      LogisticMaturity.slope.estimated = FALSE
+    ),
+    population = list(
+      Population.log_init_naa.value = log(om_output_list[[1]]$N.age[1, ])
+    )
+  )
+
+  parameters <- lengthcomp_parameters |>
+    update_parameters(
+      modified_parameters = modified_parameters
+    )
+
+  parameter_list <- initialize_fims(
+    parameters = parameters,
+    data = fims_data
+  )
+  fit <- fit_fims(parameter_list, optimize = TRUE)
+
+  clear()
+
+  validate_fims(
+    report = fit@report,
+    sdr = fit@estimates,
+    sdr_report = fit@estimates,
+    om_input = om_input_list[[iter_id]],
+    om_output = om_output_list[[iter_id]],
+    em_input = em_input_list[[iter_id]],
+    use_fimsfit = TRUE
+  )
+})