add length-age conversion matrix

tests/testthat/fixtures/simulate-length-test-data.r

@@ -38,11 +38,15 @@ for(i in seq_along(ages)){
 colnames(length_age_conversion) <- len_bins
 rownames(length_age_conversion) <- ages
 
+
+#add code to simulate length data
+length_data <- 0L
+
 on.exit(unlink(maindir, recursive = TRUE), add = TRUE)
 
 setwd(working_dir)
 on.exit(setwd(working_dir), add = TRUE)
 
-save(om_input_list, length_age_conversion,
+save(om_input_list, length_age_conversion, length_data,
   file = test_path("fixtures", "length_test_data.RData")
 )

tests/testthat/test-rcpp-fleet-interface.R

@@ -22,4 +22,30 @@ fleet module", {
   clear()
 })
 
+test_that("Fleet: length composition can be added to the
+fleet module", {
+
+   # set fishing fleet age comp data, need to set dimensions of age comps
+  fishing_fleet_length_comp <- new(LengthComp, om_input$nyr, om_input$nages)
+  fishing_fleet_length_comp$length_comp_data <- c(t(length_data)) * length(om_input_list$len_bins)
+
+  # Add selectivity to fleet
+  fleet1 <- new(Fleet)
+
+  fleet1$nages <- om_input$nages
+  fleet1$nyears <- om_input$nyr
+  fleet1$nlengths <- length(om_input_list$len_bins)
+  fleet1$age_length_conversion_matrix <- length_age_conversion #this should be a matrix of dim nages * nlengths
+  fleet1$log_Fmort <- methods::new(ParameterVector, log(om_output$f), om_input$nyr)
+  fleet1$log_Fmort$set_all_estimable(TRUE)
+  fleet1$log_q <- log(1.0)
+  fleet1$estimate_q <- FALSE
+  fleet1$random_q <- FALSE
 
+  # Set up fishery age composition data using the multinomial
+  fishing_fleet_lengthcomp_distribution <- methods::new(TMBDmultinomDistribution)
+  fishing_fleet_lengthcomp_distribution$set_observed_data(fishing_fleet_length_comp$get_id())
+  fishing_fleet_lengthcomp_distribution$set_distribution_links("data", fishing_fleet$proportion_catch_numbers_at_length$get_id())
+
+  clear()
+})