Add test file for fimsfit using pollock

content/test_fimsfit.R

@@ -0,0 +1,38 @@
+#  Load packages and input data -------------------------------------------
+# Load required packages
+packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "remotes", "lubridate")
+invisible(lapply(packages, library, character.only = TRUE))
+
+# Install the FIMS package from specific repositories
+# install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org"))
+
+# detach("package:FIMS", unload = TRUE)
+library(FIMS)
+
+# Define the years and ages for the assessment
+years <- 1970:2023
+nyears <- length(years)
+nseasons <- 1
+nages <- 10
+ages <- 1:nages
+
+# Source the script to prepare input data
+source(file.path("content", "R", "pk_prepare_dat.R"))
+
+# Run FIMS without helper functions ---------------------------------------
+clear()
+clear_logs()
+
+# Source the script to prepare FIMS inputs without using helper functions
+source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs.R"))
+
+# Create the TMB model and generate the report
+success <- CreateTMBModel()
+parameters <- list(p = get_fixed())
+parameters$p[1] = 3.5
+input <- list(data=age_frame, parameters=parameters, version='GOA pollock')
+
+## devtools::load_all('C:/Users/cole.monnahan/FIMS')
+
+fit <- fit_fims(input, verbose=FALSE)
+fit <- fit_fims(input)