Minimal Example for Running a FIMS Model

Introduction

This vignette provides the minimal steps needed to run a Fisheries Integrated Modeling System (FIMS) model.

Setup

Load the FIMS package and clear memory:

library(FIMS)

# clear memory
clear()

Data and parameters

First, load the available data and create a FIMS data frame to create a model with. Then create a set of default parameters.

# Load sample data
data("data1")
# Prepare data for FIMS model
data_4_model <- FIMSFrame(data1)

# Create parameters
parameters <- data_4_model |>
  create_default_configurations() |>
  create_default_parameters(data = data_4_model)

Initialize and Fit

Initialize the FIMS modules and fit the model.

# Run the  model with optimization
fit <- parameters |>
  initialize_fims(data = data_4_model) |>
  fit_fims(optimize = TRUE)

## ✔ Starting optimization ...
## ℹ Restarting optimizer 3 times to improve gradient.
## ℹ Maximum gradient went from 0.00915 to 0.00057 after 3 steps.
## ✔ Finished optimization
## ✔ Finished sdreport
## ℹ FIMS model version: 0.7
## ℹ Total run time was 6.45911 seconds
## ℹ Number of parameters: fixed_effects=77, random_effects=0, and total=77
## ℹ Maximum gradient= 0.00057
## ℹ Negative log likelihood (NLL):
## • Marginal NLL= 3240.1261
## • Total NLL= 3240.1261
## ℹ Terminal SB= 1803.27839

# Clear memory post-run
clear()