stockplotr

Previously named ‘satf’

The goal of stockplotr is to create a centralized package that contains all of the figures and tables for a stock assessment report used to inform management. There are multiple current packages that perform a similar function, but they are typically region and/or model dependent. Across the US, there are multiple packages that create plots that are directly used in a stock assessment report used for management. For example, an analyst that uses Stock Synthesis (SS3) to assess a stock will utilize r4ss, a package that reads outputs, plots key parameters, and more to increase throughput and reduce tedious tasks for an analyst.

Please note that this package is still in development. As such, some functions are unstable and might not perform as intended. We encourage anyone who tests out this package to leave an issue for any errors you find or for a feature request.

Installation

Install the package using one of the three following ways:

1. Using pak

install.packages("pak")
pak::pak("nmfs-ost/stockplotr")

2. Using remotes

install.packages("remotes")
remotes::install_github("nmfs-ost/stockplotr")

3. From the nmfs-ost r-universe

install.packages("stockplotr", repos = c("https://noaa-fisheries-integrated-toolbox.r-universe.dev", "https://cloud.r-project.org"))

Usage

Please refer to the asar tutorial to learn how to produce the input file necessary to create figures and tables with stockplotr.

Then, once your converted model results are saved as an object in your R environment, you can use stockplotr functions to create plots from the object.

[!TIP] stockplotr plots or tables are exported as ggplot2 or flextable objects meaning that users can use the same process to add new data, formatting, or other customizations to the plot beyond the baseline made by this package

Example

data <- stockplotr::example_data

# create a landings figure from your object
plot_spawning_biomass(data)

Example Plot	Example Table

[!NOTE] Tables are not currently included in the package due to a major overhaul. We plan to incorporate them by the end of 2025.

Contributions

Have you identified any suggestions for improvement, bugs, or questions? Please see our Contributing page for more information on how to make effective contributions to stockplotr.

Thank you for helping us improve this package!

Code of Conduct

We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

All contributors participating and contributing to the asar project are expected to adhere to the Code of Conduct.

User Community

We hope that this package will be able to be a one stop shop for plots regarding interpreting assessment models and presenting the results to managers and relevant stakeholders. We encourage interested users to contribute to this package using their custom code when they find it may be useful across the nation.

[!NOTE] An additional package to plot model diagnostics called FIMSdiags is being worked on for the Fisheries Integrated Modelling System [FIMS] that will natively work with the output used for stockplotr since the model output for FIMS works together with stockplotr.

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.