JAGGview

Static and dynamic visualization tools for interpreting model outputs generated by JABBA.

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Overview

JAGGview is an R package for preparing and plotting key diagnostics and results from JABBA model workflows.

The package includes functions to:

• prepare structured data from model output (e.g., fits, hindcast, retrospective, trajectories, Kobe, priors/posteriors, run tests);
• create publication-ready ggplot2 visualizations for each analysis component;

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Illustration

flowchart LR
  A[JABBA model list] --> B[Data builders
  fits_data / hindcast_data / ...]
  B --> C[Plot builders
  fits_ggplot / hindcast_ggplot / ...]
  C --> D[Diagnostics & communication-ready figures]

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Installation

Linux prerequisites

Before installing the package in R, install JAGS in your system terminal:

sudo apt update
sudo apt install jags

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R package installation

Open the R console and install the required dependencies:

install.packages("remotes")
library(remotes)

install.packages(c("rjags", "R2jags"))
install_github("jabbamodel/JABBA")

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Option 1: Install from GitHub

install_github("UNIVALI-LEMA/JAGGview")

Option 2: Install from a local clone

install_local(".")

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How to use

1) Load the package

library(JAGGview)

2) Prepare data from JABBA model objects

# list_fit_models should contain fit objects returned by JABBA::fit_jabba()
fits_df <- fits_data(list_fit_models)

3) Create a plot

p <- fits_ggplot(fits_df, palette = "#4285f4", title_y = "Abundance index")
print(p)

4) Example with other modules

hc_df <- hindcast_data(list_fit_models)
hc_plot <- hindcast_ggplot(hc_df)
print(hc_plot)

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Exported function groups

• Fits: fits_data(), fits_ggplot()
• Hindcast: hindcast_data(), hindcast_ggplot()
• Kobe: kobe_data(), kobe_ggplot()
• Priors vs posteriors: priors_posteriors_data(), priors_posteriors_ggplot()
• Retrospective: retrospective_analysis_data(), retrospective_analysis_ggplot()
• Run tests Cpue residuals: runs_tests_data(), runs_tests_ggplot(), cpue_residuals_ggplot()
• Trajectories: trajectories_data(), trajectories_ggplot()

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Testing

testthat::test_dir("tests/testthat")

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License

Licensed under CC BY-NC-SA 4.0.