atlantio

Read, write and manipulate Atlantis model inputs and outputs. atlantio provides an S7 class Atlantis that represents an Atlantis model, functions to read and write Atlantis files, and methods to extract diet tables, food webs and time series from a model.

Installation

atlantio is not on CRAN yet. Install the development version from GitHub with pak:

# install.packages("pak")
pak::pak("inSileco/atlantio")

Usage

library(atlantio)
mod <- new_atlantis() |>
  atlantis_load_files(c(
    atlantis_examples("outputs", "output.nc"),
    atlantis_examples("outputs", "outputBiomIndx.txt"),
    atlantis_examples("outputs", "outputBoxBiomass.txt")
  ))
mod

# ── Atlantis Model ──
# 
# ── Data availability: 
# ✖ Geometry (BGM)
# ✖ Run file
# ✖ Biology parameters
# ✖ Group file
# ✔ Main output
# ✖ Diet data
# ✖ Detailed diet data
# ✔ Biomass (system-wide)
# ✔ Biomass (per box)
# ✖ Biomass (per age)
# 
# ── Main output details: 
# • 139 variables
# • 74 time steps

See the package vignettes for details on reading models, listing parameters and calibration workflows.

License

MIT