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