In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

Installing the atlantisom R package

atlantisom requires R version 3.1.0 or greater. The package can be run on OS X, Windows, or Linux. The development version of atlantisom can be installed from GitHub with the following code:

# install.packages("devtools") # if needed
devtools::install_github("r4atlantis/atlantisom", dependencies = TRUE)

# If you would like the vignettes available with the GitHub development version:
devtools::install_github("r4atlantis/atlantisom", dependencies = TRUE, build_vignettes = TRUE)

You can then load the package with:

library("atlantisom")

You can read the help files and access the various vignettes (including this one) with:

?atlantisom
help(package = "atlantisom")
browseVignettes("atlantisom")

See @fulton2010 for a more formal (but brief) overview of atlantis.

Please direct any questions, suggestions, or bug reports to the atlantisom issue tracker: https://github.com/r4atlantis/atlantisom/issues, or to an author as listed on the title page of this vignette.

If you use atlantisom in a publication, please cite the package as indicated by running citation("atlantisom") in the R console:

citation("atlantisom")

An overview of the atlantisom simulation structure

atlantisom is an R package to make it relatively quick and easy to run simulations with the ATLANTIS output.

Units of output

In general, ATLANTIS simulates the flow of nitrogen through trophic levels in time and space. Nitrogen is typically expressed as a concentration (mgN m^-3) broken into two components, structural (structn; i.e., hard parts) and reserve (resn; i.e., soft parts). By breaking the nitrogen into two components, ATLANTIS is able to track length and condition separately.

Numbers of individuals are tracked for vertebrates, and can be used to calculate biomass with calc_biomass_age.