Ecosystem operating model. Generates data sets from ecosystem model scenarios for stock assessment models.
Installing ecosystemom
Install the most recent version of FIMSdiags using the following code:
install.packages("remotes")
remotes::install_github("NOAA-FIMS/ecosystemom")or using {pak}
pak::pak("NOAA-FIMS/ecosystemom")Why are we building {ecosystemom}?
- Connect ecosystem model outputs to stock assessment simulation testing through a flexible operating model framework.
- Support evaluation and comparison of FIMS and other assessment methods against ecosystem model outputs under realistic ecosystem dynamics.
- Enable research on ecosystem-informed stock assessment approaches.
- Foster collaboration between ecosystem modelers and stock assessment scientists.
🤝 Contributions and feedback are welcome! If you’re interested in this project or its applications, please interact with this repository or contact Bai Li at bai.li@noaa.gov
Functions
The package includes functions below:
-
load_model()— import and standardize output from ecosystem operating models (OM). For example, this function can be used to read and standardize Ecopath with Ecosim (EwE) Ecosim outputs for downstream analyses within {ecosystemom}. -
get_truth()— extract “true” population quantities from the OM, including annual or monthly biomass trajectories and biomass-at-age. -
sample_*()— generate sampled observations from OM outputs that incorporate sampling and observation error for use in estimation models such as the Fisheries Integrated Modeling System (FIMS). -
create_dsem_inputs()— prepare environmental covariates or diet composition data from the OM to support candidate model specifications for dynamic structural equation models (DSEMs) and related ecosystem-informed analyses.