{ecosystemom}

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.title[
# {ecosystemom}
]
.author[
### Bai Li <br><br> Contractor with ECS Federal LLC in support of <br> NOAA Fisheries Office of Science and Technology <br> Email: <a href="mailto:bai.li@noaa.gov" class="email">bai.li@noaa.gov</a>
]
.institute[
### GOA-CLIM Monthly All-Hands Meeting
]
.date[
### 2026/05/27
]

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.footnote[U.S. Department of Commerce | National Oceanic and Atmospheric Administration | National Marine Fisheries Service]

---
# Outline

- .hyperlink-style[[Fisheries Integrated Modeling System](https://noaa-fims.github.io/)] (FIMS) organization
- Why are we building {.hyperlink-style[[ecosystemom](https://noaa-fims.github.io/ecosystemom/)]}?
- Features
- Main challenges
- Collaboration and contributions
- Ecosystem-to-stock-assessment simulation workflow demo

---
# Fisheries Integrated Modeling System (FIMS) Organization

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???
FIMS is a flexible suite of software tools to support sustainable fishery management

---

# Why are We Building {ecosystemom}?

- 🏗️️ Create a flexible ecosystem-to-stock-assessment simulation framework

- 🧪 Test FIMS using ecosystem models as operating models

- 🔍 Explore ecosystem-informed stock assessment approaches

- 🤝 Create interdisciplinary research and collaboration opportunities

---
# Features

Import and standardize outputs from ecosystem operating models

- `load_model()`

- Current and planned ecosystem modeling platform support

- Ecopath with Ecosim (EwE): 🧪 Ecosim, 🚧️ Ecospace, 🚧 Individual-based version of Ecospace
  
  - 🔎 Atlantis

---
# Example of Loading EwE outputs

---
# Features
Extract “true” population quantities from OMs, including annual or monthly trajectories and age compositions

- `calc_truth()`

---
# Example of Extracting Truth from EwE
<iframe src="https://noaa-fims.github.io/ecosystemom/articles/ewe-ecosim-base-simulation.html#extract-truth-from-the-om" width="100%" height="400px" data-external="1"></iframe>

---
# Features
Generate sampled observations from OM outputs for use in fisheries stock assessment models such as FIMS

- `sample_lognormal()`
- `sample_multinomial()`
- `sample_dirichlet_multinomial()`

---
# Example of Generating Sampled Data

---
# Features
Reshape environmental or diet composition data from OMs to support time series analyses such as Dynamic Structural Equation Models (DSEMs)

- `create_dsem_inputs()`

---
# Example of Creating Inputs for {dsem}
<iframe src="https://noaa-fims.github.io/ecosystemom/articles/ewe-ecosim-base-simulation.html#create-dsem-inputs" width="100%" height="400px" data-external="1"></iframe>

---
# Main Challenges
Different ecosystem models

- produce different output formats
- has different spatial and temporal structures
- use different assumptions and parameterizations

---
# Collaboration and Contributions

.pull-left[
**💻Weekly coding sessions**

Mondays

- 3:30-5 PM ET
- 12:30-2 PM PT
- 9:30-11 AM HT

Starting June 1, 2026
]

.pull-right[
- Mix of development, training, and Q&A
- Topics provided beforehand 
- Work on {ecosystemom} and related workflows for sampling ecosystem model outputs to generate data for stock assessment models
]

.footnote[
[1] Weekly Google meet link: .hyperlink-style[[ https://meet.google.com/umk-toiv-ifs](https://meet.google.com/umk-toiv-ifs)] <br>
[2] GitHub issues page: .hyperlink-style[[https://github.com/NOAA-FIMS/ecosystemom/issues](https://github.com/NOAA-FIMS/ecosystemom/issues)]
]

---
# Ecosystem-to-Stock-Assessment Simulation Workflow Demo

Demo vignette: .hyperlink-style[[https://noaa-fims.github.io/ecosystemom/articles/ewe-ecosim-base-simulation.html](https://noaa-fims.github.io/ecosystemom/articles/ewe-ecosim-base-simulation.html)]

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