Ecosystem Modeling Approaches:

class: right, middle, my-title, title-slide

.title[
# Ecosystem Modeling Approaches:
]
.subtitle[
## What Questions Can We Address?
]
.author[
### Sarah Gaichas<br /> Northeast Fisheries Science Center <br /> <br /> With thanks to Gavin Fay (UMass), Sean Lucey (NOAA), and Sarah Weisberg (Stony Brook)
]

---

class: top, left

## What is an ecosystem model?
.center[
![:img ecosystem model spectrum, 85%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/ecomods.png)
]

???
# Ecosystem modelling approaches: What questions can we address?

---
# Why build a model? Identify the problem

.pull-left-60[
![:img whybuild, 85%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/piggiehippowhy.png)
]

.pull-right-40[

1. Develop clearly specified questions and objectives 
  - What does the model have to output/predict?
  - What does the user need to be able to change?
  
1. Evaluate data availability (appropriate temporal/spatial scales) 
  
1. THEN build a model, or better, model(s)  
]

---
# Today's objective

.pull-left-70[

Primary: Think about *your* research question  
  - What data do you have to address it?  
  - Would a model be useful to address your research question?  
  - If so, what would you want it to do?   
  - Advanced: How might you build it?

Secondary: Understand what a food web model is  
  - Know what questions to ask about how it was built  
  - Know what it can and cannot do 
  - Experiment: perturb the model in different ways  
    - What do you observe?  
    - Why might this be? (including model limitations)

]

.pull-right-30[
![](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/piggiegeraldbecauseok.png)
]
    
---
## What is a food web model?

.pull-left-60[
A system of linear equations

For each group, `$i$`, specify:

Biomass `$B$` [or Ecotrophic Efficiency `$EE$` ]  
   Population growth rate `$\frac{P}{B}$`  
   Consumption rate `$\frac{Q}{B}$`  
   Diet composition `$DC$`  
   Fishery catch `$C$`  
   Biomass accumulation `$BA$`  
   Im/emigration `$IM$` and `$EM$`  
   
Solving for `$EE$` [or `$B$` ] for each group:
]

.pull-right-40[
![:img toyfoodweb, 80%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/toyfw.png)
]

`$$B_i\Big(\frac{P}{B}\Big)_i*EE_i+IM_i+BA_i=\sum_{j}\Big[ B_j\Big (\frac{Q}{B}\Big)_j*DC_{ij}\Big ]+EM_i+C_i$$`
???
Mathematically identical to an "input-output" model in economics

---
## How do you build one?

Specify most parameters for each species; can solve for one

.pull-left[
How? Observations from:

1. Fishery independent surveys
  - Biomass estimates
  - Diet compositions
  - Growth and reproduction information
  
1. Catch/landings/discard data from fishery managers

1. Literature, historical information, general life history theory

1. Other transparent, reproducible processes/sources
]

.pull-right[
![:img workinprogress, 70%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/work-in-progress.png)
]

---

## What can you do with one? Lab overview
.pull-left[
Anchovy Bay food web model

1. Orientation using simple food web invented for illustration

1. Tradeoffs between fishing fleets targeting different species

]

.pull-right[
Gulf of Maine food web model

1. More complex food web model based on a real system

1. System reaction to different scenarios
    1. Changing fishing effort (combined fleet)
    1. Changing mortality for individual species
    1. Changing predator-prey dynamics

]
???
---
## The Northeast US shelf food web
.center[
![:img GOM food web 2002,  75%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/LinkNEUSfoodweb.png)
]
.footnote[Link, J. 2002. Does food web theory work for marine ecosystems? Marine ecology progress series, 230: 1–9.]

---
## The Gulf of Maine food web model
.center[
![:img GOM food web, 70%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/GOMfw.png)
]

.footnote[Link, J., Overholtz, W., O’Reilly, J., Green, J., Dow, D., Palka, D., Legault, C., et al. 2008. The Northeast U.S. continental shelf Energy Modeling and Analysis exercise (EMAX): Ecological network model development and basic ecosystem metrics. Journal of Marine Systems, 74: 453–474.

Link, J., Col, L., Guida, V., Dow, D., O’Reilly, J., Green, J., Overholtz, W., et al. 2009. Response of balanced network models to large-scale perturbation: Implications for evaluating the role of small pelagics in the Gulf of Maine. Ecological Modelling, 220: 351–369.
]

---
## New Gulf of Maine model (S. Weisberg, Stony Brook U), Atlantic herring highlighted

.center[

![:img NEW GOM food web, 100%](https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/GOMWeisberg_highlightHerring.png)
]

---
## Possible exercises: work in teams

.pull-left[
[Anchovy Bay](https://gavinfay.shinyapps.io/rpath_anchovybay/):

1. Describe impacts of different fishing scenarios

1. Describe potential catch and biomass objectives

1. Can you engineer any scenarios to achieve them?

]

.pull-right[
[Gulf of Maine](https://connect.fisheries.noaa.gov/content/6c128564-f8b2-49c4-8afc-614f9e2e7a5b/):

1. Describe impacts of different fishing scenarios

1. Describe impacts of individual species mortality scenarios

1. Describe the impacts of "as prey" scenario

1. Can you suggest mechanisms for any observed differences?

]

## Both models

1. Describe your Ecosystem Based management objective

+ Can you achieve it by changing sliders?
    + Are there any side effects (tradeoffs) of achieving your objective?

???
https://sgaichas.shinyapps.io/rpath_GOMview/

---
## The next level: uncertainty

How would you address this?
.pull-left[
Biological parameters:

1. Biomass

1. Production rate
    
1. Consumption rate

1. Diet composition

1. Predator-prey interactions

] 
.pull-right[
Management needs:

1. Species/group resolution
    
1. Fishing fleet resolution
    
1. Spatial resolution
    
1. Changing stakeholder questions
    
1. Limited time
]

---
background-image: url("https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/herrup10pann.png")
background-size: 830px
background-position: right bottom

## Herring MSE food web model results: ecosystem tradeoffs

Tradeoffs between forage groups and mixed impacts to predators apparent when multiple species and full predator prey interaction feedbacks can be included

.pull-left-30[
* Rpath <a name=cite-lucey_conducting_2020></a>([Lucey, et al., 2020](https://www.sciencedirect.com/science/article/pii/S0304380020301290)) Ecosense functions evaluate parameter uncertainty within a scenario

* Now we have MSE closed loop possibilities in Rpath <a name=cite-lucey_evaluating_2021></a>([Lucey, et al., 2021](http://www.sciencedirect.com/science/article/pii/S0165783620302976))

* Can implement HCRs with predator prey interactions

]
.pull-right-70[

]

---
background-image: url("https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/fwcompresults.png")
background-size: 780px
background-position: right bottom

## Herring MSE food web model results: ecosystem uncertainty?

.pull-left-30[
Compare 10% change (green, same as previous slide gray boxes) with more extreme "herring" biomass:  
* 50% increase from base herring biomass (red)
* 50% decrease from base herring biomass (blue)

More system uncertainty with increased herring biomass?
]

.pull-right-70[

]
---
## Additional resources
.pull-left[
* [US EBFM Policy](https://www.fisheries.noaa.gov/resource/document/ecosystem-based-fisheries-management-policy), [US EBFM Roadmap](https://www.fisheries.noaa.gov/resource/document/ecosystem-based-fisheries-management-road-map)  
* [US Integrated Ecosystem Assessments](https://www.integratedecosystemassessment.noaa.gov/)
* [Northeast US Ecosystem Reports](https://www.fisheries.noaa.gov/new-england-mid-atlantic/ecosystems/state-ecosystem-reports-northeast-us-shelf)  
* [Ecosystem Report Technical Documentation](https://noaa-edab.github.io/tech-doc)  
* [ecodata R package](https://github.com/noaa-edab/ecodata)
]
.pull-right[
* [Wikipedia: Ecosystem models](https://en.wikipedia.org/wiki/Ecosystem_model)
* [Wikipedia: Ecopath](https://en.wikipedia.org/wiki/Ecopath)
* [Rpath codebase](https://github.com/NOAA-EDAB/Rpath)
* [Rpath shiny app code](https://github.com/NOAA-EDAB/rpath_shiny)

.contrib[

* Slides available at https://noaa-edab.github.io/presentations
* Contact: <Sarah.Gaichas@noaa.gov>
]
]

## References

.contrib[
<a name=bib-lucey_evaluating_2021></a>[Lucey, S. M. et
al.](#cite-lucey_evaluating_2021) (2021). "Evaluating fishery
management strategies using an ecosystem model as an operating model".
En. In: _Fisheries Research_ 234, p. 105780. ISSN: 0165-7836. DOI:
[10.1016/j.fishres.2020.105780](https://doi.org/10.1016%2Fj.fishres.2020.105780).
URL:
[http://www.sciencedirect.com/science/article/pii/S0165783620302976](http://www.sciencedirect.com/science/article/pii/S0165783620302976)
(visited on Dec. 09, 2020).

<a name=bib-lucey_conducting_2020></a>[Lucey, S. M. et
al.](#cite-lucey_conducting_2020) (2020). "Conducting reproducible
ecosystem modeling using the open source mass balance model Rpath". En.
In: _Ecological Modelling_ 427, p. 109057. ISSN: 0304-3800. DOI:
[10.1016/j.ecolmodel.2020.109057](https://doi.org/10.1016%2Fj.ecolmodel.2020.109057).
URL:
[https://www.sciencedirect.com/science/article/pii/S0304380020301290](https://www.sciencedirect.com/science/article/pii/S0304380020301290)
(visited on Apr. 16, 2021).
]

---

background-image: url("https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/IMG_2733.jpg")
background-size: cover

## Questions?

# Thank you