An Open Science Approach to Modeling and Visualizing Cyanobacteria Blooms in Lakes and Ponds

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# An Open Science Approach to Modeling and Visualizing Cyanobacteria Blooms in Lakes and Ponds
## American Association of Geographers Annual Meeting
### Jeff Hollister, Farnaz Nojavan, Betty Kreakie
### 2017-04-05 
Boston, MA

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# Twitter?

![Yes!!!](http://www.reactiongifs.us/wp-content/uploads/2014/11/thumbs_up_waynes_world.gif)

### hashtag: \#AAG2017 
### me: @jhollist

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# Who, what, why, and how?

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# Who are we?

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- Ecologists 
- Computational focus
  - Enough to be dangerous
- 3 FTE
  - Myself
  - Betty Kreakie
  - Bryan Milstead
- 2 Post-docs
  - Farnaz Nojavan
  - Stephen Shivers
]

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<img src="figure/comp_eco_crew.jpg" style="margin-left: 75px"></img>
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# What do we do?

- Apply computational approaches to understand water quality impacts in lakes
  - Modelling (Not this talk!, but see Farnaz's talk)
- Open Science

![The workflow](figure/cyano_model_function.jpg)

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# What is open science?

- Access to materials     
- Reproducible/ Repeatable    
- The Web!                   
- A process, not a state

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# Why open science?

- Often required
  - Government/Funders/Journals
- Benefits researchers
  - [Mciernan et al. (2016) How open science helps researchers succeed](https://elifesciences.org/content/5/e16800)
- Improves quality
  - [The classic example: Reinhart and Rogoff](http://www.newyorker.com/news/john-cassidy/the-reinhart-and-rogoff-controversy-a-summing-up)
- Benefits to society
  - ["Sharing of Data Leads to Progress on Alzheimer’s"](http://www.nytimes.com/2010/08/13/health/research/13alzheimer.html)

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# How are we open?

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- R package development
- Visualization
- Sharing and collaborating
- Publishing
- Open data (not in this talk)
]

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<img src = "https://media.giphy.com/media/l0MYyv6UK0Bd4DE76/giphy.gif" style="width: 110%; height: 110%; margin-top: 50px;"></img>
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# R package development

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# `lakemorpho`

.footnote[Package URL: <https://cran.r-project.org/package=lakemorpho>]

.left-column[
- Lake morphometry metrics in R
- Version 1.0 
  - August 2014
- Version 1.1.0 
  - December 2016
- [National Lake Morphometry](https://edg.epa.gov/metadata/catalog/search/resource/details.page?uuid=%7B495CBAED-9BB9-49B4-80A7-1C91DE5FCA95%7D)
- [Hollister and Milstead (2010)](http://dx.doi.org/10.1080/07438141.2010.504321)
- [Hollister *et. al.* (2011)](http://dx.doi.org/10.1371/journal.pone.0025764)
]

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![](index_files/figure-html/unnamed-chunk-1-1.png)
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background-image: url('figure/lakemorpho_demo.png')
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# [lakemorpho: Demo](http://server.jwhollister.com:8787)

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# `elevatr`

.footnote[Package URL: <https://cran.r-project.org/package=elevatr>]

.left-column[
- Access elevation data in R
  - Mapzen
  - AWS
  - USGS
- Version 0.1.1 
  - January 2017
- Version 0.1.3 
  - March 2017
- Will be paired with `lakemorpho`
]

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![](index_files/figure-html/unnamed-chunk-2-1.png)
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background-image: url('figure/elevatr_demo.png')
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# [elevatr: Demo](http://server.jwhollister.com:8787)

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# Data Visualization

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# Shiny: Cyanobacteria Monitoring Collaborative

.footnote[Project URL: <http://cyanos.org>]

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- Started in 2013
  - New England Region Cyanobacteria Monitoring Workgroup
- Three Projects
  - bloomWatch
  - cyanoScope
  - Monitoring
- DataViz with Shiny
]

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![cyano web](figure/cyano_web.jpg)
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# [Shiny: Demo](https://cyanos.shinyapps.io/cyanoviz/)

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#  Sharing and Collaborating

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# GitHub

- What is it?
- How do we use it?

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# [GitHub: Demo](https://github.com/usepa)

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#  Open Access

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# Publishing

- Preprints
  - [Hollister *el al.* (2016) PeerJ Preprints](http://dx.doi.org/10.7287/peerj.preprints.1319v2)
- Open first
  - [Milstead *et al.* (2013) PLoS One](http://dx.doi.org/10.1371/journal.pone.0081457)
  - [Hollister and Kreakie (2016) F1000Research](https://dx.doi.org/10.12688/f1000research.7955.2)
- Money where our mouth(s) is(are)
  - [Kreakie *et al.* (2015) LakeLines](http://www.nalms.org/media.acux/beb75c9c-f812-4753-b888-79864899c6d6)

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# Thanks!
.center[
## Jeff Hollister
US EPA 
Atlantic Ecology Division 
Narragansett, RI 
email: [hollister.jeff@epa.gov](mailto:hollister.jeff@epa.gov) 
twitter: [@jhollist](https://twitter.com/jhollist) 
github: [jhollist](https://github.com/jhollist)

Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).
]