Lakes, Landscapes, and R:

class: title-slide

# Lakes, Landscapes, and R:
## A framework for open science on freshwater cyanobacteria



### Jeff Hollister and Bryan Milstead

### US-IALE 2018
#### Chicago, IL
#### 2018-04-11

---
class: center, middle, inverse

# Twitter and Photos?

[![](figure/jonah_hill_ok.gif)](https://giphy.com/gifs/reaction-R459x856IfF6w)

### \#usiale2018 \#rstats \#cyanobacteria 
### @jhollist

---
class: center, middle, inverse

# Open Science?

---

# What is open science?

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

---
# Open Science Solutions

- Open Access
- Open Data
- Open Source Code

.center[[![oa](figure/oa_dr_evil.jpg)](https://memecreator.org/meme/open-access)]

---
# Open Science Solutions

- Open Access
- Open Data
- Open Source Code

.center[[![data](figure/data_article.jpg)](https://blogs.uoregon.edu/datamanagement/2017/02/14/lydweek-2017-2/)]

---
# Open Science Solutions

- Open Access
- Open Data
- Open Source Code

.center[[![programmer](figure/programmer.png)](https://rforcats.net)]

---
# R and Landscape Ecology

.center[<a href="https://github.com/jhollist/lakes_landscapes_r/blob/master/le_r_cites.R"><img src="figure/r_lang.png" style="width: 80%;"></img></a>]

.footnote[Text mining facilitated by [rOpenSci's](https://ropensci.org) awesome [`fulltext`](https://CRAN.R-project.org/package=fulltext) package]

---
# R and Landscape Ecology

.left-column[
- Foundations
 - [`sp`](https://CRAN.R-project.org/package=sp) 
 - [`rgdal`](https://CRAN.R-project.org/package=rgdal)
 - [`raster`](https://CRAN.R-project.org/package=raster)
 - [`rgeos`](https://CRAN.R-project.org/package=rgeos)
- The Future
 - [`sf`](https://CRAN.R-project.org/package=sf)
 - [`stars`](https://github.com/r-spatial/stars)
<img src="figure/Rlogo.png" style="width: 100%; margin-top: 50px; margin-left: -50px;"></img>
]

.right-column[
- Specialty (Missing many!)
  - [`landsat`](https://CRAN.R-project.org/package=landsat)
  - [`SDMtools`](https://CRAN.R-project.org/package=SDMTools)
  - [`nlmr`](https://CRAN.R-project.org/package=NLMR)
  - [`landscapetools`](https://CRAN.R-project.org/package=landscapetools)

<img src="figure/LAND_Cover.jpg" style="width: 60%; margin-top: 10px; margin-left: 40px;"></img>
]
---
class: center, middle, inverse

# R, lakes, and cyanobacteria at USEPA

---

# Who are we?

.left-column[
- Ecologists 
- 3 FTE
  - Myself
  - Betty Kreakie
  - Bryan Milstead
- 1 Post-doc
  - Stephen Shivers
- Alum
  - Farnaz Nojavan
]

.right-column[
<img src="figure/comp_eco_crew.jpg" style="margin-left: 25px; margin-top: -50px;"></img>
]

---

# What do we do?

- Apply computational approaches to understand water quality impacts in lakes
- Focus on cyanobacteria
- Multiple Scales
- Open Science
- Use R
    - Analysis
    - Sharing code
    - Solve common problems

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

---

# R to solve common problems

- `lakemorpho`
 - `elevatr`
 - `goatscape` (in development)
 
<a href = "figure/computer GIF-source.gif"><img src="figure/computer GIF-source.gif" style="width: 80%; height: 80%; margin-left: 10%;"></img></a>
---

# `lakemorpho`

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

.left-column[
- Lake morphometry metrics in R
- `sp`, `rgdal`, `rgeos`, and `raster`
- `sf` support to be added
- [National Lake Morphometry](https://edg.epa.gov/metadata/catalog/search/resource/details.page?uuid=%7B495CBAED-9BB9-49B4-80A7-1C91DE5FCA95%7D)
- [NHD Plus](https://s3.amazonaws.com/nhdplus/NHDPlusV21/Documentation/NHDPlusV2_User_Guide.pdf#page=52)
- [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)
- [Hollister and Stachelek (2017)](https://f1000research.com/articles/6-1718/v1)
]

.right-column[

<img src="figure/lakemorpho_demo.gif" style="margin-top: -30px; margin-left: -15px; max-width: 120%;"></img>
]
---

# `elevatr`

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

.left-column[
- Access elevation data in R
 - ~~Mapzen~~
 - closed!
 - AWS
 - USGS
- Built off of `sp`, `rgdal`, `rgeos`, and `raster` suite
- `sf` support to be added
- Incorporate <https://www.nextzen.org/>

]

.right-column[

<img src="figure/elevatr_demo.gif" style="margin-top: -30px; margin-left: -15px; max-width: 120%;"></img>
]

---

# `goatscape`

.left-column[
- What's in a name?
- Summarizes ancillary data for a user-defined landscape polygon
  - Census (via `censusapi`)
  - Landcover and Impervious (via `FedData`)
- Accepts arbitrary spatial data for the landscape
- Based on `sf`
- Tidy by design
]

.right-column[

<img src="figure/goatscape_logo.jpg" style="margin-top: -70px; margin-left: -15px; max-width: 110%;"></img>
]

.footnote[
Repository URL: <https://github.com/usepa/goatscape>
]

---

# Thanks!
.left-column[
.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) 
]]

.right-column[
.center[
**Bryan Milstead**
US EPA 
Atlantic Ecology Division 
Narragansett, RI 
email: [milstead.bryan@epa.gov](mailto:milstead.bryan@epa.gov) 
twitter: [@willbmisled](https://twitter.com/willbmisled) 
github: [willbmisled](https://github.com/willbmisled) 
]]

.footnote[
**Package acknowledgements**
- Slides created with [`xaringan`](https://cran.r-project.org/package=xaringan) 
- Figures created with [`ggplot2`](https://cran.r-project.org/package=ggplot2) and [`hrbrthemes`](https://cran.r-project.org/package=hrbrthemes)
- Data analysis made **MUCH** easier with the [`tidyverse`](https://cran.r-project.org/package=tidyverse)
- Text mining of Landscape Ecology done with [`fulltext`](https://cran.r-project.org/package=fulltext) and [`rcrossref`](https://cran.r-project.org/package=rcrossref)

**Slides and Source Code**
- Slides: <https://jwhollister.com/lakes_landscapes_r>
- Repo: <https://github.com/jhollist/lakes_landscapes_r>
]