cavityuse

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.hanging[
### Stefanie E. LaZerte <br>& Elizabeth A. Gow]

# `cavityuse`

## An R Package for Detecting Cavity Use From Geolocator Data

<http://github.com/steffilazerte/cavityuse/>

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ISBE 2018

.align-bottom-left[<img src = "./Figures/logos/twitter_black.jpg" style = "height: 40px; vertical-align:middle">  @steffilazerte <img src = "./Figures/logos/github.png" style = "height: 40px; vertical-align:middle; margin-left: 25px"> steffilazerte <img src = "./Figures/logos/web.png" style = "height: 40px; vertical-align:middle; margin-left: 25px"> steffilazerte.ca <img src = "./Figures/logos/email.svg" style = "height: 25px; vertical-align:middle; margin-left: 25px"> sel@steffilazerte.ca]

---
# Cavities, caves and burrows

## Provide

- Shelter
- Nests
- Roosts

## Patterns of use indicate

- Breeding behaviour
- Parental care
- Roosting patterns
- Behavioural rhythms

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/Vaux's_Swifts-2.jpg" style = "height: 100%"><div class = "attr">Visitor7 via Wikimedia Commons</div>
<div class = "caption">e.g., Roosting Vaux's swifts</div>
</div>

---
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# Geolocators

---
## To study migration
- Record light levels
- Time of noon = Longitude
- Day length = Latitude

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/locator attachment - cropped - wide.jpg" style = "height: 100%"><div class = "attr">Scott Ramsay</div>
<div class = "caption">Placing geolocator on white-throated sparrow</div>
</div>

---

## To study cavity use

- Look for abrupt light changes
- Periods of dark during the day

---

## Benefits

- Inexpensive
- Independent of cavity location
- Individual data
- Long observation periods

---
## Used to 
- Assess activity in rodents
  - in/out of nest
  - above/below ground

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/Gilles_Gonthier_-_Tamiasciurus_hudsonicus_(by).jpg" style = "height: 100%"><div class = "attr">Gilles Gonthier via Wikimedia Commons</div>
<div class = "caption"">e.g., American red squirrels<br>Cory et al. 2014</div>
</div>

---

## Used to 
- Assess activity in rodents
  - in/out of nest
  - above/below ground
- Assess cavity use in northern flickers
  - in/out of cavity

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/Northern_Flicker_(Red-shafted) - cropped.jpg" style = "height: 100%"><div class = "attr">Dominic Sherony via Wikimedia Commons</div>
<div class = "caption">e.g., Northern flickers<br>Gow et al. 2015</div>
</div>

---

## Used to 
- Assess activity in rodents
  - in/out of nest
  - above/below ground
- Assess cavity use in northern flickers
  - in/out of cavity
- Assess incubation in shorebirds
  - incubating/non-incubating

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/Red_Knot_with_Geolocator_(9295409432) - cropped.jpg" style = "height: 100%"><div class = "attr">U. S. Fish and Wildlife Service<br>via Wikimedia Commons</div>
<div class = "caption">e.g., Red knots<br>Burger et al. 2012</div>
</div>

<div style = "padding: 10px;"></div>
.pull-left-45-c[.colourbox[But data processing!]]

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# .col[**`cavityuse`**]: An R package

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Leverage the power of

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# General Principles

---

---

---
<img src="LaZerte_ISBE_2018_files/figure-html/unnamed-chunk-6-1.png" class = 'fig-centre' style = 'width: auto; height: 78%' />

---
<img src="LaZerte_ISBE_2018_files/figure-html/unnamed-chunk-7-1.png" class = 'fig-centre' style = 'width: auto; height: 78%' />

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# Testing `cavityuse`

---

<div class = "anchorl" style = "position:absolute; bottom: 2%; left:25%; font-size:60%;">Gow, Weibe & Fox; 2015 Ibis</div>

<div class = "fig-left" style = "top:19%; height: 65%" >
<img src = "./Figures/NOFL in hand geol copy.jpg" style = "height: 100%"><div class = "attr">Elizabeth Gow</div><div class = "caption" style = "font-size: 90%">Northern flickers <span class = "small">(Colaptes auratus)</span><br><strong>Cavity nesters</strong></div>
</div>

<div class = "anchorr" style = "position:absolute; bottom:2%; right:25%;font-size:60%">Otter, Mckenna, LaZerte & Ramsay; 2017 AOS/SCO Conf.</div>

<div class = "fig-right" style = "top:19%; height: 65%" >
<img src = "./Figures/locator on bird - cropped.jpg" style = "height: 100%"><div class = "attr">Scott Ramsay</div><div class = "caption" style = "font-size: 90%">White-throated sparrows <span class = "small">(Zonotrichia albicollis)</span><br><strong>Ground nesters</strong></div>
</div>

---

.pull-left[<span style = "font-size: 300%; text-shadow: 2px 2px #919191; color: #FFB90F;">Day</span>

- Easier
- Light varies
- Look for light/dark patterns

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<img src = "./Figures/day.png" width = 500px height = 50px>]

.pull-right[<span style = "font-size: 300%; text-shadow: 2px 2px #919191; color: #440154;">Night</span>

- Harder  
- All dark
- Look for sunrise/sunset patterns

.spacer[ ]

<img src = "./Figures/night.png" width = 500px height = 50px>]

---
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# Daytime: Hypotheses

---

## a) Overall cavity use:

Birds spend more time outside than inside cavities &emsp; <img src = "./Figures/cavity_out.png" class = "align-middle" style = "width:100px"> .large[>] <img src = "./Figures/cavity_in.png" width = 100px class = "align-middle">

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Flickers use cavities more than Sparrows &emsp; &emsp; &emsp;<img src = "./Figures/flicker.png" class = "align-middle" style = "width:150px"> .large[>] <img src = "./Figures/wtsp.png" width = 150px class = "align-middle">

---

## b) Incubation cavity use:

Incubating flickers use cavities more than Non-incubating (Other) flickers & Sparrows

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.pull-left-c[<img src = "./Figures/flicker_incubating.png" class = "align-middle" style = "width:150px"> .large[>] <img src = "./Figures/flicker.png" class = "align-middle" style = "width:150px">]

.pull-right-c[<img src = "./Figures/flicker_incubating.png" class = "align-middle" style = "width:150px"> .large[>] <img src = "./Figures/wtsp.png" width = 150px class = "align-middle">]

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# Daytime: Results

## a) Overall cavity use

---

---

- Both spend more time outside than inside cavities

---

- Both spend more time outside than inside cavities
- Flickers spend more time inside than Sparrows

---
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# Daytime: Results

## b) Incubation cavity use

---

---

- Incubating flickers use cavities more than
  - Brooding flickers
  
<img src="LaZerte_ISBE_2018_files/figure-html/unnamed-chunk-14-1.png" class = 'fig-right' />

---

- Incubating flickers use cavities more than
  - Brooding flickers
  - Other flickers (without eggs or nestlings)
  
<img src="LaZerte_ISBE_2018_files/figure-html/unnamed-chunk-15-1.png" class = 'fig-right' />

---

- Incubating flickers use cavities more than
  - Brooding flickers
  - Other flickers (without eggs or nestlings)
  - Sparrows
  
<img src="LaZerte_ISBE_2018_files/figure-html/unnamed-chunk-16-1.png" class = 'fig-right' />

---
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# Nighttime: Hypotheses

---

## a) Overall cavity use

Sparrows do not use cavities &emsp; <img src = "./Figures/wtsp.png" class = "align-middle" style = "width:100px"> .large[≠] <img src = "./Figures/cavity_in.png" width = 100px class = "align-middle">

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Flickers use cavities more than Sparrows &emsp; <img src = "./Figures/flicker.png" class = "align-middle" style = "width:100px"> .large[>] <img src = "./Figures/wtsp.png" width = 100px class = "align-middle">

---

## b) Incubation/Brooding cavity use

Incubating (with eggs) and Brooding (with nestlings) flickers use cavities more than Non-Incubating/Brooding (Other) flickers & Sparrows

.spacer[ ]

.pull-left-c[<img src = "./Figures/flicker_incubating.png" class = "align-middle" style = "width:150px"> .large[>] <img src = "./Figures/flicker.png" class = "align-middle" style = "width:150px">]

.pull-right-c[<img src = "./Figures/flicker_incubating.png" class = "align-middle" style = "width:150px"> .large[>] <img src = "./Figures/wtsp.png" width = 150px class = "align-middle">]

---
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# Nighttime: Results

## a) Overall cavity use
---

---

- Flickers use cavities more than Sparrows
- Sparrows **do** use cavities at night **(?)**

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# Nighttime: Results

## b) Incubation/Brooding cavity use

---

---
Incubating and Brooding flickers:  
- Have similar cavity use

---

Incubating and Brooding flickers:  
- Have similar cavity use
- Use cavities more than Other flickers

---

Incubating and Brooding flickers:  
- Have similar cavity use
- Use cavities more than Other flickers
- Use cavities more than Sparrows

---
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# Comparing computers and humans

---

## Gow et al. 2015
- Measured nighttime cavity use in flickers
- Scored use by hand

## `cavityuse`
- Scored by computer

---

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# `cavityuse` Conclusions

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/PileatedWoodpeckerNest - cropped.jpg" style = "height: 100%"><div class = "attr">Pwieland via Wikimedia Commons</div>
</div>

## Results match expectations:

--
- Overall daytime cavity use
--

- Relative daytime vs. nighttime cavity use
--

- Behaviour
  - Cavity-users vs. Noncavity-users
  - Breeding cavity use
--

- Computer- vs. Human-scored

## Results don't match expectations:

- Overall nighttime cavity use

--
<div style = "padding: 15px;"></div>

<div class = "colourbox" style = "position:absolute; left: 6%; bottom: 2%">Good for daytime behaviour</div>

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# What next?

<div class = "fig-right" style = "top:20%; height: 70%" >
<img src = "./Figures/Marmota_marmota_01 - cropped.JPG" style = "height: 100%"><div class = "attr">H. Zell via Wikimedia Commons</div>
</div>

- Improve nighttime detections
  - Detect more types of light transitions

--
- Test different applications
  - Different species .small[(swifts? bats? squirrels?)]
  - Different cavities .small[(chimneys? caves? burrows?)]
  - Different behaviour .small[(shorebird incubation?)]

--
- Compare to ground observations

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.pull-left-c[.colourbox[Ground truthing!]]

---
# Check out `cavityuse`

## Openly developed on GitHub <img src = "./Figures/logos/github.png" style = "width: 35px; vertical-align: middle; margin-bottom: 5px;">: .small[<http://github.com/steffilazerte/cavityuse>]

- How to download/install `cavityuse`
- How to use `cavityuse`
- Contribution (feature-requests, bugs, code!)

<div style = "position:absolute; bottom: 30%">
<h1 style = "color: var(--colour1);">Thanks!</h1>
</div>
<img src = "./Figures/wtsp.png" style = "height: 150px;position:absolute;bottom:20%;left:50%;">

<div style = "position:absolute; text-align: right; bottom: 40px; right: 80px">
<div style = "margin-bottom: 20px;">
steffilazerte.ca
<img src = "./Figures/logos/web.png" style = "height: 40px; vertical-align:middle;"><br>
sel@steffilazerte.ca
<img src = "./Figures/logos/email.svg" style = "height: 25px; vertical-align:middle;margin-right:2px">
</div>
<img src = "./Figures/logos/logo_eg.png" style = "width: 350px">
</div>

.small[.align-bottom-left[Presentation Available: <https://steffilazerte.github.io/Presentations/><br>Slides created with the R package [xaringan](https://github.com/yihui/xaringan), using [remark.js](https://remarkjs.com), [knitr](http://yihui.name/knitr), and [R Markdown](https://rmarkdown.rstudio.com)<br><code class = "remark-inline-code">Compiled on 2018-08-10 with cavityuse v0.1.0</code>]]

---
# References

.small[
.hanging[
Burger J, Niles LJ, Porter RR, Dey AD (2012). Using geolocator data to reveal incubation periods and breeding biology in Red Knots Calidris canutus rufa. Wader Study Group Bull, 119:26-36. http://www.waderstudygroup.org/article/1890/

Cory TW, Wilsterman K, Kelley AD, Breton AR, Stark H, Humphries MM, McAdam AG, Barnes BM, Boutin S, Buck CL (2014). Light loggers reveal weather-driven changes in the daily activity patterns of arboreal and semifossorial rodents. Journal of Mammalogy, 95: Pages 1230–1239. https://doi.org/10.1644/14-MAMM-A-062

Gow EA, Wiebe KL, Fox JW (2015). Cavity use throughout the annual cycle of a migratory woodpecker revealed by geolocators. Ibis, 157:167-170. https://doi.org/10.1111/ibi.12206

Otter KA, Mckenna A, LaZerte SE, Ramsay SM (2017).The possible link between wintering grounds and continent-wide shifts in song dialects of white-throated sparrows (Oral). The joint meeting of the American Ornithological Society and the Society of Canadian Ornithologists/Société des ornithologistes du Canada (East Lansing, MI, USA).]]

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# Monitoring cavity use

---
## At the cavity
- Human observation
- Video surveillance
- Audio surveillance
- RFID loggers

## At the individual
- GPS/Accelerometers collars
- Temperature loggers
- Light loggers (i.e. geolocators)
- RFID loggers

<div class = "fig-right" style = "top:20%; height: 75%" >
<img src = "./Figures/steffi_muskoka_wide.JPG" style = "height: 100%"><div class = "attr">Gertrud Nürnberg</div>
</div>

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.pull-left[
## Limitations
- Knowing where potential cavities are
- Individual vs. Group patterns
- Cost (Equipment, technicians)
- Data Processing (time, reproducibility)]

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# Daytime activity for white-throated sparrows

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.small[
> White-throated sparrows spent
>  - 0.8% (0.7 - 0.8) of their time Inside
>  - 96.9% (96.7 - 97.3) of their time Outside
>  - 0.8% (0 - 2.3) of their time was ambiguous
]

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# Nighttime

## Sunrise / Sunset Detection

- See sunset and sunrise → "Out"
- See NO sunset OR sunrise →  "In"
- See either → "Ambiguous"

## Algorithm to detect sunrise/sunset
- Data from one geolocator to create the algorithm
- Tested on 4 others
- Days of calibration data

> Not bad!