animalnexus.github.io/index.html at master · animalnexus/animalnexus.github.io · GitHub

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<h1 class="title toc-ignore">About</h1>

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<p>The animal<strong>nexus</strong> project is large collaborative effort to develop tools for the observation, visualization, and analysis of animal movements registered by RFID feeders or other static recording stations.</p>
<p>Our goals are to provide a tool that is easy to use, yet powerful. We hope that this project will be useful to scientists, citizen scientists, students and educators alike.</p>
<p>If you’re interested in contributing functionality and/or coding to this project, check out our project on <a href = 'http://github.com/steffilazerte/feedr/' target = 'blank'>GitHub</a></p>
<p>We welcome all involvement!</p>
<hr />
<div id="animalnexus-and-feedr" class="section level2">
<h2>animal<strong>nexus</strong> and <code>feedr</code></h2>
<p>The <code>feedr</code> package for R is a collection of functions and shiny apps designed to help with loading, checking, transforming and visualizing RFID data, or other data types collected from static stations. The <code>feedr</code> package can be found on <a href="https://github.com/animalnexus/feedr">github</a> along with basic installation instructions.</p>
<p>This package includes a companion website, <a href="http://animalnexus.ca" class="uri">http://animalnexus.ca</a>, designed to provide a simple user-interface to access package functions and the animalnexus data base without having to use R.</p>
<p>The R package provides all the functionality and is used by the web-app. Users familiar with R can download and install the R package, users who prefer a graphical user-interface can access most of the same functionality through the animal<strong>nexus</strong> webapp.</p>
<hr />
</div>
<div id="our-reserach-projects" class="section level2">
<h2>Our Reserach Projects</h2>
<div id="tru-campus-monitoring" class="section level3">
<h3>TRU campus monitoring</h3>
<p><strong>Institution:</strong> <a href="http://tru.ca">Thompson Rivers University</a><br />
<strong>Funding Partners:</strong> <a href="http://www.nserc-crsng.gc.ca/index_eng.asp">NSERC</a><br />
<strong>People:</strong> Matt Reudink, Mark Paetkau, David J. Hill, Jackson Kusack, Alistair Sutter, Jerin Roberts, Jamie Shippit, Brandon Turner, Steffi LaZerte</p>
<p>Wifi enabled feeders automatically upload data on feeder use of common city birds (house finches, mountain chickadees, etc.). We’re currently examining barriers to movement in an urban setting.</p>
</div>
<div id="unbc-gap-crossing-in-chickadees" class="section level3">
<h3>UNBC gap-crossing in chickadees</h3>
<p><strong>Institution:</strong> <a href="http://unbc.ca">University of Northern British Columbia</a><br />
<strong>Funding Partners:</strong> <a href="http://www.nserc-crsng.gc.ca/index_eng.asp">NSERC</a>, <a href="http://www.edynamics.com/">Environmental Dynamics Inc. (EDI)</a><br />
<strong>People:</strong> Ken Otter, Jacob Baily, Steffi LaZerte</p>
<p>Habitats gaps have been well documented to act as habitat barriers to bird movement, negatively effecting the dispersal of juveniles, and reducing genetic connectivity between populations. Our work uses a novel approach (radio-frequency identification - RFID) to assess the permeability of habitat gaps, and investigate what factors influence avian gap crossing decisions. Using bird feeders outfitted with RFID readers, we tracked the movement patterns of resident, wintering black-capped chickadees individually banded with passive integrated transponder (PIT) tags. Preliminary results support the prediction that gaps are perceived as movement barriers; bird movements between feeders on opposite sides of gaps were reduced compared to feeders on the same sides of habitat gaps.</p>
</div>
<div id="slu-behaviour-and-movements-of-wintering-birds" class="section level3">
<h3>SLU behaviour and movements of wintering birds</h3>
<p><strong>Institution:</strong> <a href="http://www.slu.se/en/">Swedish University for Agricultural Sciences (SLU)</a><br />
<strong>Funding Partners:</strong> Bröderna Edlunds Fund<br />
<strong>People:</strong> Adriaan De Jong, Bo-Sören Wiklund, Holger Dettki, Ola Engman and students from Dragonskolan College</p>
<p>At SLU campus in northern Sweden, studies of behaviour and movements of wintering birds are combined with the development of rugged high-tech RFID feeder/reader units for long-term monitoring under harsh climatic conditions.</p>
</div>
<div id="osu-community-ecology-of-tropical-pollinators" class="section level3">
<h3>OSU Community ecology of tropical pollinators</h3>
<p><strong>Institution:</strong> <a href="http://oregonstate.edu/">Oregon State University</a><br />
<strong>Funding Partners:</strong> <a href="http://www.nsf.gov/">NSF</a><br />
<strong>People:</strong> Matt Betts, Evan Jackson</p>
<p>Pollination is essential to human wellbeing, as well as fundamental to maintenance of biological diversity. Research showing large-scale declines of plants and pollinators highlights the concern that pollination is an ecosystem service at risk. Habitat loss and fragmentation have been implicated as primary drivers of pollination declines, but these observations contradict most model predictions indicating that pollinator networks should be resilient. Very recent theoretical models predict that if ‘keystone’ species are lost, pollination webs may be more vulnerable, resulting in sudden network collapse. However, lack of experimental studies examining the consequences of plant or pollinator extinction means that we know little about whether such collapses occur in nature.</p>
<p>This research will focus on the idea that plant-pollinator interactions can be lost if pollinator movement is restricted due to landscape fragmentation. The tropical hummingbird-plant system is ideal for this because the large size of hummingbirds in relation to other pollinators enables tracking of movements across whole landscapes.</p>
<p>This research will address two overarching questions: (1) What are the consequences of keystone plant decline and extinction to the broader pollination network? (2) Can pollinator movement and landscape connectivity buffer pollination networks against network collapse?</p>
<p>To address these questions the research team will experimentally remove H. tortuosa in isolated and connected forest fragments to determine whether altered densities of this species affects (a) hummingbird movement, (b) plant reproduction and genetic diversity, and (c) the structure of the pollination network. Hummingbird movement will be quantified for all species in the network using Radio-Frequency Identification Devices (RFID). This method, already successfully demonstrated in this project, will enable observations of the entire hummingbird pollinator community at an unprecedented temporal resolution (seconds) and spatial extent (1000 m radius landscapes).</p>
<hr />
<p>Back to <a href="#top">top</a><br />
Start at the beginning <a href="index.html">Home</a></p>
<!-- Render entire site:
rmarkdown::render_site() -->
<!-- This is an overview of how to use the shiny webapp [animalnexus](http://animalnexus.ca).

For information on how to use the R package [`feedr`](http://github.com/animalnexus/feedr) see our [`feedr` tutorials](http://animalnexus.github.io/feedr).

Confused about the difference? See [About](#about).

1. [**Loading/Importing Data**](#load)
    Data from the animalnexus database or imported
2. [**Visualizations**](#vis)
    Interactive maps which visualize movements between and presence around the RFID loggers.
3. [**Transformations**](#trans)
    Transforming raw data into visits, presence, activity, etc

## Tutorial Data
Two data frames, `finches` and `chickadees` are included for the purpose of demonstration.

LINK TO DATA
-->
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