Six Years of Shiny in Research -- Collaborative Development of Web Tools in R

Peter Kasprzak,

Lachlan Mitchell,

Olena Kravchuk

et al.

arXiv (Cornell University), Journal Year: 2021, Volume and Issue: unknown

Published: Jan. 11, 2021

The use of Shiny in research publications is investigated. From the appearance this popular web application framework for R through to 2018, it has been utilised many diverse areas. While can be shown that complexity applications limited by background architecture, and real security concerns exist novice app developers, collaborative benefits are worth attention from wider community. simplifies complex methodologies users different specialities, at level proficiency appropriate end user. This enables a community interact efficiently, utilising cutting-edge methodologies. literature reviewed demonstrates put into practice without necessity investment professional training. It would appear opens up concurrent communication between those who analyse data other disciplines, thereby potentially enriching technology.

Language: Английский

Heat dissipation capacity influences reproductive performance in an aerial insectivore DOI Creative Commons
Simon Tapper, Joseph J. Nocera, Gary Burness

et al.

Journal of Experimental Biology, Journal Year: 2020, Volume and Issue: unknown

Published: Jan. 1, 2020

Climatic warming is predicted to increase the frequency of extreme weather events, which may reduce an individual's capacity for sustained activity because thermal limits. We tested whether risk overheating limit parental provisioning aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought operate close energetic ceiling during 2-3 week chick-rearing period. The factors determining remain unknown, although it be set by dissipate body heat (the dissipation limitation hypothesis). Over two seasons we experimentally trimmed ventral feathers female tree swallows (Tachycineta bicolor) provide a window. then monitored maternal and paternal rates, nestling growth rates fledging success. found effect our experimental treatment was context dependent. Females with enhanced fed their nestlings at higher than controls when conditions were hot, but reverse true under cool conditions. Control females mates both reduced foraging hot In contrast, male partners maintained constant feeding rate across temperatures, suggesting attempts match partners. On average, heavier controls, did not have probability fledging. suggest that removal constraint allowed additionally provided advantage via increased transfer brooding. Our data support hypothesis depending on temperature, can influence reproductive success insectivores.

Language: Английский

Citations

32

The effects of humidity on thermoregulatory physiology of a small songbird DOI Creative Commons

Cody K. Porter,

Kevin M. Cortes,

Ofir Levy

et al.

Journal of Experimental Biology, Journal Year: 2024, Volume and Issue: 227(13)

Published: June 10, 2024

Scholander-Irving curves describe the relationship between ambient temperature and metabolic rate are fundamental to understanding energetic demands of homeothermy. However, typically measured in dry air, which is not representative humidity many organisms experience nature. Consequently, it unclear (1) whether (especially below thermoneutrality) altered by humidity, given effects on thermal properties (2) physiological responses associated with lab reflect organismal performance humid field conditions. We used laboratory experiments biophysical models test thermoregulatory physiology tree swallows (Tachycineta bicolor). also tested under conditions were correlated body temperatures nestling provisioning rates. found that reduced rates evaporative water loss but did have large or rate, suggesting can decouple cooling, rate. Although effect was small, our indicated costs thermoregulation ∼8% greater simulations from birds compared Finally, we mixed evidence nest field. Our results help clarify endotherm thermoregulation, may forecast environmental change.

Language: Английский

Citations

2

A Raspberry Pi-based, RFID-equipped birdfeeder for the remote monitoring of wild bird populations DOI
Mason Youngblood

Ringing & Migration, Journal Year: 2019, Volume and Issue: 34(1), P. 25 - 32

Published: Jan. 2, 2019

Radio-frequency identification (RFID) is an increasingly popular wireless technology that allows researchers to monitor wild bird populations from fixed locations in the field. I have developed RFID-equipped birdfeeder based on Raspberry Pi Zero W, a low-cost single-board computer, collects continuous visitation data birds marked with passive integrated transponder (PIT) tags. Each has perch antenna connected RFID-reader board powered by portable battery. When tagged lands eat feeder, its unique code stored date and time Pi. These birdfeeders require only basic soldering coding skills assemble, can easily be outfitted additional hardware like video cameras microphones. outline process of assembling setting up operating system for birdfeeders. Then, describe example implementation track House Finches Haemorhous mexicanus campus Queens College New York City.

Language: Английский

Citations

18

feedr and animalnexus.ca: A paired R package and user‐friendly Web application for transforming and visualizing animal movement data from static stations DOI Creative Commons
Steffi LaZerte, Matthew W. Reudink, Ken A. Otter

et al.

Ecology and Evolution, Journal Year: 2017, Volume and Issue: 7(19), P. 7884 - 7896

Published: Aug. 30, 2017

Abstract Radio frequency identification ( RFID ) provides a simple and inexpensive approach for examining the movements of tagged animals, which can provide information on species behavior ecology, such as habitat/resource use social interactions. In addition, tracking animal is appealing to naturalists, citizen scientists, general public thus represents tool engagement in science education. Although useful tool, large amount data collected using may quickly become overwhelming. Here, we present an R package feedr have developed loading, transforming, visualizing time‐stamped, georeferenced data, from static logger stations. Using our package, be transformed raw visits, presence (regular detections by over time), between loggers, displacements, activity patterns. several conversion functions allow users format other complementary packages. Data also visualized through or interactive maps animations time. To increase accessibility, either directly, companion site: http://animalnexus.ca , online, user‐friendly, R‐based Shiny Web application. This system used professional scientists alike view study movements. We designed this flexible able handle stationary sources (e.g., hair traps, very high VHF telemetry observations marked individuals colonies staging sites), hope framework will meeting point science, education, community awareness animals. aim inspire while simultaneously enabling robust scientific analysis.

Language: Английский

Citations

12

Anthropogenic noise alters parental behavior and nestling developmental patterns, but not fledging condition DOI Creative Commons
Meelyn Pandit, James Eapen,

Gabriela Pineda-Sabillon

et al.

Behavioral Ecology, Journal Year: 2021, Volume and Issue: 32(4), P. 747 - 755

Published: Feb. 9, 2021

Abstract Anthropogenic noise is a ubiquitous feature of the American landscape, and known stressor for many bird species, leading to negative effects in behavior, physiology, reproduction, ultimately fitness. While number studies have examined how anthropogenic affects avian fitness, there are few that simultaneously examine impacts relationship between parental care behavior nestling We conducted Brownian playbacks 6 h day during nesting cycle on Eastern Bluebird (Sialia sialis) nest boxes investigate if experimentally elevated affected body conditions, stress indices. documented attendance by adult females using radio frequency identification (RFID), we assessed measuring baseline corticosterone levels telomere lengths. Based RFID data collected individual brood cycles, bluebirds exposed had significantly higher feeding rates earlier than adults control group, but reduced later cycle. Nestlings conditions nestlings at 11 days age, equalized treatments 14. found no differences or lengths two treatment groups. Our results revealed altered which corresponded with condition. However, absence indicators longer-term offspring suggests may been short-term response.

Language: Английский

Citations

10

Rapid prototyping of decision‐support tools for conservation DOI
Denis Valle, Kok Ben Toh, Justin Millar

et al.

Conservation Biology, Journal Year: 2019, Volume and Issue: 33(6), P. 1448 - 1450

Published: March 4, 2019

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by authors. Any queries (other than missing content) should be directed to corresponding author article.

Language: Английский

Citations

7

Using radio frequency identification (RFID) to investigate the gap-crossing decisions of Black-capped Chickadees (Poecile atricapillus) DOI
Jacob Bailey, Matthew W. Reudink, Steffi LaZerte

et al.

Ornithology, Journal Year: 2018, Volume and Issue: 135(3), P. 449 - 460

Published: April 18, 2018

Gaps in forest habitat are well documented to negatively impact the movements of songbirds. Much past research on avian gap-crossing decisions has utilized playback experiments. However, playbacks limited by short observation times and often cannot be used reveal differences behaviors among individuals. Here, we present a novel approach utilizing radio-frequency identification (RFID) investigate Black-capped Chickadees (Poecile atricapillus). Using bird feeders outfitted with RFID readers, were able track movement patterns wintering within forests across gaps. We logistic regression an information theoretic identify factors that best predicted behaviors. impeded predictors gap size vegetation density. Birds more likely make crossings decreasing when gaps contained matrix (1–2 m height). recommend primary way increase connectivity for birds fragmented habitats is reduce distances. Additionally, it may beneficial shrubby or woody height over 1 m, as this also increases likelihood gap-crossing.

Language: Английский

Citations

6

Introduction to the special section on Visual Movement Analytics DOI Open Access
Urška Demšar, Aidan Slingsby, Robert Weibel

et al.

Information Visualization, Journal Year: 2018, Volume and Issue: 18(1), P. 133 - 137

Published: Nov. 7, 2018

Language: Английский

Citations

3

Heat dissipation capacity influences reproductive performance in an aerial insectivore DOI Creative Commons
Simon Tapper, Joseph J. Nocera, Gary Burness

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: July 22, 2019

Abstract Climatic warming will likely increase the frequency of extreme weather events, which may reduce an individual’s capacity for sustained activity due to thermal limits. We tested whether risk overheating limit parental provisioning aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought operate close energetic ceiling during 2-3 week chick-rearing period. The factors determining remain unknown, although it be set by dissipate body heat (the dissipation limitation hypothesis). To test this hypothesis, over two seasons we experimentally trimmed ventral feathers female tree swallows ( Tachycineta bicolor ) provide a window. then monitored maternal rates, nestling growth and fledging success. found effect our experimental treatment was context-dependent varied with environmental conditions. Females plumage fed their nestlings at higher rates than controls when conditions were hot non-windy, but reverse true under cool windy On average, females heavier controls, had probability fledging. suggest that removal constraint allowed additionally provided advantage via increased transfer brooding. Our data partial support depending on patterns, can influence reproductive success insectivores.

Language: Английский

Citations

2

Why did the chickadee cross the road: effects of linear habitat gaps on the movements of black-capped chickadees DOI Open Access
Jacob Bailey

Published: Jan. 1, 2017

I present a novel approach utilizing radio frequency identification (RFID) birdfeeders, coupled with playback experiments, to investigate the gap-crossing decisions of black-capped chickadees (Poecile atricapillus). Results from my RFID experiments revealed that best predictors behaviors were gap-distance, and vegetation density. Birds less likely cross as gap distance increased. As amount within gaps increased, birds more cross. Playback showed decrease in behaviour after sampling period. Because birdfeeders put out during this time, decreases propensity suggests may be engaging tradeoff between energy reserves risk taking. both confirm do restrict movements wintering chickadees. recommend primary way increase connectivity for fragmented habitats is reduce across gaps. Furthermore, increasing also connectivity.

Language: Английский

Citations

0