Scharf, Anne K.
MoveApps : a serverless no-code analysis platform for animal tracking data
2022-07-18, Kölzsch, Andrea, Davidson, Sarah C., Gauggel, Dominik, Hahn, Clemens, Lang, Ilona, Scharf, Anne K., Schneider, Gabriel, Vinciguerra, Candace M., Wikelski, Martin, Safi, Kamran
Bio-logging and animal tracking datasets continuously grow in volume and complexity, documenting animal behaviour and ecology in unprecedented extent and detail, but greatly increasing the challenge of extracting knowledge from the data obtained. A large variety of analysis methods are being developed, many of which in effect are inaccessible to potential users, because they remain unpublished, depend on proprietary software or require significant coding skills.
We developed MoveApps, an open analysis platform for animal tracking data, to make sophisticated analytical tools accessible to a global community of movement ecologists and wildlife managers. As part of the Movebank ecosystem, MoveApps allows users to design and share workflows composed of analysis modules (Apps) that access and analyse tracking data. Users browse Apps, build workflows, customise parameters, execute analyses and access results through an intuitive web-based interface.
Apps, coded in R or other programming languages, have been developed by the MoveApps team and can be contributed by anyone developing analysis code. They become available to all user of the platform. To allow long-term and cross-system reproducibility, Apps have public source code and are compiled and run in Docker containers that form the basis of a serverless cloud computing system. To support reproducible science and help contributors document and benefit from their efforts, workflows of Apps can be shared, published and archived with DOIs in the Movebank Data Repository.
The platform was beta launched in spring 2021 and currently contains 49 Apps that are used by 316 registered users. We illustrate its use through two workflows that (1) provide a daily report on active tag deployments and (2) segment and map migratory movements.
The MoveApps platform is meant to empower the community to supply, exchange and use analysis code in an intuitive environment that allows fast and traceable results and feedback. By bringing together analytical experts developing movement analysis methods and code with those in need of tools to explore, answer questions and inform decisions based on data they collect, we intend to increase the pace of knowledge generation and integration to match the huge growth rate in bio-logging data acquisition.
Habitat suitability does not capture the essence of animal-defined corridors
2018, Scharf, Anne K., Belant, Jerrold L., Beyer, Dean E., Wikelski, Martin, Safi, Kamran
Increases in landscape connectivity can improve a species’ ability to cope with habitat fragmentation and degradation. Wildlife corridors increase landscape connectivity and it is therefore important to identify and maintain them. Currently, corridors are mostly identified using methods that rely on generic habitat suitability measures. One important and widely held assumption is that corridors represent swaths of suitable habitat connecting larger patches of suitable habitat in an otherwise unsuitable environment. Using high-resolution GPS data of four large carnivore species, we identified corridors based on animal movement behavior within each individual’s home range and quantified the spatial overlap of these corridors. We thus tested whether corridors were in fact spatial bottle necks in habitat suitability surrounded by unsuitable habitat, and if they could be characterized by their coarse-scale environmental composition.
We found that most individuals used corridors within their home ranges and that several corridors were used simultaneously by individuals of the same species, but also by individuals of different species. When we compared the predicted habitat suitability of corridors and their immediate surrounding area we found, however, no differences.
We could not find a direct correspondence between corridors chosen and used by wildlife on the one hand, and a priori habitat suitability measurements on the other hand. This leads us to speculate that identifying corridors relying on typically-used habitat suitability methods alone may misplace corridors at the level of space use within an individual’s home range. We suggest future studies to rely more on movement data to directly identify wildlife corridors based on the observed behavior of the animals.
The Movebank system for studying global animal movement and demography
2022, Kays, Roland, Davidson, Sarah C., Fiedler, Wolfgang, Flack, Andrea, Kölzsch, Andrea, Partecke, Jesko, Quetting, Michael, Safi, Kamran, Scharf, Anne K., Schneider, Gabriel, Lang, Ilona, Landwehr, Matthias, van Schalkwyk, Louis, Weinzierl, Rolf, Wikelski, Martin
Quantifying movement and demographic events of free-ranging animals is fundamental to studying their ecology, evolution and conservation. Technological advances have led to an explosion in sensor-based methods for remotely observing these phenomena. This transition to big data creates new challenges for data management, analysis and collaboration. We present the Movebank ecosystem of tools used by thousands of researchers to collect, manage, share, visualize, analyse and archive their animal tracking and other animal-borne sensor data. Users add sensor data through file uploads or live data streams and further organize and complete quality control within the Movebank system. All data are harmonized to a data model and vocabulary. The public can discover, view and download data for which they have been given access to through the website, the Animal Tracker mobile app or by API. Advanced analysis tools are available through the EnvDATA System, the MoveApps platform and a variety of user-developed applications. Data owners can share studies with select users or the public, with options for embargos, licenses and formal archiving in a data repository. Movebank is used by over 3,100 data owners globally, who manage over 6 billion animal location and sensor measurements across more than 6,500 studies, with thousands of active tags sending over 3 million new data records daily. These data underlie >700 published papers and reports. We present a case study demonstrating the use of Movebank to assess life-history events and demography, and engage with citizen scientists to identify mortalities and causes of death for a migratory bird. A growing number of researchers, government agencies and conservation organizations use Movebank to manage research and conservation projects and to meet legislative requirements. The combination of historic and new data with collaboration tools enables broad comparative analyses and data acquisition and mapping efforts. Movebank offers an integrated system for real-time monitoring of animals at a global scale and represents a digital museum of animal movement and behaviour. Resources and coordination across countries and organizations are needed to ensure that these data, including those that cannot be made public, remain accessible to future generations.
Acceleration Data Reveal Highly Individually Structured Energetic Landscapes in Free-Ranging Fishers (Pekania pennanti)
2016-02-03, Scharf, Anne K., LaPoint, Scott, Wikelski, Martin, Safi, Kamran
Investigating animal energy expenditure across space and time may provide more detailed insight into how animals interact with their environment. This insight should improve our understanding of how changes in the environment affect animal energy budgets and is particularly relevant for animals living near or within human altered environments where habitat change can occur rapidly. We modeled fisher (Pekania pennanti) energy expenditure within their home ranges and investigated the potential environmental and spatial drivers of the predicted spatial patterns. As a proxy for energy expenditure we used overall dynamic body acceleration (ODBA) that we quantified from tri-axial accelerometer data during the active phases of 12 individuals. We used a generalized additive model (GAM) to investigate the spatial distribution of ODBA by associating the acceleration data to the animals' GPS-recorded locations. We related the spatial patterns of ODBA to the utilization distributions and habitat suitability estimates across individuals. The ODBA of fishers appears highly structured in space and was related to individual utilization distribution and habitat suitability estimates. However, we were not able to predict ODBA using the environmental data we selected. Our results suggest an unexpected complexity in the space use of animals that was only captured partially by re-location data-based concepts of home range and habitat suitability. We suggest future studies recognize the limits of ODBA that arise from the fact that acceleration is often collected at much finer spatio-temporal scales than the environmental data and that ODBA lacks a behavioral correspondence. Overcoming these limits would improve the interpretation of energy expenditure in relation to the environment.
Overall Dynamic Body Acceleration in Straw-Colored Fruit Bats Increases in Headwinds but Not With Airspeed
2019-05-31, O'Mara, Michael Teague, Scharf, Anne K., Fahr, Jakob, Abedi-Lartey, Michael, Wikelski, Martin, Dechmann, Dina K. N., Safi, Kamran
Atmospheric conditions impact how animals use the aerosphere, and birds and bats should modify their flight to minimize energetic expenditure relative to changing wind conditions. To investigate how free-ranging straw-colored fruit bats (Eidolon helvum) fly with changing wind support, we use data collected from bats fit with GPS loggers and an integrated triaxial accelerometer and measure flight speeds, wingbeat frequency, and overall dynamic body acceleration (ODBA) as an estimate for energetic expenditure. We predicted that if ODBA reflects energetic expenditure, then we should find a curvilinear relationship between ODBA and airspeed consistent with aerodynamic theory. We expected that bats would lower their airspeed with tailwind support and that ODBA will decrease with increasing tailwinds and increase with wingbeat frequency. We found that wingbeat frequency has the strongest positive relationship with ODBA. There was a small, but negative, relationship between airspeed and ODBA, and bats decreased ODBA with increasing tailwind. Bats flew at ground speeds of 9.6 ± 2.4 ms−1 (Mean ± SD, range: 4.3–23.9 ms−1) and airspeeds of 10.2 ± 2.5 ms−1, and did not modify their wingbeat frequency with speed. Free-ranging straw-colored fruit bats therefore exerted more total ODBA in headwinds but not when they changed their airspeed. It is possible that the flexibility in wingbeat kinematics may make flight of free-ranging bats less costly than currently predicted or alternatively that the combination of ODBA and airspeed at our scales of measurement does not reflect this relationship in straw-colored fruit bats. Further work is needed to understand the full potential of free-ranging bat flight and how well bio-logging techniques reflect the costs of bat flight.