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Scharf, A. K.

Publications and source records attributed to Scharf, A. K..

4 recordsLinked to original sources

move2utils: a utility toolkit for the move2 ecosystem

1. Studying animal movement at the population scale requires a stable, modern software substrate. Within R, the legacy move package supplied that substrate for over a decade, but its sp/rgeos backbone has been retired. The successor package move2 deliberately confined its scope to the data class and core movebank API functions. 2. The analytical machinery of move, namely dynamic Brownian-bridge utilisation distributions, the directional bivariate-Gaussian variant, corridor segmentation, and along-track thinning, was left to port to the modern sf/terra stack. 3. We present move2utils, an R package that completes and complements that transition. move2utils provides move2-native ports of the move analytical functions, preserves the original C kernels where they exist, and replaces the deprecated spatial scaffolding around them. It additionally ports some of the legacy R code to faster C kernels. move2utils also exposes novel outlier-detection methodology described in detail in a companion paper. 4. The package is open-source (GPL [≥] 3), is developed on the MPCDF GitLab and mirrored on GitHub for public installation, and ships with vignettes and a CI-tested check suite. We illustrate it with a worked example on real tracking data and synthetic datasets.

ecology↗

MoveTraits - A database for integrating animal behaviour into trait-based ecology

Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits - standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure, and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species acclimation and adaptive capacity to environmental change. We outline a vision for a living global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology, and (3) providing information on multi-level (species, individual, within-individual) trait variation. We present a proof-of-concept MoveTraits database with 55 mammal and 108 bird species, demonstrating calculation workflows for 5 traits across multiple time scales. Movement traits have significant potential to improve trait-based global change predictions and contribute to global biodiversity assessments as Essential Biodiversity Variables. By making animal movement data more accessible and interpretable, this database could bridge the gap between movement ecology and biodiversity policy, facilitating evidence-based conservation.

ecology↗

MoveApps - a serverless no-code analysis platform for animal tracking data

BackgroundBio-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. ResultsWe 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 44 Apps that are used by 156 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. ConclusionsThe 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.

ecology↗

A comprehensive framework for handling location error in animal tracking data

Animal tracking data are being collected more frequently, in greater detail, and on smaller taxa than ever before. These data hold the promise to increase the relevance of animal movement for understanding ecological processes, but this potential will only be fully realized if their accompanying location error is properly addressed. Historically, coarsely-sampled movement data have proved invaluable for understanding large scale processes (e.g., home range, habitat selection, etc.), but modern fine-scale data promise to unlock far more ecological information. While GPS location error can often be ignored in coarsely sampled data, fine-scale data require more care, and tools to do this have not kept pace. Current approaches to dealing with location error largely fall into two categories--either discarding the least accurate location estimates prior to analysis or simultaneously fitting movement and error parameters in a hidden-state model. In some cases these approaches can provide a level of correction, but they have known limitations, and in some cases they can be worse than doing nothing. Here, we provide a general framework to account for location error in the analysis of triangulated and trilatcralizcd animal tracking data, which includes GPS, Argos Doppler-shift, triangulated VHF, trilatcralized acoustic and cellular location data. We apply our error-modelselection framework to 190 GPS, cellular, and acoustic devices representing 27 models from 14 manufacturers. Collectively, these devices were used to track a wide range of taxa comprising birds, fish, reptiles, and mammals of different sizes and with different behaviors, in urban, suburban, and wild settings. In almost half of the tested device models, error-model selection was necessary to obtain the best performing error model, and in almost a quarter of tested device models, the reported DOP values were actually misinformative. Then, using empirical tracking data from multiple species, we provide an overview of modern, error-informed movement analyses, including continuous-time path reconstruction, home-range distribution, home-range overlap, speed, and distance estimation. Adding to these techniques, we introduce new error-informed estimators for outlier detection and autocorrelation visualization. Because error-induced biases depend on many factors--sampling schedule, movement characteristics, tracking device, habitat, etc.--differential bias can easily confound biological inference and lead researchers to draw false conclusions. We demonstrate how error-informed analyses on calibrated tracking data can provide more accurate estimates are that are insensitive to location error, and allow researchers to use all of their data.

ecology↗