R package for animal behavior classification from accelerometer data-rabc.
Ontology highlight
ABSTRACT:
SUBMITTER: Yu H
PROVIDER: S-EPMC8462134 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Accurate and low-cost sleep measurement tools are needed in both clinical and epidemiological research. To this end, wearable accelerometers are widely used as they are both low in price and provide reasonably accurate estimates of movement. Techniques to classify sleep from the high-resolution accelerometer data primarily rely on heuristic algorithms. In this paper, we explore the potential of detecting sleep using Random forests. Models were trained using data from three different studies where 134 adult participants (70 with sleep disorder and 64 good healthy sleepers) wore an accelerometer on their wrist during a one-night polysomnography recording in the clinic. The Random forests were able to distinguish sleep-wake states with an F1 score of 73.93% on a previously unseen test set of 24 participants. Detecting when the accelerometer is not worn was also successful using machine learning ([Formula: see text]), and when combined with our sleep detection models on day-time data provide a sleep estimate that is correlated with self-reported habitual nap behaviour ([Formula: see text]). These Random forest models have been made open-source to aid further research. In line with literature, sleep stage classification turned out to be difficult using only accelerometer data.
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Project description:Collar-mounted canine activity monitors can use accelerometer data to estimate dog activity levels, step counts, and distance traveled. With recent advances in machine learning and embedded computing, much more nuanced and accurate behavior classification has become possible, giving these affordable consumer devices the potential to improve the efficiency and effectiveness of pet healthcare. Here, we describe a novel deep learning algorithm that classifies dog behavior at sub-second resolution using commercial pet activity monitors. We built machine learning training databases from more than 5000 videos of more than 2500 dogs and ran the algorithms in production on more than 11 million days of device data. We then surveyed project participants representing 10,550 dogs, which provided 163,110 event responses to validate real-world detection of eating and drinking behavior. The resultant algorithm displayed a sensitivity and specificity for detecting drinking behavior (0.949 and 0.999, respectively) and eating behavior (0.988, 0.983). We also demonstrated detection of licking (0.772, 0.990), petting (0.305, 0.991), rubbing (0.729, 0.996), scratching (0.870, 0.997), and sniffing (0.610, 0.968). We show that the devices' position on the collar had no measurable impact on performance. In production, users reported a true positive rate of 95.3% for eating (among 1514 users), and of 94.9% for drinking (among 1491 users). The study demonstrates the accurate detection of important health-related canine behaviors using a collar-mounted accelerometer. We trained and validated our algorithms on a large and realistic training dataset, and we assessed and confirmed accuracy in production via user validation.
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Project description:Identification and classification of behavior states in animal movement data can be complex, temporally biased, time-intensive, scale-dependent, and unstandardized across studies and taxa. Large movement datasets are increasingly common and there is a need for efficient methods of data exploration that adjust to the individual variability of each track. We present the Residence in Space and Time (RST) method to classify behavior patterns in movement data based on the concept that behavior states can be partitioned by the amount of space and time occupied in an area of constant scale. Using normalized values of Residence Time and Residence Distance within a constant search radius, RST is able to differentiate behavior patterns that are time-intensive (e.g., rest), time & distance-intensive (e.g., area restricted search), and transit (short time and distance). We use grey-headed albatross (Thalassarche chrysostoma) GPS tracks to demonstrate RST's ability to classify behavior patterns and adjust to the inherent scale and individuality of each track. Next, we evaluate RST's ability to discriminate between behavior states relative to other classical movement metrics. We then temporally sub-sample albatross track data to illustrate RST's response to less resolved data. Finally, we evaluate RST's performance using datasets from four taxa with diverse ecology, functional scales, ecosystems, and data-types. We conclude that RST is a robust, rapid, and flexible method for detailed exploratory analysis and meta-analyses of behavioral states in animal movement data based on its ability to integrate distance and time measurements into one descriptive metric of behavior groupings. Given the increasing amount of animal movement data collected, it is timely and useful to implement a consistent metric of behavior classification to enable efficient and comparative analyses. Overall, the application of RST to objectively explore and compare behavior patterns in movement data can enhance our fine- and broad- scale understanding of animal movement ecology.
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Project description:Our aim in this study was to investigate whether the behaviors of dairy cows on pasture, predicted with accelerometer data and combined with GPS data, can be used to better understand the relationship between behaviors and pasture characteristics. During spring 2018, 26 Holstein cows were equipped with a 3D-accelerometer and a GPS sensor fixed on a neck-collar for five days. The cows grazed alternatively in permanent and in temporary grasslands. The structural elements, soil moisture, slope and botanical characteristics were identified. Behaviors were predicted every 10 s from the accelerometer data and combined with the GPS data. The time-budgets expressed in each characterized zone of 8 m × 8 m were calculated. The relation between the time-budgets and pasture characteristics was explored with a linear mixed model. In the permanent grassland, dairy cows spent more time under a tree to ruminate (p < 0.001) and to rest (p < 0.001) and more time to graze in areas with Holcus lanatus (p < 0.001). In the temporary grassland, behavior was influenced by the external environment (presence of other animals on the farm; p < 0.05). Thus, this methodology seems relevant to better understand the relationship between the behaviors of dairy cows and grazing conditions to develop precision grazing.
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Project description:Accelerometer-based activity monitors are widely used in research and surveillance applications for quantifying sedentary behavior (SB) and physical activity (PA). Considerable research has been done to refine methods for assessing PA, but relatively little attention has been given to operationalizing SB parameters (i.e., sedentary time and breaks) from accelerometer data - particularly in relation to health outcomes. This study investigated: (a) the accrued patterns of sedentary time and breaks; and (b) the associations of sedentary time and breaks in different bout durations with cardiovascular risk factors.Accelerometer data on 5,917 adults from the National Health Examination and Nutrition Survey (NHANES) 2003-2006 were used. Sedentary time and breaks at different bout durations (i.e., 1, 2-4, 5-9, 10-14, 15-19, 20-24, 25-29, and ≥ 30-min) were obtained using a threshold of < 100 counts per minute. Sedentary time and breaks were regressed on cardiovascular risk factors (waist circumference, triglyceride, and high-density lipoprotein cholesterol) and body mass index across bout durations.The results revealed that the majority of sedentary time occurred within relatively short bout durations (≈ 70% and ≈ 85% for < 5-min and < 10-min, respectively). The associations of sedentary time and breaks with health outcomes varied depending on how bout time was defined. Estimates of SB parameters based on bout durations of 5 min or shorter were associated with reduced cardiovascular risk factors while durations longer than 10-min were generally associated with increased risk factors.The present study demonstrates that the duration of sedentary bouts should be further considered when operationalizing the SB parameters from accelerometer data. The threshold of 5 minutes to define a bout is defensible, but a 10 minute threshold would provide a more conservative estimate to clearly capture the prolonged nature of sedentary behavior. Additional research is needed to determine the relative sensitivity and specificity of these thresholds.
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Project description:Advances in tracking technology have led to an exponential increase in animal location data, greatly enhancing our ability to address interesting questions in movement ecology, but also presenting new challenges related to data management and analysis. Step-selection functions (SSFs) are commonly used to link environmental covariates to animal location data collected at fine temporal resolution. SSFs are estimated by comparing observed steps connecting successive animal locations to random steps, using a likelihood equivalent of a Cox proportional hazards model. By using common statistical distributions to model step length and turn angle distributions, and including habitat- and movement-related covariates (functions of distances between points, angular deviations), it is possible to make inference regarding habitat selection and movement processes or to control one process while investigating the other. The fitted model can also be used to estimate utilization distributions and mechanistic home ranges. Here, we present the R package amt (animal movement tools) that allows users to fit SSFs to data and to simulate space use of animals from fitted models. The amt package also provides tools for managing telemetry data. Using fisher (Pekania pennanti) data as a case study, we illustrate a four-step approach to the analysis of animal movement data, consisting of data management, exploratory data analysis, fitting of models, and simulating from fitted models.
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Project description:the use of movement monitors (accelerometers) for measuring physical activity (PA) in intervention and population-based studies is becoming a standard methodology for the objective measurement of sedentary and active behaviors and for the validation of subjective PA self-reports. A vital step in PA measurement is the classification of daily time into accelerometer wear and nonwear intervals using its recordings (counts) and an accelerometer-specific algorithm.the purpose of this study was to validate and improve a commonly used algorithm for classifying accelerometer wear and nonwear time intervals using objective movement data obtained in the whole-room indirect calorimeter.we conducted a validation study of a wear or nonwear automatic algorithm using data obtained from 49 adults and 76 youth wearing accelerometers during a strictly monitored 24-h stay in a room calorimeter. The accelerometer wear and nonwear time classified by the algorithm was compared with actual wearing time. Potential improvements to the algorithm were examined using the minimum classification error as an optimization target.the recommended elements in the new algorithm are as follows: 1) zero-count threshold during a nonwear time interval, 2) 90-min time window for consecutive zero or nonzero counts, and 3) allowance of 2-min interval of nonzero counts with the upstream or downstream 30-min consecutive zero-count window for detection of artifactual movements. Compared with the true wearing status, improvements to the algorithm decreased nonwear time misclassification during the waking and the 24-h periods (all P values < 0.001).the accelerometer wear or nonwear time algorithm improvements may lead to more accurate estimation of time spent in sedentary and active behaviors.
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