More Like this

1. Estimating encounter location distributions from animal tracking data

   https://doi.org/10.1111/2041-210X.13597  

   Noonan, Michael J. ; Martinez‐Garcia, Ricardo ; Davis, Grace H. ; Crofoot, Margaret C. ; Kays, Roland ; Hirsch, Ben T. ; Caillaud, Damien ; Payne, Eric ; Sih, Andrew ; Sinn, David L. ; et al ( May 2021 , Methods in Ecology and Evolution)

   Ecologists have long been interested in linking individual behaviour with higher level processes. For motile species, this ‘upscaling’ is governed by how well any given movement strategy maximizes encounters with positive factors and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modelling. Furthermore, existing work has focused primarily on the relationship between animal movement and encounterrateswhile the relationship between individual movement and the spatiallocationsof encounter events in the environment has remained conspicuously understudied.

   Here, we bridge this gap by introducing a method for describing the long‐term encounter location probabilities for movement within home ranges, termed the conditional distribution of encounters (CDE). We then derive this distribution, as well as confidence intervals, implement its statistical estimator into open‐source software and demonstrate the broad ecological relevance of this distribution.

   We first use simulated data to show how our estimator provides asymptotically consistent estimates. We then demonstrate the general utility of this method for three simulation‐based scenarios that occur routinely in biological systems: (a) a population of individuals with home ranges that overlap with neighbours; (b) a pair of individuals with a hard territorial border between their home ranges; and (c) a predator with a large home range that encompassed the home ranges of multiple prey individuals. Using GPS data from white‐faced capuchinsCebus capucinus, tracked on Barro Colorado Island, Panama, and sleepy lizardsTiliqua rugosa,tracked in Bundey, South Australia, we then show how the CDE can be used to estimate the locations of territorial borders, identify key resources, quantify the potential for competitive or predatory interactions and/or identify any changes in behaviour that directly result from location‐specific encounter probability.

   The CDE enables researchers to better understand the dynamics of populations of interacting individuals. Notably, the general estimation framework developed in this work builds straightforwardly off of home range estimation and requires no specialized data collection protocols. This method is now openly available via thectmm Rpackage.

    

   more » « less
2. movedesign: Shiny R app to evaluate sampling design for animal movement studies

   https://doi.org/10.1111/2041-210X.14153  

   Silva, Inês ; Fleming, Christen H. ; Noonan, Michael J. ; Fagan, William F. ; Calabrese, Justin M. ( June 2023 , Methods in Ecology and Evolution)

   Projects focused on movement behaviour and home range are commonplace, but beyond a focus on choosing appropriate research questions, there are no clear guidelines for such studies. Without these guidelines, designing an animal tracking study to produce reliable estimates of space‐use and movement properties (necessary to answer basic movement ecology questions), is often done in an ad hoc manner.

   We developed ‘movedesign’, a user‐friendly Shiny application, which can be utilized to investigate the precision of three estimates regularly reported in movement and spatial ecology studies: home range area, speed and distance travelled. Conceptually similar to statistical power analysis, this application enables users to assess the degree of estimate precision that may be achieved with a given sampling design; that is, the choices regarding data resolution (sampling interval) and battery life (sampling duration).

   Leveraging the ‘ctmm’Rpackage, we utilize two methods proven to handle many common biases in animal movement datasets: autocorrelated kernel density estimators (AKDEs) and continuous‐time speed and distance (CTSD) estimators. Longer sampling durations are required to reliably estimate home range areas via the detection of a sufficient number of home range crossings. In contrast, speed and distance estimation requires a sampling interval short enough to ensure that a statistically significant signature of the animal's velocity remains in the data.

   This application addresses key challenges faced by researchers when designing tracking studies, including the trade‐off between long battery life and high resolution of GPS locations collected by the devices, which may result in a compromise between reliably estimating home range or speed and distance. ‘movedesign’ has broad applications for researchers and decision‐makers, supporting them to focus efforts and resources in achieving the optimal sampling design strategy for their research questions, prioritizing the correct deployment decisions for insightful and reliable outputs, while understanding the trade‐off associated with these choices.

    

   more » « less
3. Overcoming the challenge of small effective sample sizes in home‐range estimation

   https://doi.org/10.1111/2041-210X.13270  

   Fleming, Christen H. ; Noonan, Michael J. ; Medici, Emilia Patricia ; Calabrese, Justin M. ; Matthiopoulos, ed., Jason ( August 2019 , Methods in Ecology and Evolution)

   Technological advances have steadily increased the detail of animal tracking datasets, yet fundamental data limitations exist for many species that cause substantial biases in home‐range estimation. Specifically, the effective sample size of a range estimate is proportional to the number of observed range crossings, not the number of sampled locations. Currently, the most accurate home‐range estimators condition on an autocorrelation model, for which the standard estimation frame‐works are based on likelihood functions, even though these methods are known to underestimate variance—and therefore ranging area—when effective sample sizes are small.

   Residual maximum likelihood (REML) is a widely used method for reducing bias in maximum‐likelihood (ML) variance estimation at small sample sizes. Unfortunately, we find that REML is too unstable for practical application to continuous‐time movement models. When the effective sample sizeNis decreased toN ≤ (10), which is common in tracking applications, REML undergoes a sudden divergence in variance estimation. To avoid this issue, while retaining REML’s first‐order bias correction, we derive a family of estimators that leverage REML to make a perturbative correction to ML. We also derive AIC values for REML and our estimators, including cases where model structures differ, which is not generally understood to be possible.

   Using both simulated data and GPS data from lowland tapir (Tapirus terrestris), we show how our perturbative estimators are more accurate than traditional ML and REML methods. Specifically, when(5) home‐range crossings are observed, REML is unreliable by orders of magnitude, ML home ranges are ~30% underestimated, and our perturbative estimators yield home ranges that are only ~10% underestimated. A parametric bootstrap can then reduce the ML and perturbative home‐range underestimation to ~10% and ~3%, respectively.

   Home‐range estimation is one of the primary reasons for collecting animal tracking data, and small effective sample sizes are a more common problem than is currently realized. The methods introduced here allow for more accurate movement‐model and home‐range estimation at small effective sample sizes, and thus fill an important role for animal movement analysis. Given REML’s widespread use, our methods may also be useful in other contexts where effective sample sizes are small.

    

   more » « less
4. Identifying latent behavioural states in animal movement with M4, a nonparametric Bayesian method

   https://doi.org/10.1111/2041-210X.13745  

   Cullen, Joshua A. ; Poli, Caroline L. ; Fletcher, Jr., Robert J. ; Valle, Denis ( October 2021 , Methods in Ecology and Evolution)

   Understanding animal movement often relies upon telemetry and biologging devices. These data are frequently used to estimate latent behavioural states to help understand why animals move across the landscape. While there are a variety of methods that make behavioural inferences from biotelemetry data, some features of these methods (e.g. analysis of a single data stream, use of parametric distributions) may limit their generality to reliably discriminate among behavioural states.

   To address some of the limitations of existing behavioural state estimation models, we introduce a nonparametric Bayesian framework called the mixed‐membership method for movement (M4), which is available within the open‐sourcebayesmoveR package. This framework can analyse multiple data streams (e.g. step length, turning angle, acceleration) without relying on parametric distributions, which may capture complex behaviours more successfully than current methods. We tested our Bayesian framework using simulated trajectories and compared model performance against two segmentation methods (behavioural change point analysis (BCPA) and segclust2d), one machine learning method [expectation‐maximization binary clustering (EMbC)] and one type of state‐space model [hidden Markov model (HMM)]. We also illustrated this Bayesian framework using movements of juvenile snail kitesRostrhamus sociabilisin Florida, USA.

   The Bayesian framework estimated breakpoints more accurately than the other segmentation methods for tracks of different lengths. Likewise, the Bayesian framework provided more accurate estimates of behaviour than the other state estimation methods when simulations were generated from less frequently considered distributions (e.g. truncated normal, beta, uniform). Three behavioural states were estimated from snail kite movements, which were labelled as ‘encamped’, ‘area‐restricted search’ and ‘transit’. Changes in these behaviours over time were associated with known dispersal events from the nest site, as well as movements to and from possible breeding locations.

   Our nonparametric Bayesian framework estimated behavioural states with comparable or superior accuracy compared to the other methods when step lengths and turning angles of simulations were generated from less frequently considered distributions. Since the most appropriate parametric distributions may not be obvious a priori, methods (such as M4) that are agnostic to the underlying distributions can provide powerful alternatives to address questions in movement ecology.

    

   more » « less
5. Resource selection of a nomadic ungulate in a dynamic landscape

   https://doi.org/10.1371/journal.pone.0246809  

   Stratmann, Theresa S. ; Dejid, Nandintsetseg ; Calabrese, Justin M. ; Fagan, William F. ; Fleming, Christen H. ; Olson, Kirk A. ; Mueller, Thomas ( February 2021 , PLOS ONE)

   Weckerly, Floyd W. (Ed.)

   Nomadic movements are often a consequence of unpredictable resource dynamics. However, how nomadic ungulates select dynamic resources is still understudied. Here we examined resource selection of nomadic Mongolian gazelles ( Procapra gutturosa ) in the Eastern Steppe of Mongolia. We used daily GPS locations of 33 gazelles tracked up to 3.5 years. We examined selection for forage during the growing season using the Normalized Difference Vegetation Index (NDVI). In winter we examined selection for snow cover which mediates access to forage and drinking water. We studied selection at the population level using resource selection functions (RSFs) as well as on the individual level using step-selection functions (SSFs) at varying spatio-temporal scales from 1 to 10 days. Results from the population and the individual level analyses differed. At the population level we found selection for higher than average NDVI during the growing season. This may indicate selection for areas with more forage cover within the arid steppe landscape. In winter, gazelles selected for intermediate snow cover, which may indicate preference for areas which offer some snow for hydration but not so much as to hinder movement. At the individual level, in both seasons and across scales, we were not able to detect selection in the majority of individuals, but selection was similar to that seen in the RSFs for those individuals showing selection. Difficulty in finding selection with SSFs may indicate that Mongolian gazelles are using a random search strategy to find forage in a landscape with large, homogeneous areas of vegetation. The combination of random searches and landscape characteristics could therefore obscure results at the fine scale of SSFs. The significant results on the broader scale used for the population level RSF highlight that, although individuals show uncoordinated movement trajectories, they ultimately select for similar vegetation and snow cover. 

   more » « less