Automated call detection for acoustic surveys with structured calls of varying length

Funding: Y.W. is partly funded by the China Scholarship Council (CSC) for Ph.D. study at the University of St Andrews, UK.1. When recorders are used to survey acoustically conspicuous species, identification calls of the target species in recordings is essential for estimating density and abundance. We investigate how well deep neural networks identify vocalisations consisting of phrases of varying lengths, each containing a variable number of syllables. We use recordings of Hainan gibbon (Nomascus hainanus) vocalisations to develop and test the methods. 2. We propose two methods for exploiting the two-level structure of such data. The first combines convolutional neural network (CNN) models with a hidden Markov model (HMM) and the second uses a convolutional recurrent neural network (CRNN). Both models learn acoustic features of syllables via a CNN and temporal correlations of syllables into phrases either via an HMM or recurrent network. We compare their performance to commonly used CNNs LeNet and VGGNet, and support vector machine (SVM). We also propose a dynamic programming method to evaluate how well phrases are predicted. This is useful for evaluating performance when vocalisations are labelled by phrases, not syllables. 3. Our methods perform substantially better than the commonly used methods when applied to the gibbon acoustic recordings. The CRNN has an F-score of 90% on phrase prediction, which is 18% higher than the best of the SVM or LeNet and VGGNet methods. HMM post-processing raised the F-score of these last three methods to as much as 87%. The number of phrases is overestimated by CNNs and SVM, leading to error rates between 49% and 54%. With HMM, these error rates can be reduced to 0.4% at the lowest. Similarly, the error rate of CRNN's prediction is no more than 0.5%. 4. CRNNs are better at identifying phrases of varying lengths composed of a varying number of syllables than simpler CNN or SVM models. We find a CRNN model to be best at this task, with a CNN combined with an HMM performing almost as well. We recommend that these kinds of models are used for species whose vocalisations are structured into phrases of varying lengths.Publisher PDFPeer reviewe

Towards Automated Animal Density Estimation with Acoustic Spatial Capture-Recapture

Passive acoustic monitoring can be an effective way of monitoring wildlife populations that are acoustically active but difficult to survey visually. Digital recorders allow surveyors to gather large volumes of data at low cost, but identifying target species vocalisations in these data is non-trivial. Machine learning (ML) methods are often used to do the identification. They can process large volumes of data quickly, but they do not detect all vocalisations and they do generate some false positives (vocalisations that are not from the target species). Existing wildlife abundance survey methods have been designed specifically to deal with the first of these mistakes, but current methods of dealing with false positives are not well-developed. They do not take account of features of individual vocalisations, some of which are more likely to be false positives than others. We propose three methods for acoustic spatial capture-recapture inference that integrate individual-level measures of confidence from ML vocalisation identification into the likelihood and hence integrate ML uncertainty into inference. The methods include a mixture model in which species identity is a latent variable. We test the methods by simulation and find that in a scenario based on acoustic data from Hainan gibbons, in which ignoring false positives results in 17% positive bias, our methods give negligible bias and coverage probabilities that are close to the nominal 95% level.Comment: 35 pages, 5 figure

Exact Likelihoods for N-mixture models with Time-to-Detection Data

This paper is concerned with the formulation of $N$-mixture models for estimating the abundance and probability of detection of a species from binary response, count and time-to-detection data. A modelling framework, which encompasses time-to-first-detection within the context of detection/non-detection and time-to-each-detection and time-to-first-detection within the context of count data, is introduced. Two observation processes which depend on whether or not double counting is assumed to occur are also considered. The main focus of the paper is on the derivation of explicit forms for the likelihoods associated with each of the proposed models. Closed-form expressions for the likelihoods associated with time-to-detection data are new and are developed from the theory of order statistics. A key finding of the study is that, based on the assumption of no double counting, the likelihoods associated with times-to-detection together with count data are the product of the likelihood for the counts alone and a term which depends on the detection probability parameter. This result demonstrates that, in this case, recording times-to-detection could well improve precision in estimation over recording counts alone. In contrast, for the double counting protocol with exponential arrival times, no information was found to be gained by recording times-to-detection in addition to the count data. An R package and an accompanying vignette are also introduced in order to complement the algebraic results and to demonstrate the use of the models in practice.Comment: 21 pages, 1 figur

inlabru: an R package for Bayesian spatial modelling from ecological survey data

1. Spatial processes are central to many ecological processes, but fitting models that incorporate spatial correlation to data from ecological surveys is computationally challenging. This is particularly true of point pattern data (in which the primary data are the locations at which target species are found), but also true of gridded data, and of georeferenced samples from continuous spatial fields. 2. We describe here the R package inlabru that builds on the widely used RINLA package to provide easier access to Bayesian inference from spatial point process, spatial count, gridded, and georeferenced data, using integrated nested Laplace approximation (INLA, Rue et al., 2009). 3. The package provides methods for fitting spatial density surfaces and estimating abundance, as well as for plotting and prediction. It accommodates data that are points, counts, georeferenced samples, or distance sampling data. 4. This paper describes the main features of the package, illustrated by fitting models to the gorilla nest data contained in the package spatstat (Baddeley, & Turner, 2005), a line transect survey dataset contained in the package dsm (Miller, Rexstad, Burt, Bravington, & Hedley, 2018), and to a georeferenced sample from a simulated continuous spatial field

A latent capture history model for digital aerial surveys

Funding: This work was part-funded by the Royal Society of New Zealand Marsden grant UOA-1418, Leverhulme grant RF-2018-213\9 and EPSRC IAA grant ‘High Definition digital aerial survey software’.We anticipate that unmanned aerial vehicles will become popular wildlife survey platforms. Because detecting animals from the air is imperfect, we develop a mark‐recapture line transect method using two digital cameras, possibly mounted on one aircraft, which cover the same area with a short time delay between them. Animal movement between the passage of the cameras introduces uncertainty in individual identity, so individual capture histories are unobservable and are treated as latent variables. We obtain the likelihood for mark‐recapture line transects without capture histories by automatically enumerating all possibilities within segments of the transect that contain ambiguous identities, instead of attempting to decide identities in a prior step. We call this method “Latent Capture‐history Enumeration” (LCE). We include an availability model for species that are periodically unavailable for detection, such as cetaceans that are undetectable while diving. External data are needed to estimate the availability cycle length, but not the mean availability rate, if the full availability model is employed. We compare the LCE method with the recently developed cluster capture‐recapture method (CCR), which uses a Palm likelihood approximation, providing the first comparison of CCR with maximum likelihood. The LCE estimator has slightly lower variance, more so as sample size increases, and close to nominal coverage probabilities. Both methods are approximately unbiased. We illustrate with semisynthetic data from a harbor porpoise survey.PostprintPeer reviewe

Using continuous-time spatial capture–recapture models to make inference about animal activity patterns

This work was part‐funded by EPSRC Grant EP/I000917/1, by the research fellowship RF‐2018‐213/9, and the fieldwork was funded by the Summerlee Foundation and Panthera.1. Quantifying the distribution of daily activity is an important component of behavioral ecology. Historically, it has been difficult to obtain data on activity patterns, especially for elusive species. However, the development of affordable camera traps and their widespread usage has led to an explosion of available data from which activity patterns can be estimated. 2. Continuous-time spatial capture?recapture (CT SCR) models drop the occasion structure seen in traditional spatial and nonspatial capture?recapture (CR) models and use the actual times of capture. In addition to estimating density, CT SCR models estimate expected encounters through time. Cyclic splines can be used to allow flexible shapes for modeling cyclic activity patterns, and the fact that SCR models also incorporate distance means that space-time interactions can be explored. This method is applied to a jaguar dataset. 3. Jaguars in Belize are most active and range furthest in the evening and early morning and when they are located closer to the network of trails. There is some evidence that females have a less variable pattern than males. The comparison between sexes demonstrates how CT SCR can be used to explore hypotheses about animal behavior within a formal modeling framework. 4. SCR models were developed primarily to estimate and model density, but the models can be used to explore processes that interact across space and time, especially when using the CT SCR framework that models the temporal dimension at a finer resolution.Publisher PDFPeer reviewe

Open population maximum likelihood spatial capture-recapture

Funding: Part-funded by UK EPSRC grant EP/K041061/1 (DB); Richard Glennie was funded by the Carnegie Trust.Open population capture‐recapture models are widely used to estimate population demographics and abundance over time. Bayesian methods exist to incorporate open population modeling with spatial capture‐recapture (SCR), allowing for estimation of the effective area sampled and population density. Here, open population SCR is formulated as a hidden Markov model (HMM), allowing inference by maximum likelihood for both Cormack‐Jolly‐Seber and Jolly‐Seber models, with and without activity center movement. The method is applied to a 12‐year survey of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary, Belize, to estimate survival probability and population abundance over time. For this application, inference is shown to be biased when assuming activity centers are fixed over time, while including a model for activity center movement provides negligible bias and nominal confidence interval coverage, as demonstrated by a simulation study. The HMM approach is compared with Bayesian data augmentation and closed population models for this application. The method is substantially more computationally efficient than the Bayesian approach and provides a lower root‐mean‐square error in predicting population density compared to closed population models.PostprintPeer reviewe

Counting chirps : acoustic monitoring of cryptic frogs

Funding for the frog survey was received from the National Geographic Society/Waitt Grants Program (No. W184-11). The EPSRC and NERC helped to fund this research through a PhD grant (No. EP/1000917/1) to D.L.B. R.A. and G.J.M. acknowledge initiative funding from the National Research Foundation of South Africa.1 .  Global amphibian declines have resulted in a vital need for monitoring programmes that follow population trends. Monitoring using advertisement calls is ideal as choruses are undisturbed during data collection. However, methods currently employed by managers frequently rely on trained observers, and/or do not provide density data on which to base trends. 2 .  This study explores the utility of monitoring using acoustic spatially explicit capture-recapture (aSECR) with time of arrival (ToA) and signal strength (SS) as a quantitative monitoring technique to measure call density of a threatened but visually cryptic anuran, the Cape peninsula moss frog Arthroleptella lightfooti. 3 .  The relationships between temporal and environmental variables (date, rainfall, temperature) and A. lightfooti call density at three study sites on the Cape peninsula, South Africa were examined. Acoustic data, collected from an array of six microphones over four months during the winter breeding season, provided a time series of call density estimates. 4 .  Model selection indicated that call density was primarily associated with seasonality fitted as a quadratic function. Call density peaked mid-breeding season. At the main study site, the lowest recorded mean call density (0·160 calls m-2 min-1) occurred in May and reached its peak mid-July (1·259 calls m-2 min-1). The sites differed in call density, but also the effective sampling area. 5 .  Synthesis and applications.The monitoring technique, acoustic spatially explicit capture–recapture (aSCR), quantitatively estimates call density without disturbing the calling animals or their environment, while time of arrival (ToA) and signal strength (SS) significantly add to the accuracy of call localisation, which in turn increases precision of call density estimates without the need for specialist field staff. This technique appears ideally suited to aid the monitoring of visually cryptic, acoustically active species.Publisher PDFPeer reviewe

A general framework for animal density estimation from acoustic detections across a fixed microphone array

Acoustic monitoring can be an efficient, cheap, non‐invasive alternative to physical trapping of individuals. Spatially explicit capture–recapture (SECR) methods have been proposed to estimate calling animal abundance and density from data collected by a fixed array of microphones. However, these methods make some assumptions that are unlikely to hold in many situations, and the consequences of violating these are yet to be investigated. We generalize existing acoustic SECR methodology, enabling these methods to be used in a much wider variety of situations. We incorporate time‐of‐arrival (TOA) data collected by the microphone array, increasing the precision of calling animal density estimates. We use our method to estimate calling male density of the Cape Peninsula Moss Frog Arthroleptella lightfooti. Our method gives rise to an estimator of calling animal density that has negligible bias, and 95% confidence intervals with appropriate coverage. We show that using TOA information can substantially improve estimate precision. Our analysis of the A. lightfooti data provides the first statistically rigorous estimate of calling male density for an anuran population using a microphone array. This method fills a methodological gap in the monitoring of frog populations and is applicable to acoustic monitoring of other species that call or vocalize

Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales

Distance sampling is a widely used method for estimating wildlife population abundance. The fact that conventional distance sampling methods are partly design-based constrains the spatial resolution at which animal density can be estimated using these methods. Estimates are usually obtained at survey stratum level. For an endangered species such as the blue whale, it is desirable to estimate density and abundance at a finer spatial scale than stratum. Temporal variation in the spatial structure is also important. We formulate the process generating distance sampling data as a thinned spatial point process and propose model-based inference using a spatial log-Gaussian Cox process. The method adopts a flexible stochastic partial differential equation (SPDE) approach to model spatial structure in density that is not accounted for by explanatory variables, and integrated nested Laplace approximation (INLA) for Bayesian inference. It allows simultaneous fitting of detection and density models and permits prediction of density at an arbitrarily fine scale. We estimate blue whale density in the Eastern Tropical Pacific Ocean from thirteen shipboard surveys conducted over 22 years. We find that higher blue whale density is associated with colder sea surface temperatures in space, and although there is some positive association between density and mean annual temperature, our estimates are consitent with no trend in density across years. Our analysis also indicates that there is substantial spatially structured variation in density that is not explained by available covariates.Comment: 33 pages 19 figure