The Effect of Animal Movement on Line Transect Estimates of Abundance

Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.     

Improving Aquatic Warbler Population Assessments by Accounting for Imperfect Detection

Monitoring programs designed to assess changes in population size over time need to account for imperfect detection and provide estimates of precision around annual abundance estimates. Especially for species dependent on conservation management, robust monitoring is essential to evaluate the effectiveness of management. Many bird species of temperate grasslands depend on specific conservation management to maintain suitable breeding habitat. One such species is the Aquatic Warbler (Acrocephalus paludicola), which breeds in open fen mires in Central Europe. Aquatic Warbler populations have so far been assessed using a complete survey that aims to enumerate all singing males over a large area. Because this approach provides no estimate of precision and does not account for observation error, detecting moderate population changes is challenging. From 2011 to 2013 we trialled a new line transect sampling monitoring design in the Biebrza valley, Poland, to estimate abundance of singing male Aquatic Warblers. We surveyed Aquatic Warblers repeatedly along 50 randomly placed 1-km transects, and used binomial mixture models to estimate abundances per transect. The repeated line transect sampling required 150 observer days, and thus less effort than the traditional ‘full count’ approach (175 observer days). Aquatic Warbler abundance was highest at intermediate water levels, and detection probability varied between years and was influenced by vegetation height. A power analysis indicated that our line transect sampling design had a power of 68% to detect a 20% population change over 10 years, whereas raw count data had a 9% power to detect the same trend. Thus, by accounting for imperfect detection we increased the power to detect population changes. We recommend to adopt the repeated line transect sampling approach for monitoring Aquatic Warblers in Poland and in other important breeding areas to monitor changes in population size and the effects of habitat management.     

Effect of observer differences on abundance estimates of seabirds from ship-based strip transect surveys

Data from four ship-based strip transect surveys of seabirds, in which six observer teams from several countries cooperated, were used to estimate observer differences. The numbers of birds per sampled area as reported by the various observer teams were used to estimate differences among observer teams. As overlap in effort was not complete (all teams did not work in exactly the same areas at the same times), a log-linear model was used to correct for differences due to survey and region effects and the state of the sea. Considerable observer differences were found. For example, three teams out of five observed less than 16% of Guillemot Uria aalge and even less than 10% of Kittiwake Rissa tridactyla relative to the team that reported the highest densities.     

Response to human presence during nocturnal line transect surveys in fallow deer (<Emphasis Type="Italic">Dama dama</Emphasis>) and wild boar (<Emphasis Type="Italic">Sus scrofa</Emphasis>)

The use of line transect methodology and portable thermal imaging for ground survey of wildlife should require a good knowledge of the behavioural response of the animals to the presence of an observer, in order to take into account the potential bias in density estimate caused by deviation from the assumption that distances are recorded at the initial position. We used ten fallow deer and eight wild boar fitted with radiocollars to investigate animals’ response during simulated nocturnal line transect surveys, carried out in a Mediterranean plain forest. The experiment consisted in radiolocating a focal animal before and after an observer walked a transect nearby (<100 m). Each transect line was followed using a Global Positioning System (GPS) navigator. We carried out a total of 64 trials on fallow deer and 57 on wild boar. Results showed that despite most of the animals moved significantly in response to the observer (mean ± standard error, wild boar—95.3 ± 10.0 m; fallow deer—149.6 ± 14.2 m), the flying patterns were different in the two species: the reaction of fallow deer turned out to be more intense and directional with respect to that showed by wild boar. Although these results sound explorative, the experiment attempted here, for the first time, is relevant for an appropriate design of nocturnal distance-sampling surveys and gives information about potential bias arising from animal’s behavioural response. We believe that these first results may foster more in-deep analyses which are now made possible with the adoption of GPS technology for animal location.     

A hierarchical modeling framework for multiple observer transect surveys

Ecologists often use multiple observer transect surveys to census animal populations. In addition to animal counts, these surveys produce sequences of detections and non-detections for each observer. When combined with additional data (i.e. covariates such as distance from the transect line), these sequences provide the additional information to estimate absolute abundance when detectability on the transect line is less than one. Although existing analysis approaches for such data have proven extremely useful, they have some limitations. For instance, it is difficult to extrapolate from observed areas to unobserved areas unless a rigorous sampling design is adhered to; it is also difficult to share information across spatial and temporal domains or to accommodate habitat-abundance relationships. In this paper, we introduce a hierarchical modeling framework for multiple observer line transects that removes these limitations. In particular, abundance intensities can be modeled as a function of habitat covariates, making it easier to extrapolate to unsampled areas. Our approach relies on a complete data representation of the state space, where unobserved animals and their covariates are modeled using a reversible jump Markov chain Monte Carlo algorithm. Observer detections are modeled via a bivariate normal distribution on the probit scale, with dependence induced by a distance-dependent correlation parameter. We illustrate performance of our approach with simulated data and on a known population of golf tees. In both cases, we show that our hierarchical modeling approach yields accurate inference about abundance and related parameters. In addition, we obtain accurate inference about population-level covariates (e.g. group size). We recommend that ecologists consider using hierarchical models when analyzing multiple-observer transect data, especially when it is difficult to rigorously follow pre-specified sampling designs. We provide a new R package, hierarchicalDS, to facilitate the building and fitting of these models.     

Correcting observer effect bias in estimates of nesting success of a coastal bird,the White-fronted Plover Charadrius marginatus

Capsule A recently developed observer-effects model gives better estimates than the survival model.

Aims To compare the performance of the traditional survival model with that of an observer-effects model in estimating nesting success.

Methods We used survival data from 654 nests in a covariate-dependent extension of a maximum-likelihood estimator model to simultaneously estimate daily survival rate and observer effect on nesting success in four different sectors of a study site. Standard likelihood-ratio tests and Akaike's information criterion differences were used to compare model performances.

Results A significant (negative) observer effect was detected in one of four sectors of the study area, and was probably attributable to small mammal predators. Despite significantly higher predation risk during the laying period, there was a significant positive observer effect during the laying period, contrasting with a weak negative effect during the incubation period, suggesting that an observer's tracks around unattended nests reduced predation risk. Likelihood-ratio tests indicated a significantly better fit using the observer effects model versus the Mayfield survival model in four of six scenarios.

Conclusion The observer-effects model accounts for bias in estimates of nest survival rates, and is preferred over the survival model because the inclusion of observer effect as a variable does not over-parameterize the model.     

Towards a density measure for assessments of arid plant populations – examples from the southern Namib Desert

Plant species in arid environments are often widely spaced making population assessments difficult. In order to minimise observer bias we tested two repeatable simple methods during red data assessments in the southern Namib Desert. Both the transect‐based and the quadrat‐based method resulted in over‐estimates of the true population size. However, because of case of application, the transect method warrants further development.     

截线抽样法在中国水域鲸豚考察中的应用及其局限性与改进建议

截线抽样法广泛应用于鲸豚类动物的考察。通过文献调查并结合我们自己的研究工作,本文从考察设计、
野外考察和数据分析三个方面分析了截线抽样法在我国水域应用时可能出现的问题。针对考察设计,提出了截
线设计的建议。针对野外考察,主要从观察平台、人员配置、观察方法和记录方法几个方面提出建议。针对分
析过程,介绍了使用R 编程平台和Distance 软件进行数据预处理和数据分析的简要过程。笔者期望本文的相关
建议有助于促进我国鲸豚类考察方法的规范化。     

Line transect estimators for left-truncated distributions

Left-truncated line transect data sets may occur when surveying with certain types of aircraft where the observer cannot look straight down. A general model of left-truncation in line transect sampling is developed and parametric estimators are derived in such cases when the underlying distribution of right-angle distances is either exponentially or half-normally distributed. Computer simulations demonstrate the validity of the derived estimators and the expected nonrobustness against alternative distributions. An aerial survey example using dolphin data is presented.     

Abundance of Diurnal Primates in Mwanihana Forest, Udzungwa Mountains, Tanzania

Many individual researchers have used line transect counts to estimate forest primate abundance. They have devoted less attention to the interpretation of line transect data obtained by several observers, as is often the case in long-term monitoring programs. We present primate relative abundance data that 5 observers collected over 6 yr (not continuous) along 4 different transects each 4 km long in the Mwanihana Forest, Udzungwa Mountains National Park, Tanzania. Total distance walked during transect repetitions is ca. 700 km. The species we saw most frequently was the endemic Udzungwa red colobus Procolobus gordonorum (mean 0.59 groups/km walked), followed by the Angolan black-and-white colobus Colobus angolensis (0.43 groups/km) and Sykes’s monkey Cercopithecus mitis (0.35 groups/km). We sighted the endemic Sanje mangabey Cercocebus galeritus sanjei and the yellow baboon Papio cynocephalus infrequently, the latter being confined to the deciduous forest parts of the transects. We analyzed sighting frequency by gross habitat type, transect, season, and observer. Interobserver differences in the relative abundance of each species were moderate and the few cases of significant variations were due to discordance of only 1 observer from the others. Estimated distances of primate group sightings differ significantly among observers, thus preventing us from deriving estimates of absolute density. Frequency distributions of distance-class intervals are not significantly different among observers, which may indicate gross interobserver consistency in the width of the area sampled. We conclude that unless consistency in data collection is checked, as we did for 2 observers who collected data simultaneously, potential interobserver differences remain an underlying source of variance in the results that cannot be separated from other sources of variance.     

Performance evaluation of contrast-detail in full field digital mammography systems using ideal (Hotelling) observer vs. conventional automated analysis of CDMAM images for quality control of contrast-detail characteristics

PurposeThe purpose of this work was to evaluate the contrast-detail performance of full field digital mammography (FFDM) systems using ideal (Hotelling) observer Signal-to-Noise Ratio (SNR) methodology and ascertain whether it can be considered an alternative to the conventional, automated analysis of CDMAM phantom images.MethodsFive FFDM units currently used in the national breast screening programme were evaluated, which differed with respect to age, detector, Automatic Exposure Control (AEC) and target/filter combination. Contrast-detail performance was analysed using CDMAM and ideal observer SNR methodology. The ideal observer SNR was calculated for input signal originating from gold discs of varying thicknesses and diameters, and then used to estimate the threshold gold thickness for each diameter as per CDMAM analysis. The variability of both methods and the dependence of CDMAM analysis on phantom manufacturing discrepancies also investigated.ResultsResults from both CDMAM and ideal observer methodologies were informative differentiators of FFDM systems' contrast-detail performance, displaying comparable patterns with respect to the FFDM systems' type and age. CDMAM results suggested higher threshold gold thickness values compared with the ideal observer methodology, especially for small-diameter details, which can be attributed to the behaviour of the CDMAM phantom used in this study. In addition, ideal observer methodology results showed lower variability than CDMAM results.ConclusionThe Ideal observer SNR methodology can provide a useful metric of the FFDM systems' contrast detail characteristics and could be considered a surrogate for conventional, automated analysis of CDMAM images.     

Field and simulation analyses of visual methods for sampling coral cover

The consensus view that coral reefs are declining urges the need to test the short-term effects of conservation. Visual sampling methods are a low cost, technically simple, and potentially highly accurate means of monitoring reef status or calibrating larger scale aerial and satellite surveys. We studied the recent literature and found that of the three most commonly used visual methods, the belt transect (BT) method was used twice as much as the line transect (LT) method and 2.5 times as often as the linear point intercept (LPI) method. We tested the repeatability, cost-efficiency, precision, and accuracy of these three methods in the field and in computer simulations. In the field, the observer repeatability was uniformly high among the three methods (R>0.9). Surprisingly, our study indicates that the least used method (LPI) was the most cost-effective means of measuring coral cover while being at least as precise and accurate as the other two methods. Our simulation study indicated that both the accuracy and precision of the three methods decrease sharply with decreasing coral cover, and that using between 5 and 10 transects over a homogeneous area is an appropriate sample size at either low or high coral cover.     

TEMP/TDM et scintigraphie osseuse en cancérologie : impact d’une acquisition scannographique basse dose chez les patients avec foyer isolé suspect ou de nature indéterminée

AimTo evaluate the usefulness of a low dose SPECT/CT and the added value of an additional “diagnostic” centred CT-scan in cancer patients with a solitary focus observed on planar whole-body bone scintigraphy (PWBS) and classified as indeterminate or suspicious.Material and methodsSixty consecutive patients underwent a low dose SPECT/CT acquisition (120 kV, 30 mAs, 3 mm slice thickness) followed by a “diagnostic” CT-scan (120 kV, 100 mAs, 1.25 mm slice thickness) centred on the focus. The first observer considered prospectively WBS, low-dose SPECT/CT and finally the centred SPECT/CT. A blinded review was performed by a second observer.ResultsPWBS depicted solitary indeterminate or suspicious foci in 38 and 22 patients, respectively. SPECT/CT acquisitions clarified 73% (44/60) of the foci. Additional diagnostic CT-scan altered low-dose SPECT/CT results in nine patients. Additional foci (not found by PWBS) located outside the scanning area of the centred diagnostic CT-scan were found in 20 patients. Inter observer agreement for PWBS, low-dose SPECT/CT and diagnostic SPECT/CT was equal to 0.542, 0.68 and 0.694, respectively. ROC analysis showed no difference between low-dose SPECT/CT and diagnostic SPECT/CT for observer 1 and observer 2.ConclusionThis study shows that a conventional low-dose SPECT/CT in patients presenting with a solitary focus on PWBS is sufficient to improve both accuracy and inter observer variability of bone scanning. A CT volume session should not be limited to the area of the solitary focus since additional foci located outside the centred CT-scan frequently occurred.     

Using counts of begging young to estimate post-fledging survival in Tawny Owls Strix aluco

Capsule The method reliably accounted for variation in brood size when used by a ‘naive’ observer.     

Roll of the Botanical Society of Edinburgh

Summary

The succession of vascular plants and lichens along a 131m transect, representing 70 – 80 years accretion to a sand-dune system, was studied at Tentsmuir Point National Nature Reserve, Fife. Its flora is compared to other dune areas and the reasons why some such areas are lichen-rich and others lichen-poor are discussed.     

Improving multispecies rocky reef fish censuses by counting different groups of species using different procedures

Synopsis A number of factors can influence the accuracy and precision of underwater visual transect techniques. Among these are observer swimming speed and, during multispecies surveys, the effect of counting all fishes on estimates of particular species. This paper examines the effect of these factors on population estimates of inconspicuous fishes (defined as Type 1) in a temperate reef fish assemblage near Sydney, Australia. Counting Type 1 fishes with all others yielded significantly lower estimates of species richness and abundance than when counted alone. This suggests that multispecies surveys should be split into 2 or more counts, using a census procedure that is appropriate to the group of species cencused. Further, the effect of counting all other fishes on estimates of Type 1 fishes varied according to the relative abundance of the former: their effect was lowest when abundance of other fishes was lowest. There was a negative relationship between observer speed and estimated abundance for Type 1 fishes. Survey precision of Type 1 fishes was generally improved by surveying at slower observer speeds.     

Edge detection in vegetation: Jornada revisited

Abstract. We return to the problem of pattern detection with focus on locating vegetation edges. We assume transect sampling with contiguous quadrats and we postulate a vegetation model in which pattern confounds responses to random, serial, and possibly edge-generating effects. Realizing that strong serial effects will enhance the appearance of vegetation continuity, we probe the residuals for evidence of edges. Two independently derived structures furnish the evidence: a deviations profile and an ordination map. The profile displays compositional changes along the transect as deviations from a theoretical continuum state. The ordination traces the transect as an irregular line in vegetation hyperspace. On this irregular line, the transect segments appear as apices and the compositional dissimilarities of the transect segments as inter-apex distances. Sharp apices (in full dimension) isolated by long inter-apex distances (also in full dimension) indicate possible edges. While the subtending angle to an apex reflects changes in population proportions, the criterion for measuring edge sharpness, the height of the deviations profile expresses quantitative effects, the criterion for measuring edge intensity. The deviations profile does not seem to have direct parallel in past edge detection. The inter-apex distance has a parallel in the Ludwig-Cornelius compositional distance. We describe the details of sampling and analysis, and present numerical results. We also include a short glossary in App. 5.     

Effects of ambient noise on detectability and localization of avian songs and tones by observers in grasslands

Probability of detection and accuracy of distance estimates in aural avian surveys may be affected by the presence of anthropogenic noise, and this may lead to inaccurate evaluations of the effects of noisy infrastructure on wildlife. We used arrays of speakers broadcasting recordings of grassland bird songs and pure tones to assess the probability of detection, and localization accuracy, by observers at sites with and without noisy oil and gas infrastructure in south‐central Alberta from 2012 to 2014. Probability of detection varied with species and with speaker distance from transect line, but there were few effects of noisy infrastructure. Accuracy of distance estimates for songs and tones decreased as distance to observer increased, and distance estimation error was higher for tones at sites with infrastructure noise. Our results suggest that quiet to moderately loud anthropogenic noise may not mask detection of bird songs; however, errors in distance estimates during aural surveys may lead to inaccurate estimates of avian densities calculated using distance sampling. We recommend caution when applying distance sampling if most birds are unseen, and where ambient noise varies among treatments.