Flexible density surface estimation for spatially explicit capture-recapture surveys

1. Existing spatially explicit capture-recapture (SECR) software does not have the ability to fit flexible nonparametric models of animal density. 2. We describe and implement in the R package secrgam, a flexible method for estimating density surfaces from SECR data, using regression splines. 3. Package secrgam is an extension of package secr to implement some models available in the generalised additive model package mvcv. It accommodates density models that are arbitrarily flexible functions of spatially- and temporally-referenced variables. This includes one-dimensional and multi-dimensional smooths of covariates and smooths with interactions. The shape and smoothness of the fitted density surfaces is data-driven and can be determined using AIC or similar criteria. We illustrate use of the package by estimating the density surface from a simulated camera trap survey of leopards. 4. Package secrgam provides a flexible tool for species distribution modelling using SECR data.Postprin

The lemur diversity of the Fiherenana-Manombo Complex, southwest Madagascar

We conducted the first comprehensive lemur survey of the Fiherenana - Manombo Complex (Atsimo-Andrefana Region), site of PK32-Ranobe, a new protected area within the Madagascar Protected Area System. Our cross-seasonal surveys of three sites revealed the presence of eight lemur species representing seven genera and four families, of which three are diurnal and five are nocturnal species. Six species were only recorded in the riparian and transitional forests of the Fiherenana and Manombo river valleys, while the spiny thicket at Ranobe contains only Microcebus (two species), all larger species having been extirpated by hunting in recent years. Two of our records (Mirza coquereli and Cheirogaleus sp.) represent new locality records or range extensions, but we failed to record one species (Phaner pallescens) expected to occur in the area, and question the literature supporting its presence south of the Manombo river. Our findings highlight the importance of the Fiherenana-Manombo Complex for the conservation of lemurs in southwest Madagascar, but also show that PK32 - Ranobe fails to protect the full lemur diversity of the Complex. The protected area does not include the riparian forests of the Manombo and Fiherenana rivers, and at least three lemur species are therefore unprotected. We strongly support the proposed extension of the protected area to include these riparian forests as well as other important habitats for locally endemic bird and reptile taxa.RÉSUMÉ La zone du Complexe Fiherenana - Manombo (Région d’Atsimo- Andrefana), site de PK32-Ranobe, une nouvelle aire protégée dans le Système des Aires Protégées de Madagascar (SAPM), a fait l’objet d’un premier inventaire de lémuriens. Nos prospections dans trois sites à différentes saisons ont révélé la présence de huit espèces de lémuriens représentés dans sept genres et trois familles, dont trois sont des espèces diurnes et cinq sont des espèces nocturnes. Nous n’avons pas pu identifier l’espèce du genre Lepilemur ni celle du genre Cheirogaleus à défaut de disposer de spécimens. Six espèces ne se trouvaient que dans les forêts riveraines et les forêts de transition des vallées des fleuves Fiherenana et Manombo. Le fourré épineux de Ranobe n’abrite que des Microcebus (deux espèces), toutes les espèces plus grandes ayant déjà été exterminées par la chasse au cours des dernières années. Nos estimations de densité indiquent que la population des Microcebus est deux fois plus importante dans le fourré épineux que dans la forêt riveraine (1,078 individus / km² vs. 546 individus / km²). Nous avons estimé la densité d’Eulemur rufus à 40 groupes / km² dans la vallée du Fiherenana, mais nos transects ne nous ont pas permis d’obtenir des estimations fiables pour les densités de Lemur catta et de Propithecus verreauxi. Deux des espèces répertoriées (Mirza coquereli et Cheirogaleus sp.) représentent de nouvelles observations pour la zone ou des extensions de leurs aires de répartition connues, mais nous n’avons pas pu trouver l’espèce Phaner pallescens qui devait être présente dans la zone et nous émettons des doutes portant sur les références publiées rapportant la présence de l’espèce au sud du fleuve Manombo. Nos résultats mettent en exergue l’importance du Complexe Fiherenana - Manombo pour la conservation des lémuriens dans le sud-ouest de Madagascar, mais ils indiquent que l’aire protégée de PK32 - Ranobe ne protège pas la diversité complète des lémuriens du Complexe. Les forêts riveraines des fleuves Fiherenana et Manombo ne sont pas incluses dans l’aire protégée de sorte qu’au moins trois espèces de lémuriens ne bénéficient alors d’aucune protection. Compte tenu des objectifs du SAPM et plus particulièrement de l’Objectif 1, à savoir ‘Conserver l’ensemble de la biodiversité unique de Madagascar’, nous estimons que la nouvelle aire protégée du PK32-Ranobe n’atteint pas ces objectifs et nous appuyons les efforts des promoteurs afin de re-délimiter l’aire protégée pour inclure les forêts riveraines ainsi que d’autres habitats importants pour la conservation des oiseaux et des reptiles localement endémiques

Capture-Recapture Abundance Estimation using a Semi-complete Data Likelihood Approach

Capture–recapture data are often collected when abundance estimation is of interest. In this manuscript we focus on abundance estimation of closed populations. In the presence of unobserved individual heterogeneity, specified on a continuous scale for the capture probabilities, the likelihood is not generally available in closed form, but expressible only as an analytically intractable integral. Model-fitting algorithms to estimate abundance most notably include a numerical approximation for the likelihood or use of a Bayesian data augmentation technique considering the complete data likelihood. We consider a Bayesian hybrid approach, defining a “semi-complete” data likelihood, composed of the product of a complete data likelihood component for individuals seen at least once within the study and a marginal data likelihood component for the individuals not seen within the study, approximated using numerical integration. This approach combines the advantages of the two different approaches, with the semi-complete likelihood component specified as a single integral (over the dimension of the individual heterogeneity component). In addition, the models can be fitted within BUGS/JAGS (commonly used for the Bayesian complete data likelihood approach) but with significantly improved computational efficiency compared to the commonly used superpopulation data augmentation approaches (between about 10 and 77 times more efficient in the two examples we consider). The semi-complete likelihood approach is flexible and applicable to a range of models, including spatially explicit capture–recapture models. The model-fitting approach is applied to two different data sets: the first relates to snowshoe hares where model Mh is applied and the second to gibbons where a spatially explicit capture–recapture model is applied.Publisher PDFPeer reviewe

An assessment of the population of cotton-top tamarins (Saguinus oedipus) and their habitat in Colombia

Numerous animals have declining populations due to habitat loss, illegal wildlife trade, and climate change. The cotton-top tamarin (Saguinus oedipus) is a Critically Endangered primate species, endemic to northwest Colombia, threatened by deforestation and illegal trade. In order to assess the current state of this species, we analyzed changes in the population of cotton-top tamarins and its habitat from 2005 to 2012. We used a tailor-made "lure strip transect" method to survey 43 accessible forest parcels that represent 30% of the species' range. Estimated population size in the surveyed region was approximately 2,050 in 2005 and 1,900 in 2012, with a coefficient of variation of approximately 10%. The estimated population change between surveys was -7% (a decline of approximately 1.3% per year) suggesting a relatively stable population. If densities of inaccessible forest parcels are similar to those of surveyed samples, the estimated population of cotton-top tamarins in the wild in 2012 was 6,946 individuals. We also recorded little change in the amount of suitable habitat for cotton-top tamarins between sample periods: in 2005, 18% of surveyed forest was preferred habitat for cotton-top tamarins, while in 2012, 17% percent was preferred. We attribute the relatively stable population of this Critically Endangered species to increased conservation efforts of Proyecto Tití, conservation NGOs, and the Colombian government. Due to continued threats to cotton-top tamarins and their habitat such as agriculture and urban expansion, ongoing conservation efforts are needed to ensure the long-term survival of cotton-top tamarins in Colombia.Publisher PDFPeer reviewe

Classification of animal dive tracks via automatic landmarking, principal components analysis and clustering

The BRS study was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) Grants N00014‐07‐10988, N00014‐07‐11023, N00014‐08‐10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) Grant SI‐1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).The behaviour of animals and their interactions with the environment can be inferred by tracking their movement. For this reason, biologgers are an important source of ecological data, but analysing the shape of the tracks they record is difficult. In this paper we present a technique for automatically determining landmarks that can be used to analyse the shape of animal tracks. The approach uses a parametric version of the SALSA algorithm to fit regression splines to 1‐dimensional curves in N dimensions (in practice N = 2 or 3). The knots of these splines are used as landmarks in a subsequent Principal Components Analysis, and the dives classified via agglomerative clustering. We demonstrate the efficacy of this algorithm on simulated 2‐dimensional dive data, and apply our method to real 3‐dimensional whale dive data from the Behavioral Response Study (BRS) in the Bahamas. The BRS is a series of experiments to quantify shifts in behavior due to SONAR. Our analysis of 3‐dimensional track data supports an alteration in the dive behavior post‐ensonification.Publisher PDFPeer reviewe

Random coeffcient models for complex longitudinal data

Longitudinal data are common in biological research. However, real data sets vary considerably in terms of their structure and complexity and present many challenges for statistical modelling. This thesis proposes a series of methods using random coefficients for modelling two broad types of longitudinal response: normally distributed measurements and binary recapture data. Biased inference can occur in linear mixed-effects modelling if subjects are drawn from a number of unknown sub-populations, or if the residual covariance is poorly specified. To address some of the shortcomings of previous approaches in terms of model selection and flexibility, this thesis presents methods for: (i) determining the presence of latent grouping structures using a two-step approach, involving regression splines for modelling functional random effects and mixture modelling of the fitted random effects; and (ii) flexible of modelling of the residual covariance matrix using regression splines to specify smooth and potentially non-monotonic variance and correlation functions. Spatially explicit capture-recapture methods for estimating the density of animal populations have shown a rapid increase in popularity over recent years. However, further refinements to existing theory and fitting software are required to apply these methods in many situations. This thesis presents: (i) an analysis of recapture data from an acoustic survey of gibbons using supplementary data in the form of estimated angles to detections, (ii) the development of a multi-occasion likelihood including a model for stochastic availability using a partially observed random effect (interpreted in terms of calling behaviour in the case of gibbons), and (iii) an analysis of recapture data from a population of radio-tagged skates using a conditional likelihood that allows the density of animal activity centres to be modelled as functions of time, space and animal-level covariates

Flexible density surface estimation for spatially explicit capture-recapture surveys

1. Existing spatially explicit capture-recapture (SECR) software does not have the ability to fit flexible nonparametric models of animal density. 2. We describe and implement in the R package secrgam, a flexible method for estimating density surfaces from SECR data, using regression splines. 3. Package secrgam is an extension of package secr to implement some models available in the generalised additive model package mvcv. It accommodates density models that are arbitrarily flexible functions of spatially- and temporally-referenced variables. This includes one-dimensional and multi-dimensional smooths of covariates and smooths with interactions. The shape and smoothness of the fitted density surfaces is data-driven and can be determined using AIC or similar criteria. We illustrate use of the package by estimating the density surface from a simulated camera trap survey of leopards.4. Package secrgam provides a flexible tool for species distribution modelling using SECR data

Lagebericht 1996 zur Angewandten Supraleitung

Der Lagebericht gibt den an den Anwendungen der Supraleitung interessierten Wissenschaftlern und Ingenieuren einen Ueberblick ueber den aktuellen internationalen Entwicklungsstand (Oktober 1996). Der Bericht beschaeftigt sich vor allem mit den in den letzten 12 bis 18 Monaten erzielten Fortschritten. Im Kapitel Materialentwicklung werden behandelt: Duenne Schichten, Josephsonkontakte, Draehte und Baender sowie Volumenproben. Im Kapitel Anwendungen werden Sensoren, Hochfrequenztechnik (z.B. Filter, Transistoren), Digitalschaltungen, Magnettechnik, Energietechnik angesprochen. Das letzte Kapitel befasst sich mit der Kuehlung (z.B. Pulsrohrkuehler, Stirlingkuehler). (MM)The report outlines the international situation of applied superconductivity as of October 1996. The advances made in the past 12-18 months re reviewed. The chapter 'Material Development' discusses thin films, Josephson contacts, wires and bands, volume samples. The chapter 'Applications' goes into sensors, high-frequency technology (filters, transistors), digital circuits, magnets, energy engineering. The final chapter presents a review of coolers (pulsed-tube coolers, Stirling coolers). (MM)SIGLEAvailable from TIB Hannover: ZO 9098(1996) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekDEGerman

Classification of animal dive tracks via automatic landmarking, principal components analysis and clustering

The behaviour of animals and their interactions with the environment can be inferred by tracking their movement. For this reason, biologgers are an important source of ecological data, but analysing the shape of the tracks they record is difficult. In this paper we present a technique for automatically determining landmarks that can be used to analyse the shape of animal tracks. The approach uses a parametric version of the SALSA algorithm to fit regression splines to 1‐dimensional curves in N dimensions (in practice N = 2 or 3). The knots of these splines are used as landmarks in a subsequent Principal Components Analysis, and the dives classified via agglomerative clustering. We demonstrate the efficacy of this algorithm on simulated 2‐dimensional dive data, and apply our method to real 3‐dimensional whale dive data from the Behavioral Response Study (BRS) in the Bahamas. The BRS is a series of experiments to quantify shifts in behavior due to SONAR. Our analysis of 3‐dimensional track data supports an alteration in the dive behavior post‐ensonification