momentuHMM: R package for generalized hidden Markov models of animal movement

1. Discrete‐time hidden Markov models (HMMs) have become an immensely popular tool for inferring latent animal behaviours from telemetry data. While movement HMMs typically rely solely on location data (e.g. step length and turning angle), auxiliary biotelemetry and environmental data are powerful and readily‐available resources for incorporating much more ecological and behavioural realism. However, complex movement or observation process models often necessitate custom and computationally demanding HMM model‐fitting techniques that are impractical for most practitioners, and there is a paucity of generalized user‐friendly software available for implementing multivariate HMMs of animal movement. 2. Here, we introduce an open‐source R package, momentuHMM, that addresses many of the deficiencies in existing HMM software. Features include: (1) data pre‐processing and visualization; (2) user‐specified probability distributions for an unlimited number of data streams and latent behaviour states; (3) biased and correlated random walk movement models, including dynamic “activity centres” associated with attractive or repulsive forces; (4) user‐specified design matrices and constraints for covariate modelling of parameters using formulas familiar to most R users; (5) multiple imputation methods that account for measurement error and temporally irregular or missing data; (6) seamless integration of spatio‐temporal covariate raster data; (7) cosinor and spline models for cyclical and other complicated patterns; (8) model checking and selection; and (9) simulation. 3. After providing an overview of the main features of the package, we demonstrate some of the capabilities of momentuHMM using real‐world examples. These include models for cyclical movement patterns of African elephants, foraging trips of northern fur seals, loggerhead turtle movements relative to ocean surface currents, and grey seal movements among three activity centres. 4. momentuHMM considerably extends the capabilities of existing HMM software while accounting for common challenges associated with telemetry data. It therefore facilitates more realistic hypothesis‐driven animal movement analyses that have hitherto been largely inaccessible to non‐statisticians. While motivated by telemetry data, the package can be used for analysing any type of data that is amenable to HMMs. Practitioners interested in additional features are encouraged to contact the authors

Probit models for capture-recapture data subject to imperfect detection, individual heterogeneity and misidentification

As noninvasive sampling techniques for animal populations have become more popular, there has been increasing interest in the development of capture-recapture models that can accommodate both imperfect detection and misidentification of individuals (e.g., due to genotyping error). However, current methods do not allow for individual variation in parameters, such as detection or survival probability. Here we develop misidentification models for capture-recapture data that can simultaneously account for temporal variation, behavioral effects and individual heterogeneity in parameters. To facilitate Bayesian inference using our approach, we extend standard probit regression techniques to latent multinomial models where the dimension and zeros of the response cannot be observed. We also present a novel Metropolis-Hastings within Gibbs algorithm for fitting these models using Markov chain Monte Carlo. Using closed population abundance models for illustration, we re-visit a DNA capture-recapture population study of black bears in Michigan, USA and find evidence of misidentification due to genotyping error, as well as temporal, behavioral and individual variation in detection probability. We also estimate a salamander population of known size from laboratory experiments evaluating the effectiveness of a marking technique commonly used for amphibians and fish. Our model was able to reliably estimate the size of this population and provided evidence of individual heterogeneity in misidentification probability that is attributable to variable mark quality. Our approach is more computationally demanding than previously proposed methods, but it provides the flexibility necessary for a much broader suite of models to be explored while properly accounting for uncertainty introduced by misidentification and imperfect detection. In the absence of misidentification, our probit formulation also provides a convenient and efficient Gibbs sampler for Bayesian analysis of traditional closed population capture-recapture data.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS783 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

X-ray reflected spectra from accretion disk models. III. A complete grid of ionized reflection calculations

We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code XILLVER that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index \Gamma of the illuminating radiation, the ionization parameter \xi at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A_{Fe} relative to the solar value. The ranges of the parameters covered are: 1.2 \leq \Gamma \leq 3.4, 1 \leq \xi \leq 10^4, and 0.5 \leq A_{Fe} \leq 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file{\url{http://hea-www.cfa.harvard.edu/~javier/xillver/}} suitable for the analysis of X-ray observations via the atable model in XSPEC. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of XILLVER.Comment: 70 pages, 21 figures, submitted to Ap

Constraints on the Size of Extra Dimensions from the Orbital Evolution of the Black-Hole X-Ray Binary XTE J1118+480

In a universe of the Randall-Sundrum type, black holes are unstable and emit gravitational modes in the extra dimension. This leads to dramatically shortened lifetimes of astrophysical black holes and to an observable change of the orbital period of black-hole binaries. I obtain an upper limit on the rate of change of the orbital period of the binary XTE J1118+480 and constrain the asymptotic curvature radius of the extra dimension to a value that is of the same order as the constraints from other astrophysical sources. A unique property of XTE J1118+480 is that the expected rate of change of the orbital period due to magnetic braking alone is so large that only one additional measurement of the orbital period would lead to the first detection of orbital evolution of a black-hole binary and impose the tightest constraint to date on the size of one extra dimension of the order of 35 microns.Comment: accepted for publication in A&

HST/STIS UV Spectroscopy of Two Quiescent X-ray Novae: A0620-00 and Centaurus X-4

In 1998 we made UV spectroscopic observations with HST/STIS of A0620-00 and Cen X-4, which are two X-ray novae (aka soft X-ray transients). These binary systems are similar in all respects except that the former contains a black hole and the latter contains a neutron star. A UV spectrum (1700-3100A) is presented for the quiescent state of each system in the context of previously published UV/optical and X-ray data. The non-stellar, continuum spectrum of black hole A0620-00 has a prominent UV/optical peak centered at about 3500A. In contrast the spectrum of neutron-star Cen X-4 lacks a peak and rises steadily with frequency over the entire UV/optical band. In the optical, the two systems are comparably luminous. However, black hole A0620-00 is about 6 times less luminous at 1700A, and about 40 times less luminous in the X-ray band. The broadband spectrum of A0620-00 is discussed in terms of the advection-dominated accretion flow model.Comment: 18 pages including 4 figures; tentatively scheduled for the March 10, 2000 issue of ApJ; minor revision

The Oral Administration of Antitoxins for Prevention of Diphtheria, Tetanus, and Possibly Sepsis, with Some Observations on the Influence of Certain Drugs in Preventing Digestion and Promoting Absorption from the Alimentary Canal

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Inclination Effects and Beaming in Black Hole X-ray Binaries

We investigate the dependence of observational properties of black hole X-ray binaries on the inclination angle i of their orbits. We find the following: (1) Transient black hole binaries show no trend in their quiescent X-ray luminosities as a function of i, suggesting that the radiation is not significantly beamed. This is consistent with emission from an accretion disk. If the X-rays are from a jet, then the Lorentz factor gamma of the jet is less than 1.24 at the 90% confidence level. (2) The X-ray binary 4U1543-47 with i of order 21 degrees has a surprisingly strong fluorescent iron line in the high soft state. Quantifying an earlier argument by Park et al. (2004), we conclude that if the continuum X-ray emission in this source is from a jet, then gamma < 1.04. (3) None of the known binaries has cos i 75 degrees. This fact, plus the lack of eclipses among the 20 black hole binaries in our sample, strongly suggests at the 99.5% confidence level that systems with large inclination angles are hidden from view. The obscuration could be the result of disk flaring, as suggested by Milgrom (1978) for neutron star X-ray binaries. (4) Transient black hole binaries with i ~ 70-75 degrees have significantly more complex X-ray light curves than systems with i < 65 degrees. This may be the result of variable obscuration and/or variable height above the disk of the radiating gas.Comment: 26 pages, to appear in The Astrophysical Journal, vol. 624, May 1, 200