Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

The effectiveness of traffic policing in reducing traffic crashes

Many governments throughout the world rely heavily on traffic law enforcement programs to modify driver behaviour and enhance road safety. There are two related functions of traffic law enforcement, apprehension and deterrence, and these are achieved through three processes: the establishment of traffic laws, the policing of those laws, and the application of penalties and sanctions to offenders. Traffic policing programs can vary by visibility (overt or covert) and deployment methods (scheduled and non-scheduled), while sanctions can serve to constrain, deter or reform offending behaviour. This chapter will review the effectiveness of traffic law enforcement strategies from the perspective of a range of high-risk, illegal driving behaviours including drink/drug driving, speeding, seat belt use and red light running. Additionally, this chapter discusses how traffic police are increasingly using technology to enforce traffic laws and thus reduce crashes. The chapter concludes that effective traffic policing involves a range of both overt and covert operations and includes a mix of automatic and more traditional manual enforcement methods. It is important to increase both the perceived and actual risk of detection by ensuring that traffic law enforcement operations are sufficiently intensive, unpredictable in nature and conducted as widely as possible across the road network. A key means of maintaining the unpredictability of operations is through the random deployment of enforcement and/or the random checking of drivers. The impact of traffic enforcement is also heightened when it is supported by public education campaigns. In the future, technological improvements will allow the use of more innovative enforcement strategies. Finally, further research is needed to continue the development of traffic policing approaches and address emerging road safety issues.

Navigational traffic conflict technique: a proactive approach to quantitative measurement of collision risks in port waters

Navigational safety analysis relying on collision statistics is often hampered because of low number of observations. A promising alternative approach that overcomes this problem is proposed in this paper. By analyzing critical vessel interactions this approach proactively measures collision risk in port waters. The proposed method is illustrated for quantitative measurement of collision risks in Singapore port fairways, and validated by examining correlations between the measured risks with those perceived by pilots. This method is an ethically appealing alternative to the collision-based analysis for fast, reliable and effective safety assessment, thus possesses great potential for managing collision risks in port waters.

On the significance of omitted variables in intersection crash modeling

Advances in safety research—trying to improve the collective understanding of motor vehicle crash causes and contributing factors—rest upon the pursuit of numerous lines of research inquiry. The research community has focused considerable attention on analytical methods development (negative binomial models, simultaneous equations, etc.), on better experimental designs (before-after studies, comparison sites, etc.), on improving exposure measures, and on model specification improvements (additive terms, non-linear relations, etc.). One might logically seek to know which lines of inquiry might provide the most significant improvements in understanding crash causation and/or prediction. It is the contention of this paper that the exclusion of important variables (causal or surrogate measures of causal variables) cause omitted variable bias in model estimation and is an important and neglected line of inquiry in safety research. In particular, spatially related variables are often difficult to collect and omitted from crash models—but offer significant opportunities to better understand contributing factors and/or causes of crashes. This study examines the role of important variables (other than Average Annual Daily Traffic (AADT)) that are generally omitted from intersection crash prediction models. In addition to the geometric and traffic regulatory information of intersection, the proposed model includes many spatial factors such as local influences of weather, sun glare, proximity to drinking establishments, and proximity to schools—representing a mix of potential environmental and human factors that are theoretically important, but rarely used. Results suggest that these variables in addition to AADT have significant explanatory power, and their exclusion leads to omitted variable bias. Provided is evidence that variable exclusion overstates the effect of minor road AADT by as much as 40% and major road AADT by 14%.

Empirical analysis on relationship between traffic conditions and crash occurrences

This paper investigates relationship between traffic conditions and the crash occurrence likelihood (COL) using the I-880 data. To remedy the data limitations and the methodological shortcomings suffered by previous studies, a multiresolution data processing method is proposed and implemented, upon which binary logistic models were developed. The major findings of this paper are: 1) traffic conditions have significant impacts on COL at the study site; Specifically, COL in a congested (transitioning) traffic flow is about 6 (1.6) times of that in a free flow condition; 2)Speed variance alone is not sufficient to capture traffic dynamics’ impact on COL; a traffic chaos indicator that integrates speed, speed variance, and flow is proposed and shows a promising performance; 3) Models based on aggregated data shall be interpreted with caution. Generally, conclusions obtained from such models shall not be generalized to individual vehicles (drivers) without further evidences using high-resolution data and it is dubious to either claim or disclaim speed kills based on aggregated data.

Severity of driver injury and vehicle damage in traffic crashes at intersections: A Bayesian hierarchical analysis

Most crash severity studies ignored severity correlations between driver-vehicle units involved in the same crashes. Models without accounting for these within-crash correlations will result in biased estimates in the factor effects. This study developed a Bayesian hierarchical binomial logistic model to identify the significant factors affecting the severity level of driver injury and vehicle damage in traffic crashes at signalized intersections. Crash data in Singapore were employed to calibrate the model. Model fitness assessment and comparison using Intra-class Correlation Coefficient (ICC) and Deviance Information Criterion (DIC) ensured the suitability of introducing the crash-level random effects. Crashes occurring in peak time, in good street lighting condition, involving pedestrian injuries are associated with a lower severity, while those in night time, at T/Y type intersections, on right-most lane, and installed with red light camera have larger odds of being severe. Moreover, heavy vehicles have a better resistance on severe crash, while crashes involving two-wheel vehicles, young or aged drivers, and the involvement of offending party are more likely to result in severe injuries.

Modeling random effect and excess zeros in road traffic accident prediction

Poisson distribution has often been used for count like accident data. Negative Binomial (NB) distribution has been adopted in the count data to take care of the over-dispersion problem. However, Poisson and NB distributions are incapable of taking into account some unobserved heterogeneities due to spatial and temporal effects of accident data. To overcome this problem, Random Effect models have been developed. Again another challenge with existing traffic accident prediction models is the distribution of excess zero accident observations in some accident data. Although Zero-Inflated Poisson (ZIP) model is capable of handling the dual-state system in accident data with excess zero observations, it does not accommodate the within-location correlation and between-location correlation heterogeneities which are the basic motivations for the need of the Random Effect models. This paper proposes an effective way of fitting ZIP model with location specific random effects and for model calibration and assessment the Bayesian analysis is recommended.

Proactive management of collision risks in port waters using navigational traffic conflicts

Navigational collisions are one of the major safety concerns in many seaports. To address this safety concern, a comprehensive and structured method of collision risk management is necessary. Traditionally management of port water collision risks has been relied on historical collision data. However, this collision-data-based approach is hampered by several shortcomings, such as randomness and rarity of collision occurrence leading to obtaining insufficient number of samples for a sound statistical analysis, insufficiency in explaining collision causation, and reactive approach to safety. A promising alternative approach that overcomes these shortcomings is the navigational traffic conflict technique that uses traffic conflicts as an alternative to the collision data. This paper proposes a collision risk management method by utilizing the principles of this technique. This risk management method allows safety analysts to diagnose safety deficiencies in a proactive manner, which, consequently, has great potential for managing collision risks in a fast, reliable and efficient manner.

Monotonous trend estimation using recursive prony analysis

This paper presents a solution to the problem of estimating the monotonous tendency of a slow-varying oscillating system. A recursive Prony Analysis (PA) scheme is developed which involves obtaining a dynamic model with parameters identified by implementing the forgetting factor recursive least square (FFRLS) method. A box threshold principle is proposed to separate the dominant components, which results in an accurate estimation of the trend of oscillating systems. Performance of the proposed PA is evaluated using real-time measurements when random noise and vibration effects are present. Moreover, the proposed method is used to estimate monotonous tendency of deck displacement to assist in a safe landing of an unmanned aerial vehicle (UAV). It is shown that the proposed method can estimate instantaneous mean deck satisfactorily, making it well suited for integration into ship-UAV approach and landing guidance systems.

System identification, estimation and control for a cost effective open-source quadcopter

This paper describes system identification, estimation and control of translational motion and heading angle for a cost effective open-source quadcopter — the MikroKopter. The dynamics of its built-in sensors, roll and pitch attitude controller, and system latencies are determined and used to design a computationally inexpensive multi-rate velocity estimator that fuses data from the built-in inertial sensors and a low-rate onboard laser range finder. Control is performed using a nested loop structure that is also computationally inexpensive and incorporates different sensors. Experimental results for the estimator and closed-loop positioning are presented and compared with ground truth from a motion capture system.

Integrated vision-based attitude estimation

For many years, computer vision has lured researchers with promises of a low-cost, passive, lightweight and information-rich sensor suitable for navigation purposes. The prime difficulty in vision-based navigation is that the navigation solution will continually drift with time unless external information is available, whether it be cues from the appearance of the scene, a map of features (whether built online or known a priori), or from an externally-referenced sensor. It is not merely position that is of interest in the navigation problem. Attitude (i.e. the angular orientation of a body with respect to a reference frame) is integral to a visionbased navigation solution and is often of interest in its own right (e.g. flight control). This thesis examines vision-based attitude estimation in an aerospace environment, and two methods are proposed for constraining drift in the attitude solution; one through a novel integration of optical flow and the detection of the sky horizon, and the other through a loosely-coupled integration of Visual Odometry and GPS position measurements. In the first method, roll angle, pitch angle and the three aircraft body rates are recovered though a novel method of tracking the horizon over time and integrating the horizonderived attitude information with optical flow. An image processing front-end is used to select several candidate lines in a image that may or may not correspond to the true horizon, and the optical flow is calculated for each candidate line. Using an Extended Kalman Filter (EKF), the previously estimated aircraft state is propagated using a motion model and a candidate horizon line is associated using a statistical test based on the optical flow measurements and location of the horizon in the image. Once associated, the selected horizon line, along with the associated optical flow, is used as a measurement to the EKF. To evaluate the accuracy of the algorithm, two flights were conducted, one using a highly dynamic Uninhabited Airborne Vehicle (UAV) in clear flight conditions and the other in a human-piloted Cessna 172 in conditions where the horizon was partially obscured by terrain, haze and smoke. The UAV flight resulted in pitch and roll error standard deviations of 0.42° and 0.71° respectively when compared with a truth attitude source. The Cessna 172 flight resulted in pitch and roll error standard deviations of 1.79° and 1.75° respectively. In the second method for estimating attitude, a novel integrated GPS/Visual Odometry (GPS/VO) navigation filter is proposed, using a structure similar to a classic looselycoupled GPS/INS error-state navigation filter. Under such an arrangement, the error dynamics of the system are derived and a Kalman Filter is developed for estimating the errors in position and attitude. Through similar analysis to the GPS/INS problem, it is shown that the proposed filter is capable of recovering the complete attitude (i.e. pitch, roll and yaw) of the platform when subjected to acceleration not parallel to velocity for both the monocular and stereo variants of the filter. Furthermore, it is shown that under general straight line motion (e.g. constant velocity), only the component of attitude in the direction of motion is unobservable. Numerical simulations are performed to demonstrate the observability properties of the GPS/VO filter in both the monocular and stereo camera configurations. Furthermore, the proposed filter is tested on imagery collected using a Cessna 172 to demonstrate the observability properties on real-world data. The proposed GPS/VO filter does not require additional restrictions or assumptions such as platform-specific dynamics, map-matching, feature-tracking, visual loop-closing, gravity vector or additional sensors such as an IMU or magnetic compass. Since no platformspecific dynamics are required, the proposed filter is not limited to the aerospace domain and has the potential to be deployed in other platforms such as ground robots or mobile phones.