The Bayesian conditional independence model for measurement error: applications in ecology

The measurement error model is a well established statistical method for regression problems in medical sciences, although rarely used in ecological studies. While the situations in which it is appropriate may be less common in ecology, there are instances in which there may be benefits in its use for prediction and estimation of parameters of interest. We have chosen to explore this topic using a conditional independence model in a Bayesian framework using a Gibbs sampler, as this gives a great deal of flexibility, allowing us to analyse a number of different models without losing generality. Using simulations and two examples, we show how the conditional independence model can be used in ecology, and when it is appropriate.

Error analysis and attitude observability of a monocular GPS/visual odometry integrated navigation filter

In this paper, we present a method for the recovery of position and absolute attitude (including pitch, roll and yaw) using a novel fusion of monocular Visual Odometry and GPS measurements in a similar manner to a classic loosely-coupled GPS/INS error state navigation filter. The proposed 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. An observability analysis of the proposed filter is performed, showing that the scale factor, position and attitude errors are fully observable under acceleration that is non-parallel to velocity vector in the navigation frame. The observability properties of the proposed filter are demonstrated using numerical simulations. We conclude the article with an implementation of the proposed filter using real flight data collected from a Cessna 172 equipped with a downwards-looking camera and GPS, showing the feasibility of the algorithm in real-world conditions.

The effect of simulated astigmatic refractive error on reading performance

Background: Few studies have specifically investigated the functional effects of uncorrected astigmatism on measures of reading fluency. This information is important to provide evidence for the development of clinical guidelines for the correction of astigmatism. Methods: Participants included 30 visually normal, young adults (mean age 21.7 ± 3.4 years). Distance and near visual acuity and reading fluency were assessed with optimal spectacle correction (baseline) and for two levels of astigmatism, 1.00DC and 2.00DC, at two axes (90° and 180°) to induce both against-the-rule (ATR) and with-the-rule (WTR) astigmatism. Reading and eye movement fluency were assessed using standardized clinical measures including the test of Discrete Reading Rate (DRR), the Developmental Eye Movement (DEM) test and by recording eye movement patterns with the Visagraph (III) during reading for comprehension. Results: Both distance and near acuity were significantly decreased compared to baseline for all of the astigmatic lens conditions (p < 0.001). Reading speed with the DRR for N16 print size was significantly reduced for the 2.00DC ATR condition (a reduction of 10%), while for smaller text sizes reading speed was reduced by up to 24% for the 1.00DC ATR and 2.00DC condition in both axis directions (p<0.05). For the DEM, sub-test completion speeds were significantly impaired, with the 2.00DC condition affecting both vertical and horizontal times and the 1.00DC ATR condition affecting only horizontal times (p<0.05). Visagraph reading eye movements were not significantly affected by the induced astigmatism. Conclusions: Induced astigmatism impaired performance on selected tests of reading fluency, with ATR astigmatism having significantly greater effects on performance than did WTR, even for relatively small amounts of astigmatic blur of 1.00DC. These findings have implications for the minimal prescribing criteria for astigmatic refractive errors.

Effect of geometry on the melting rates of iron rods burning in high pressure oxygen

The effect of sample geometry on the melting rates of burning iron rods was assessed. Promoted-ignition tests were conducted with rods having cylindrical, rectangular, and triangular cross-sectional shapes over a range of cross-sectional areas. The regression rate of the melting interface (RRMI) was assessed using a statistical approach which enabled the quantification of confidence levels for the observed differences in RRMI. Statistically significant differences in RRMI were observed for rods with the same cross-sectional area but different cross-sectional shape. The magnitude of the proportional difference in RRMI increased with the cross-sectional area. Triangular rods had the highest RRMI, followed by rectangular rods, and then cylindrical rods. The dependence of RRMI on rod shape is shown to relate to the action of molten metal at corners. The corners of the rectangular and triangular rods melted faster than the faces due to their locally higher surface area to volume ratios. This phenomenon altered the attachment geometry between liquid and solid phases, increasing the surface area available for heat transfer, causing faster melting. Findings relating to the application of standard flammability test results in industrial situations are also presented.

Thresholds for error probability measures of business process models

The quality of conceptual business process models is highly relevant for the design of corresponding information systems. In particular, a precise measurement of model characteristics can be beneficial from a business perspective, helping to save costs thanks to early error detection. This is just as true from a software engineering point of view. In this latter case, models facilitate stakeholder communication and software system design. Research has investigated several proposals as regards measures for business process models, from a rather correlational perspective. This is helpful for understanding, for example size and complexity as general driving forces of error probability. Yet, design decisions usually have to build on thresholds, which can reliably indicate that a certain counter-action has to be taken. This cannot be achieved only by providing measures; it requires a systematic identification of effective and meaningful thresholds. In this paper, we derive thresholds for a set of structural measures for predicting errors in conceptual process models. To this end, we use a collection of 2,000 business process models from practice as a means of determining thresholds, applying an adaptation of the ROC curves method. Furthermore, an extensive validation of the derived thresholds was conducted by using 429 EPC models from an Australian financial institution. Finally, significant thresholds were adapted to refine existing modeling guidelines in a quantitative way.

Wear it or wear the cost : current seatbelt wearing rates in Queensland

Observational seatbelt wearing studies are a valuable tool for obtaining up-to-date information about rates of use. Given that one quarter of vehicle occupants killed on Queensland roads in recent years were not wearing seatbelts, it is important that authorities are able to identify non-wearers and take steps to increase compliance with seatbelt laws to reduce the severity of crashes and, therefore, the road toll. An observational study of seatbelt use was conducted in metropolitan, regional and rural locations throughout Queensland in May and June, 2010. Trained observers took note of seatbelt use of all occupants of passenger vehicles, noting their gender, approximate age group, seating position, vehicle type, licence type (i.e. visible L or P plates), mobile phone use, and the date, time and location of the observation. Of 19,579 observations, 99.04% (19,391) of occupants were observed wearing seatbelts, as only 0.96% of occupants (188) were not wearing a seatbelt. There were differences in seatbelt wearing rates for a number of study variables, although most were very small. However, seatbelt wearing rates were 3.84% lower for drivers observed using a mobile phone than for those who were not. While compliance with seatbelt laws seems to be very high, it is still concerning that so few non-wearers represent a disproportionately large proportion of road fatalities and serious injuries in Queensland. Road safety authorities must therefore continue to find ways to improve seatbelt use, as small gains in wearing rates will translate into significant fatality reductions.

Error correction in second language writing : teachers’ beliefs, practices, and students’ preferences

Error correction is perhaps the most widely used method for responding to student writing. While various studies have investigated the effectiveness of providing error correction, there has been relatively little research incorporating teachers' beliefs, practices, and students' preferences in written error correction. The current study adopted features of an ethnographic research design in order to explore the beliefs and practices of ESL teachers, and investigate the preferences of L2 students regarding written error correction in the context of a language institute situated in the Brisbane metropolitan district. In this study, two ESL teachers and two groups of adult intermediate L2 students were interviewed and observed. The beliefs and practices of the teachers were elicited through interviews and classroom observations. The preferences of L2 students were elicited through focus group interviews. Responses of the participants were encoded and analysed. Results of the teacher interviews showed that teachers believe that providing written error correction has advantages and disadvantages. Teachers believe that providing written error correction helps students improve their proof-reading skills in order to revise their writing more efficiently. However, results also indicate that providing written error correction is very time consuming. Furthermore, teachers prefer to provide explicit written feedback strategies during the early stages of the language course, and move to a more implicit strategy of providing written error correction in order to facilitate language learning. On the other hand, results of the focus group interviews suggest that students regard their teachers' practice of written error correction as important in helping them locate their errors and revise their writing. However, students also feel that the process of providing written error correction is time consuming. Nevertheless, students want and expect their teachers to provide written feedback because they believe that the benefits they gain from receiving feedback on their writing outweigh the apparent disadvantages of their teachers' written error correction strategies.

Using approximate Bayesian computation to estimate transmission rates of nosocomial pathogens

In this paper, we apply a simulation based approach for estimating transmission rates of nosocomial pathogens. In particular, the objective is to infer the transmission rate between colonised health-care practitioners and uncolonised patients (and vice versa) solely from routinely collected incidence data. The method, using approximate Bayesian computation, is substantially less computer intensive and easier to implement than likelihood-based approaches we refer to here. We find through replacing the likelihood with a comparison of an efficient summary statistic between observed and simulated data that little is lost in the precision of estimated transmission rates. Furthermore, we investigate the impact of incorporating uncertainty in previously fixed parameters on the precision of the estimated transmission rates.

Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Can rodents enhance germination rates in rainforest seeds?

The decline of large coevolved frugivorous species within fragmented habitats can have an effect on ecological processes, for example, seed dispersal and germination. It is therefore necessary for more resilient species to ensure essential processes are maintained within the system. This study investigates the influence of two rodent species, Melomys cervinipes (Fawn-footed Melomys) and Rattus fuscipes (Bush Rat), on the germination process of rainforest fruits. Both species are endemic to north Queensland rainforest and commonly found in fragmented habitats in high densities. We found in 85% of fruit species tested, rodent feeding increased seed germination rate by a factor of 3.5. Our results suggest that rodents can play a significant role in enhancing germination rates of fruits in the tropical rainforest of far north Queensland.

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.