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).

Calibration uncertainty estimation for internal aerodynamic balance

Aerodynamic balances are employed in wind tunnels to estimate the forces and moments acting on the model under test. This paper proposes a methodology for the assessment of uncertainty in the calibration of an internal multi-component aerodynamic balance. In order to obtain a suitable model to provide aerodynamic loads from the balance sensor responses, a calibration is performed prior to the tests by applying known weights to the balance. A multivariate polynomial fitting by the least squares method is used to interpolate the calibration data points. The uncertainties of both the applied loads and the readings of the sensors are considered in the regression. The data reduction includes the estimation of the calibration coefficients, the predicted values of the load components and their corresponding uncertainties, as well as the goodness of fit.

Evaluación y análisis de la trazabilidad metrológica en redes para la verificación y calibración de instrumental GNSS (Global Navigation Satellite System)

Los estudios realizados hasta el momento para la determinación de la calidad de medida del instrumental geodésico han estado dirigidos, fundamentalmente, a las medidas angulares y de distancias. Sin embargo, en los últimos años se ha impuesto la tendencia generalizada de utilizar equipos GNSS (Global Navigation Satellite System) en el campo de las aplicaciones geomáticas sin que se haya establecido una metodología que permita obtener la corrección de calibración y su incertidumbre para estos equipos. La finalidad de esta Tesis es establecer los requisitos que debe satisfacer una red para ser considerada Red Patrón con trazabilidad metrológica, así como la metodología para la verificación y calibración de instrumental GNSS en redes patrón. Para ello, se ha diseñado y elaborado un procedimiento técnico de calibración de equipos GNSS en el que se han definido las contribuciones a la incertidumbre de medida. El procedimiento, que se ha aplicado en diferentes redes para distintos equipos, ha permitido obtener la incertidumbre expandida de dichos equipos siguiendo las recomendaciones de la Guide to the Expression of Uncertainty in Measurement del Joint Committee for Guides in Metrology. Asimismo, se han determinado mediante técnicas de observación por satélite las coordenadas tridimensionales de las bases que conforman las redes consideradas en la investigación, y se han desarrollado simulaciones en función de diversos valores de las desviaciones típicas experimentales de los puntos fijos que se han utilizado en el ajuste mínimo cuadrático de los vectores o líneas base. Los resultados obtenidos han puesto de manifiesto la importancia que tiene el conocimiento de las desviaciones típicas experimentales en el cálculo de incertidumbres de las coordenadas tridimensionales de las bases. Basándose en estudios y observaciones de gran calidad técnica, llevados a cabo en estas redes con anterioridad, se ha realizado un exhaustivo análisis que ha permitido determinar las condiciones que debe satisfacer una red patrón. Además, se han diseñado procedimientos técnicos de calibración que permiten calcular la incertidumbre expandida de medida de los instrumentos geodésicos que proporcionan ángulos y distancias obtenidas por métodos electromagnéticos, ya que dichos instrumentos son los que van a permitir la diseminación de la trazabilidad metrológica a las redes patrón para la verificación y calibración de los equipos GNSS. De este modo, ha sido posible la determinación de las correcciones de calibración local de equipos GNSS de alta exactitud en las redes patrón. En esta Tesis se ha obtenido la incertidumbre de la corrección de calibración mediante dos metodologías diferentes; en la primera se ha aplicado la propagación de incertidumbres, mientras que en la segunda se ha aplicado el método de Monte Carlo de simulación de variables aleatorias. El análisis de los resultados obtenidos confirma la validez de ambas metodologías para la determinación de la incertidumbre de calibración de instrumental GNSS. ABSTRACT The studies carried out so far for the determination of the quality of measurement of geodetic instruments have been aimed, primarily, to measure angles and distances. However, in recent years it has been accepted to use GNSS (Global Navigation Satellite System) equipment in the field of Geomatic applications, for data capture, without establishing a methodology that allows obtaining the calibration correction and its uncertainty. The purpose of this Thesis is to establish the requirements that a network must meet to be considered a StandardNetwork with metrological traceability, as well as the methodology for the verification and calibration of GNSS instrumental in those standard networks. To do this, a technical calibration procedure has been designed, developed and defined for GNSS equipment determining the contributions to the uncertainty of measurement. The procedure, which has been applied in different networks for different equipment, has alloweddetermining the expanded uncertainty of such equipment following the recommendations of the Guide to the Expression of Uncertainty in Measurement of the Joint Committee for Guides in Metrology. In addition, the three-dimensional coordinates of the bases which constitute the networks considered in the investigationhave been determined by satellite-based techniques. There have been several developed simulations based on different values of experimental standard deviations of the fixed points that have been used in the least squares vectors or base lines calculations. The results have shown the importance that the knowledge of experimental standard deviations has in the calculation of uncertainties of the three-dimensional coordinates of the bases. Based on high technical quality studies and observations carried out in these networks previously, it has been possible to make an exhaustive analysis that has allowed determining the requirements that a standard network must meet. In addition, technical calibration procedures have been developed to allow the uncertainty estimation of measurement carried outby geodetic instruments that provide angles and distances obtained by electromagnetic methods. These instruments provide the metrological traceability to standard networks used for verification and calibration of GNSS equipment. As a result, it has been possible the estimation of local calibration corrections for high accuracy GNSS equipment in standardnetworks. In this Thesis, the uncertainty of calibration correction has been calculated using two different methodologies: the first one by applying the law of propagation of uncertainty, while the second has applied the propagation of distributions using the Monte Carlo method. The analysis of the obtained results confirms the validity of both methodologies for estimating the calibration uncertainty of GNSS equipment.

Avaliação da incerteza de medição no Setor Médico-hospitalar

This study aims to evaluate the uncertainty associated with measurements made by aneroid sphygmomanometer, neonatal electronic balance and electrocautery. Therefore, were performing repeatability tests on all devices for the subsequent execution of normality tests using Shapiro-Wilk; identification of influencing factors that affect the measurement result of each measurement; proposition of mathematical models to calculate the measurement uncertainty associated with measuring evaluated for all equipament and calibration for neonatal electronic balance; evaluation of the measurement uncertainty; and development of a computer program in Java language to systematize the calibration uncertainty of estimates and measurement uncertainty. It was proposed and carried out 23 factorial design for aneroid sphygmomanometer order to investigate the effect of temperature factors, patient and operator and another 32 planning for electrocautery, where it investigated the effects of temperature factors and output electrical power. The expanded uncertainty associated with the measurement of blood pressure significantly reduced the extent of the patient classification tracks. In turn, the expanded uncertainty associated with the mass measurement with neonatal balance indicated a variation of about 1% in the dosage of medication to neonates. Analysis of variance (ANOVA) and the Turkey test indicated significant and indirectly proportional effects of temperature factor in cutting power values and clotting indicated by electrocautery and no significant effect of factors investigated for aneroid sphygmomanometer.

Recommended practice, symbols, terms, units, and uncertainty analysis for radiometric sensor calibration /

"September 1998."

Integrated sensitivity analysis, calibration, and uncertainty propagation analysis approaches for supporting hydrological modeling

The successful performance of a hydrological model is usually challenged by the quality of the sensitivity analysis, calibration and uncertainty analysis carried out in the modeling exercise and subsequent simulation results. This is especially important under changing climatic conditions where there are more uncertainties associated with climate models and downscaling processes that increase the complexities of the hydrological modeling system. In response to these challenges and to improve the performance of the hydrological models under changing climatic conditions, this research proposed five new methods for supporting hydrological modeling. First, a design of experiment aided sensitivity analysis and parameterization (DOE-SAP) method was proposed to investigate the significant parameters and provide more reliable sensitivity analysis for improving parameterization during hydrological modeling. The better calibration results along with the advanced sensitivity analysis for significant parameters and their interactions were achieved in the case study. Second, a comprehensive uncertainty evaluation scheme was developed to evaluate three uncertainty analysis methods, the sequential uncertainty fitting version 2 (SUFI-2), generalized likelihood uncertainty estimation (GLUE) and Parameter solution (ParaSol) methods. The results showed that the SUFI-2 performed better than the other two methods based on calibration and uncertainty analysis results. The proposed evaluation scheme demonstrated that it is capable of selecting the most suitable uncertainty method for case studies. Third, a novel sequential multi-criteria based calibration and uncertainty analysis (SMC-CUA) method was proposed to improve the efficiency of calibration and uncertainty analysis and control the phenomenon of equifinality. The results showed that the SMC-CUA method was able to provide better uncertainty analysis results with high computational efficiency compared to the SUFI-2 and GLUE methods and control parameter uncertainty and the equifinality effect without sacrificing simulation performance. Fourth, an innovative response based statistical evaluation method (RESEM) was proposed for estimating the uncertainty propagated effects and providing long-term prediction for hydrological responses under changing climatic conditions. By using RESEM, the uncertainty propagated from statistical downscaling to hydrological modeling can be evaluated. Fifth, an integrated simulation-based evaluation system for uncertainty propagation analysis (ISES-UPA) was proposed for investigating the effects and contributions of different uncertainty components to the total propagated uncertainty from statistical downscaling. Using ISES-UPA, the uncertainty from statistical downscaling, uncertainty from hydrological modeling, and the total uncertainty from two uncertainty sources can be compared and quantified. The feasibility of all the methods has been tested using hypothetical and real-world case studies. The proposed methods can also be integrated as a hydrological modeling system to better support hydrological studies under changing climatic conditions. The results from the proposed integrated hydrological modeling system can be used as scientific references for decision makers to reduce the potential risk of damages caused by extreme events for long-term water resource management and planning.

Solving navigational uncertainty using grid cells on robots

To successfully navigate their habitats, many mammals use a combination of two mechanisms, path integration and calibration using landmarks, which together enable them to estimate their location and orientation, or pose. In large natural environments, both these mechanisms are characterized by uncertainty: the path integration process is subject to the accumulation of error, while landmark calibration is limited by perceptual ambiguity. It remains unclear how animals form coherent spatial representations in the presence of such uncertainty. Navigation research using robots has determined that uncertainty can be effectively addressed by maintaining multiple probabilistic estimates of a robot's pose. Here we show how conjunctive grid cells in dorsocaudal medial entorhinal cortex (dMEC) may maintain multiple estimates of pose using a brain-based robot navigation system known as RatSLAM. Based both on rodent spatially-responsive cells and functional engineering principles, the cells at the core of the RatSLAM computational model have similar characteristics to rodent grid cells, which we demonstrate by replicating the seminal Moser experiments. We apply the RatSLAM model to a new experimental paradigm designed to examine the responses of a robot or animal in the presence of perceptual ambiguity. Our computational approach enables us to observe short-term population coding of multiple location hypotheses, a phenomenon which would not be easily observable in rodent recordings. We present behavioral and neural evidence demonstrating that the conjunctive grid cells maintain and propagate multiple estimates of pose, enabling the correct pose estimate to be resolved over time even without uniquely identifying cues. While recent research has focused on the grid-like firing characteristics, accuracy and representational capacity of grid cells, our results identify a possible critical and unique role for conjunctive grid cells in filtering sensory uncertainty. We anticipate our study to be a starting point for animal experiments that test navigation in perceptually ambiguous environments.

Internal calibration of gel dosimeters : a feasibility study

In this work we test the feasibility of a new calibration method for gel dosimetry. We examine, through Monte Carlo modelling, whether the inclusion of an organic plastic scintillator system at key points within the gel phantom would perturb the dose map. Such a system would remove the requirement for a separate calibration gel, removing many sources of uncertainty.

Soil nitrogen—crop response calibration relationships and criteria for winter cereal crops grown in Australia

More than 1200 wheat and 120 barley experiments conducted in Australia to examine yield responses to applied nitrogen (N) fertiliser are contained in a national database of field crops nutrient research (BFDC National Database). The yield responses are accompanied by various pre-plant soil test data to quantify plant-available N and other indicators of soil fertility status or mineralisable N. A web application (BFDC Interrogator), developed to access the database, enables construction of calibrations between relative crop yield ((Y0/Ymax) × 100) and N soil test value. In this paper we report the critical soil test values for 90% RY (CV90) and the associated critical ranges (CR90, defined as the 70% confidence interval around that CV90) derived from analysis of various subsets of these winter cereal experiments. Experimental programs were conducted throughout Australia’s main grain-production regions in different eras, starting from the 1960s in Queensland through to Victoria during 2000s. Improved management practices adopted during the period were reflected in increasing potential yields with research era, increasing from an average Ymax of 2.2 t/ha in Queensland in the 1960s and 1970s, to 3.4 t/ha in South Australia (SA) in the 1980s, to 4.3 t/ha in New South Wales (NSW) in the 1990s, and 4.2 t/ha in Victoria in the 2000s. Various sampling depths (0.1–1.2 m) and methods of quantifying available N (nitrate-N or mineral-N) from pre-planting soil samples were used and provided useful guides to the need for supplementary N. The most regionally consistent relationships were established using nitrate-N (kg/ha) in the top 0.6 m of the soil profile, with regional and seasonal variation in CV90 largely accounted for through impacts on experimental Ymax. The CV90 for nitrate-N within the top 0.6 m of the soil profile for wheat crops increased from 36 to 110 kg nitrate-N/ha as Ymax increased over the range 1 to >5 t/ha. Apparent variation in CV90 with seasonal moisture availability was entirely consistent with impacts on experimental Ymax. Further analyses of wheat trials with available grain protein (~45% of all experiments) established that grain yield and not grain N content was the major driver of crop N demand and CV90. Subsets of data explored the impact of crop management practices such as crop rotation or fallow length on both pre-planting profile mineral-N and CV90. Analyses showed that while management practices influenced profile mineral-N at planting and the likelihood and size of yield response to applied N fertiliser, they had no significant impact on CV90. A level of risk is involved with the use of pre-plant testing to determine the need for supplementary N application in all Australian dryland systems. In southern and western regions, where crop performance is based almost entirely on in-crop rainfall, this risk is offset by the management opportunity to split N applications during crop growth in response to changing crop yield potential. In northern cropping systems, where stored soil moisture at sowing is indicative of minimum yield potential, erratic winter rainfall increases uncertainty about actual yield potential as well as reducing the opportunity for effective in-season applications.

Managing uncertainty to improve the cost performance of complex infrastructure projects

There has been a recent spate of high profile infrastructure cost overruns in Australia and internationally. This is just the tip of a longer-term and more deeply-seated problem with initial budget estimating practice, well recognised in both academic research and industry reviews: the problem of uncertainty. A case study of the Sydney Opera House is used to identify and illustrate the key causal factors and system dynamics of cost overruns. It is conventionally the role of risk management to deal with such uncertainty, but the type and extent of the uncertainty involved in complex projects is shown to render established risk management techniques ineffective. This paper considers a radical advance on current budget estimating practice which involves a particular approach to statistical modelling complemented by explicit training in estimating practice. The statistical modelling approach combines the probability management techniques of Savage, which operate on actual distributions of values rather than flawed representations of distributions, and the data pooling technique of Skitmore, where the size of the reference set is optimised. Estimating training employs particular calibration development methods pioneered by Hubbard, which reduce the bias of experts caused by over-confidence and improve the consistency of subjective decision-making. A new framework for initial budget estimating practice is developed based on the combined statistical and training methods, with each technique being explained and discussed.

Estimation of soil hydraulic properties and their uncertainty: comparison between laboratory and field experiment

Often the soil hydraulic parameters are obtained by the inversion of measured data (e.g. soil moisture, pressure head, and cumulative infiltration, etc.). However, the inverse problem in unsaturated zone is ill-posed due to various reasons, and hence the parameters become non-unique. The presence of multiple soil layers brings the additional complexities in the inverse modelling. The generalized likelihood uncertainty estimate (GLUE) is a useful approach to estimate the parameters and their uncertainty when dealing with soil moisture dynamics which is a highly non-linear problem. Because the estimated parameters depend on the modelling scale, inverse modelling carried out on laboratory data and field data may provide independent estimates. The objective of this paper is to compare the parameters and their uncertainty estimated through experiments in the laboratory and in the field and to assess which of the soil hydraulic parameters are independent of the experiment. The first two layers in the field site are characterized by Loamy sand and Loamy. The mean soil moisture and pressure head at three depths are measured with an interval of half hour for a period of 1 week using the evaporation method for the laboratory experiment, whereas soil moisture at three different depths (60, 110, and 200 cm) is measured with an interval of 1 h for 2 years for the field experiment. A one-dimensional soil moisture model on the basis of the finite difference method was used. The calibration and validation are approximately for 1 year each. The model performance was found to be good with root mean square error (RMSE) varying from 2 to 4 cm(3) cm(-3). It is found from the two experiments that mean and uncertainty in the saturated soil moisture (theta(s)) and shape parameter (n) of van Genuchten equations are similar for both the soil types. Copyright (C) 2010 John Wiley & Sons, Ltd.

Handling uncertainty in housing stock models

Housing stock models can be useful tools in helping to assess the environmental and socio-economic impacts of retrofits to residential buildings; however, existing housing stock models are not able to quantify the uncertainties that arise in the modelling process from various sources, thus limiting the role that they can play in helping decision makers. This paper examines the different sources of uncertainty involved in housing stock models and proposes a framework for handling these uncertainties. This framework involves integrating probabilistic sensitivity analysis with a Bayesian calibration process in order to quantify uncertain parameters more accurately. The proposed framework is tested on a case study building, and suggestions are made on how to expand the framework for retrofit analysis at an urban-scale. © 2011 Elsevier Ltd.