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We propose Generalized Linear Models for understanding errors in SEE rate due to uncertainties in LET of the ion responsible for the event. Applications are suggested and assessed for suitability of treatment by the model.
Purpose: The purpose of this work was to develop and evaluate the accuracy of several predictive models of variation in tumor volume throughout the course of radiation therapy. Methods: Nineteen patients with oropharyngeal cancers were imaged daily with CT-on-rails for image-guided alignment per an institutional protocol. The daily volumes of 35 tumors in these 19 patients were determined and used to generate (1) a linear model in which tumor volume changed at a constant rate, (2) a general linear model that utilized the power fit relationship between the daily and initial tumor volumes, and (3) a functional general linear model that identified and exploited the primary modes of variation between time series describing the changing tumor volumes. Primary and nodal tumor volumes were examined separately. The accuracy of these models in predicting daily tumor volumes were compared with those of static and linear reference models using leave-one-out cross-validation. Results: In predicting the daily volume of primary tumors, the general linear model and the functional general linear model were more accurate than the static reference model by 9.9% (range: −11.6%–23.8%) and 14.6% (range: −7.3%–27.5%), respectively, and were more accurate than the linear reference model by 14.2% (range: −6.8%–40.3%) and 13.1% (range: −1.5%–52.5%), respectively. In predicting the daily volume of nodal tumors, only the 14.4% (range: −11.1%–20.5%) improvement in accuracy of the functional general linear model compared to the static reference model was statistically significant. Conclusions: A general linear model and a functional general linear model trained on data from a small population of patients can predict the primary tumor volume throughout the course of radiation therapy with greater accuracy than standard reference models. These more accurate models may increase the prognostic value of information about the tumor garnered from pretreatment computed tomography images and facilitate improved treatment management.
Although most SEE rate estimation methods presume a fit to SEE cross section vs. LET, fitting SEE data is challenging because the data are not compatible with the assumptions of many common fitting techniques (e.g. linear regression. The difficulty of fitting such data is compounded when the LET of the ion responsible for an SEE is uncertain. We modify a Generalized Linear Model SEE data fitting methodology to accommodate uncertain LET and apply the method to the problem of backside heavy-ion SEE testing to demonstrate the utility of the method, explore the dependence of systematic errors that arise from improper treatment of LET uncertainty and develop guidelines for minimizing such systematic errors when proper treatment is not possible. Additional applications are suggested and assessed for suitability of treatment by the model.
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Here, effective sensitivity analysis approaches are needed to identify important parameters or factors and their uncertainties in complex Earth system models composed of multi-phase multi-component phenomena and multiple biogeophysical-biogeochemical processes. In this study, the impacts of 10 hydrologic parameters in the Community Land Model on simulations of runoff and latent heat flux are evaluated using data from a watershed. Different metrics, including residual statistics, the Nash-Sutcliffe coefficient, and log mean square error, are used as alternative measures of the deviations between the simulated and field observed values. Four sensitivity analysis (SA) approaches, including analysis of variance based on the generalized linear model, generalized cross validation based on the multivariate adaptive regression splines model, standardized regression coefficients based on a linear regression model, and analysis of variance based on support vector machine, are investigated. Results suggest that these approaches show consistent measurement of the impacts of major hydrologic parameters on response variables, but with differences in the relative contributions, particularly for the secondary parameters. The convergence behaviors of the SA with respect to the number of sampling points are also examined with different combinations of input parameter sets and output response variables and their alternative metrics. This study helps identify the optimal SA approach, provides guidance for the calibration of the Community Land Model parameters to improve the model simulations of land surface fluxes, and approximates the magnitudes to be adjusted in the parameter values during parametric model optimization.
Repeated measurement will be a feature of the survey data collected during the Quesst missionX-59 community response tests (CRT). Since each participant will report his or her categorical level of annoyance in response to multiple events, the responses from any single individual may be correlated with one another. Several models within the class of generalized linear mixed models (GLMM) are pertinent to the analysis of correlated categorical outcomes; the random intercept logistic regression model is one example. Both Bayesian and frequentist methods for fitting these models are available, with frequentist methods relying on some form of approximation (of either an integral or the integrand) that appears in the marginal likelihood function. Given several anticipated similarities of the X-59 CRT data to data collected during a past risk reduction, Quiet Supersonic Flights 2018 (QSF18), this short note is intended to create awareness. It documents an instance in which a reported population average dose-response relationship derived from QSF18 single event data was distorted by the integral approximation applied in likelihood-based methods. We review some of the available literature on the topic, compare the outputs of several different computational approaches implemented in available statistical software, and present simple corrective actions that may be useful during the Quesst mission.
Previous studies have found that the relationship between wildlife road mortality and traffic volume follows a threshold effect on low traffic volume roads. We aimed at evaluating the response of several species to increasing traffic intensity on highways over a large geographic area and temporal period. We used data of four terrestrial vertebrate species with different biological and ecological features known by their high road-kill rates: the barn owl (Tyto alba), hedgehog (Erinaceus europaeus), red fox (Vulpes vulpes) and European rabbit (Oryctolagus cuniculus). Additionally, we checked whether road-kill likelihood varies when traffic patterns depart from the average. We used annual average daily traffic (AADT) and road-kill records observed along 1000 km of highways in Portugal over seven consecutive years (2003–2009). We fitted candidate models using Generalized Linear Models with a binomial distribution through a sample unit of 1 km segments to describe the effect of traffic on the probability of finding at least one victim in each segment during the study. We also assigned for each road-kill record the traffic of that day and the AADT on that year to test for differences using Paired Student's t-test. Mortality risk declined significantly with traffic volume but varied among species: the probability of finding road-killed red foxes and rabbits occurs up to moderate traffic volumes (< 20,000 AADT) whereas barn owls and hedgehogs occurred up to higher traffic volumes (40,000 AADT). Perception of risk may explain differences in responses towards high traffic highway segments. Road-kill rates did not vary significantly when traffic intensity departed from the average. In summary, we did not find evidence of traffic thresholds for the analysed species and traffic intensities. We suggest mitigation measures to reduce mortality be applied in particular on low traffic roads (< 5000 AADT) while additional measures to reduce barrier effects should take into account species-specific behavioural traits. - Highlights: • Traffic and road-kills were analysed along 1000 km of highways over seven years. • Mortality risk declined significantly with traffic volume. • Perception of risk may explain different responses towards high traffic sections. • Reducing barrier effects should take into account species behavioural traits.
Background: The transmission of vectorborne infectious diseases is often influenced by environmental, meteorological and climatic parameters, because the vector life cycle depends on these factors. For example, the geophysical parameters relevant to malaria transmission include precipitation, surface temperature, humidity, elevation, and vegetation type. Because these parameters are routinely measured by satellites, remote sensing is an important technological tool for predicting, preventing, and containing a number of vectorborne infectious diseases, such as malaria, dengue, West Nile virus, etc. Methods: A variety of NASA remote sensing data can be used for modeling vectorborne infectious disease transmission. We will discuss both the well known and less known remote sensing data, including Landsat, AVHRR (Advanced Very High Resolution Radiometer), MODIS (Moderate Resolution Imaging Spectroradiometer), TRMM (Tropical Rainfall Measuring Mission), ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer), EO-1 (Earth Observing One) ALI (Advanced Land Imager), and SIESIP (Seasonal to Interannual Earth Science Information Partner) dataset. Giovanni is a Web-based application developed by the NASA Goddard Earth Sciences Data and Information Services Center. It provides a simple and intuitive way to visualize, analyze, and access vast amounts of Earth science remote sensing data. After remote sensing data is obtained, a variety of techniques, including generalized linear models and artificial intelligence oriented methods, t 3 can be used to model the dependency of disease transmission on these parameters. Results: The processes of accessing, visualizing and utilizing precipitation data using Giovanni, and acquiring other data at additional websites are illustrated. Malaria incidence time series for some parts of Thailand and Indonesia are used to demonstrate that malaria incidences are reasonably well modeled with generalized linear models and artificial intelligence based techniques. Conclusions: Remote sensing data relevant to the transmission of vectorborne infectious diseases can be conveniently accessed at NASA and some other websites. These data are useful for vectorborne infectious disease surveillance and modeling.
We evaluate the sensitivity of simulated turbine-height winds to 26 parameters applied in a planetary boundary layer (PBL) scheme and a surface layer scheme of the Weather Research and Forecasting (WRF) model over an area of complex terrain during the Columbia Basin Wind Energy Study. An efficient sampling algorithm and a generalized linear model are used to explore the multiple-dimensional parameter space and quantify the parametric sensitivity of modeled turbine-height winds. The results indicate that most of the variability in the ensemble simulations is contributed by parameters related to the dissipation of the turbulence kinetic energy (TKE), Prandtl number, turbulence length scales, surface roughness, and the von Kármán constant. The relative contributions of individual parameters are found to be dependent on both the terrain slope and atmospheric stability. The parameter associated with the TKE dissipation rate is found to be the most important one, and a larger dissipation rate can produce larger hub-height winds. A larger Prandtl number results in weaker nighttime winds. Increasing surface roughness reduces the frequencies of both extremely weak and strong winds, implying a reduction in the variability of the wind speed. All of the above parameters can significantly affect the vertical profiles of wind speed, the altitude of the low-level jet and the magnitude of the wind shear strength. The wind direction is found to be modulated by the same subset of influential parameters. Remainder of abstract is in attachment.
The goal of this paper is to offer a rigorous analysis of the sigmoid shape single toxin dose-response relationship. The toxin efficacy function is introduced and four special points, including maximum toxin efficacy and inflection points, on the dose-response curve are defined. The special points define three phases of the toxin effect on mortality: (1) toxin concentrations smaller than the first inflection point or (2) larger then the second inflection point imply low mortality rate, and (3) concentrations between the first and the second inflection points imply high mortality rate. Probabilistic interpretation and mathematical analysis for each of the four models, Hill, logit, probit, and Weibull is provided. Two general model extensions are introduced: (1) the multi-target hit model that accounts for the existence of several vital receptors affected by the toxin, and (2) model with a nonzero mortality at zero concentration to account for natural mortality. Special attention is given to statistical estimation in the framework of the generalized linear model with the binomial dependent variable as the mortality count in each experiment, contrary to the widespread nonlinear regression treating the mortality rate as continuous variable. The models are illustrated using standard EPA Daphnia acute (48 h) toxicity tests with mortality as a function of NiCl or CuSO{sub 4} toxin. - Highlights: • The paper offers a rigorous study of a sigmoid dose-response relationship. • The concentration with highest mortality rate is rigorously defined. • A table with four special points for five morality curves is presented. • Two new sigmoid dose-response models have been introduced. • The generalized linear model is advocated for estimation of sigmoid dose-response relationship.
Despite the widespread application of statistical downscaling tools, uncertainty remains regarding the role of model formulation in determining model skill for daily maximum and minimum temperature (Tmax and Tmin), and precipitation occurrence and intensity. Impacts of several key aspects of statistical transfer function form on model skill are evaluated using a framework resistant to model overspecification. We focus on: (a) model structure: simple (generalized linear models, GLMs) versus complex (artificial neural networks, ANNs) models. (b) Predictor selection: Fixed number of predictors chosen a priori versus stepwise selection of predictors and inclusion of grid point values versus predictors derived from application of principal components analysis (PCA) to spatial fields. We also examine the influence of domain size on model performance. For precipitation downscaling, we consider the role of the threshold used to characterize a wet day and apply three approaches (Poisson and Gamma distributions in GLM and ANN) to downscale wet-day precipitation amounts. While no downscaling formulation is optimal for all predictands and at 10 locations representing diverse U.S. climates, and due to the exclusion of variance inflation all of the downscaling formulations fail to reproduce the range of observed variability, models with larger suites of prospective predictors generally have higher skill. For temperature downscaling, ANNs generally outperform GLM, with greater improvements for T min than T max . Furthermore, use of PCA-derived predictors does not systematically improve model skill, but does improve skill for temperature extremes. Model skill for precipitation occurrence generally increases as the wet-day threshold increases and models using PCA-derived predictors tend to outperform those based on grid cell predictors. Each model for wet-day precipitation intensity overestimates annual total precipitation and underestimates the proportion derived from extreme precipitation events, but ANN-based models and those with larger predictor suites tend to have the smallest bias.
Sim-SEQ is a model comparison initiative for geologic carbon storage (GCS). In Sim-SEQ, fifteen different modeling teams are developing conceptual models for flow and transport of an injected CO 2 plume at the Sim-SEQ study site (or the S-3 site) located near Cranfield, Mississippi. The objective of the project is to understand the sources of model uncertainty in GCS, and if possible, to quantify these uncertainties through comparison of the different conceptual models and also through comparison with observed data from the S-3 site. In this paper, we compare six different conceptual models of the S-3 site, and present a preliminary uncertainty analysis of these six models using a generalized linear model approach. We show that differences in model conceptualization and interpretation of site characterization data caus a significant range in predictions.
Abstract Summary MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results. Availability and implementation The MWASTools R package is implemented in R (version > =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/. Supplementary information Supplementary data are available at Bioinformatics online.
In this study, we investigated the sensitivity of net radiative fluxes (FNET) at the top of atmosphere (TOA) to 16 selected uncertain parameters mainly related to the cloud microphysics and aerosol schemes in the Community Atmosphere Model version 5 (CAM5). We adopted a quasi-Monte Carlo (QMC) sampling approach to effectively explore the high dimensional parameter space. The output response variables (e.g., FNET) were simulated using CAM5 for each parameter set, and then evaluated using generalized linear model analysis. In response to the perturbations of these 16 parameters, the CAM5-simulated global annual mean FNET ranges from -9.8 to 3.5 W m-2 compared to the CAM5-simulated FNET of 1.9 W m-2 with the default parameter values. Variance-based sensitivity analysis was conducted to show the relative contributions of individual parameter perturbation to the global FNET variance. The results indicate that the changes in the global mean FNET are dominated by those of cloud forcing (CF) within the parameter ranges being investigated. The size threshold parameter related to auto-conversion of cloud ice to snow is confirmed as one of the most influential parameters for FNET in the CAM5 simulation. The strong heterogeneous geographic distribution of FNET variation shows parameters have a clear localized effect over regions where they are acting. However, some parameters also have non-local impacts on FNET variance. Although external factors, such as perturbations of anthropogenic and natural emissions, largely affect FNET variations at the regional scale, their impact is weaker than that of model internal parameters in terms of simulating global mean FNET in this study. The interactions among the 16 selected parameters contribute a relatively small portion of the total FNET variations over most regions of the globe. This study helps us better understand the CAM5 model behavior associated with parameter uncertainties, which will aid the next step of reducing model uncertainty via calibration of uncertain model parameters with the largest sensitivity.