Exploratory movement analysis and report building with R package stmove

Abstract Background As GPS tags and data loggers have become lighter, cheaper, and longer-lasting, there has been a growing influx of data on animal movement. Simultaneously, methods of analyses and software to apply such methods to movement data have expanded dramatically. Even so, for many interdisciplinary researchers and managers without familiarity with the field of movement ecology and the open-source tools that have been developed, the analysis of movement data has remained an overwhelming challenge. Description Here we present stmove , an R package designed to take individual relocation data and generate a visually rich report containing a set of preliminary results that ecologists and managers can use to guide further exploration of their data. Not only does this package make report building and exploratory data analysis (EDA) simple for users who may not be familiar with the extent of available analytical tools, but it sets forth a framework of best practice analyses, which offers a common starting point for the interpretation of terrestrial movement data. Results Using data from African elephants ( Loxodonta africana ) collected in southern Africa, we demonstrate stmove ’s report building function through the main analyses included: path visualization, primary statistic calculation, summary in space and time, and space-use construction. Conclusions The stmove package provides consistency and increased accessibility to managers and researchers who are interested in movement analysis but who may be unfamiliar with the full scope of movement packages and analytical tools. If widely adopted, the package will promote comparability of results across movement ecology studies

Forecasting electricity demand using univariate time series volatility forecasting models : a case study of Uganda and South Africa.

Master of Science in Statistics. University of KwaZulu-Natal, Pietermaritzburg 2016.Different sectors of economies are significantly affected by the supply of electricity. However, with the available limited resources, supply and demand of electricity in Africa are strongly correlated. In order to efficiently improve electricity supply, its demand has to be accurately predicted. In this research, we analyse electricity demand in two cases; peak monthly electricity demand in Uganda from January 2008 to December 2013, and daily electricity demand for South Africa from 1st January 2004 to 30th June 2008, using ARIMA and ARCH/GARCH models. We use this data to forecast future demand for both countries in order to help policy makers in the electricity sector make decisions for sustainable development of both countries. GARCH models are introduced to correct the volatility found in South Africa's daily demand data. Results from the study show that; for Uganda, a seasonal ARIMA(0,0,0)(1,1,1)[12] model describes the data better, with RMSE of 4.872027 and MAPE of 2.347028, and gives better forecasts which display a continued increase in electricity demand for months ahead. For South African data, a seasonal ARIMA(1,0,1)(0,1,0)[365] describes the data better but a standard GARCH(1,1) with normally distributed error terms accommodates volatility. Therefore, a combination of the two models produces better forecast accuracy

Regional groundwater levels in crystalline aquifers: structural domains, groundwater level monitoring, and factors controlling the response time and variability

This thesis aims to determine the degree to which fracture networks control the response time and fluctuation of groundwater levels in regional crystalline aquifers in comparison to topography, sediment deposits, precipitation and snowmelt. In this respect, the compartmentalization of the crystalline aquifer into structural domains is necessary, in order to take into account the heterogeneity of the crystalline aquifer in relation to the different fracture networks existing in the rock mass. Field investigations were conducted in the Lanaudiere region, Quebec, Canada, where the underlying crystalline rock outcrops in several locations, allowing access to outcrops for fracture sampling. In addition, four unequipped boreholes drilled into the crystalline rock were available for fracture sampling. Typically, fracture sampling involves the collection of multiple fracture samples, which involve numerous fracture clusters. Grouping fracture samples into structural domains is generally useful for geologists, hydrogeologists, and geomechanicians as a region of fractured rocks is subdivided into sub-regions with similar behavior in terms of their hydromechanical properties. One of the commonly used methods to group fracture samples into structural domains is Mahtab and Yegulalp's method, considering the orientation of fracture clusters and ignoring several fracture parameters, such as fracture spacing, aperture, and persistence, that are important for fluid circulation in the rock mass. In this thesis, we proposed a new cluster-based similarity method that considers cluster orientation as well as the aperture, persistence and spacing. In addition, a method for compartmentalizing a given study area into structural domains using Voronoi diagrams has also been proposed. The proposed method is more suitable than the previous method for applications in hydrogeology and rock mechanics, especially for regional studies of fluid flow in the rock mass. The study of response time and variability of groundwater levels requires a groundwater level monitoring network. The inclusion of private boreholes in these monitoring networks can provide a cost-effective means of obtaining a larger data set; however, the use of these boreholes is limited by the fact that frequent pumping, in these boreholes, generates outliers in the recorded time series. In this thesis, a slope criterion is applied to identify and remove outliers from groundwater level time series from exploited private boreholes. Nevertheless, the removal of outliers creates a missing value problem, which biases the subsequent time series analysis. Thus, 14 imputation methods were used to replace missing values. The proposed approach is applied to groundwater level time series from a monitoring network of 20 boreholes in the Lanaudiere region, Quebec, Canada. The slope criterion is shown to be very effective in identifying outliers in exploited private boreholes. Among the characteristics of the missing value pattern, the gap size and gap position in the time series are the most important parameters that affect the performance of the imputation methods. Among the imputation methods tested, linear and Stineman interpolations, and Kalman filtering were the most effective. This thesis demonstrates that privately operated boreholes can be used for groundwater monitoring by removing outliers and imputing missing values. At local and regional scales, groundwater level is controlled by several factors. The most commonly studied factors are climatic, geologic and geomorphologic controls on groundwater level variability and response time, and in many cases only one controlling factor is considered in the analysis. However, many other factors can affect groundwater level variability and response time, such as the sediment deposit properties and fracture network characteristics in crystalline aquifers. In this study, a more inclusive approach is used to consider climatic, geomorphological, and fracture network parameters as potential controlling factors. A total of 18 parameters were analyzed for interrelationships as each controlling factor is described by several parameters. The study analyzed a two-year record of groundwater levels in 20 boreholes, drilled into the crystalline rock of the Canadian Shield in the Lanaudière region, Québec, Canada. Factors associated to geomorpgology and fracture network are related to groundwater level variability and its response time. Of the various parameters analyzed in each control factor, sediment thickness and local slope of the geomorphological factor, as well as average persistence and equivalent hydraulic conductivity of the fracture network factor, are most closely related to groundwater level variability and response time. However, further studies are needed to elucidate the physical processes behind certain interrelationships between fracture network parameters and groundwater level variability parameters. Cette thèse a pour but de déterminer le degré auquel les réseaux de fractures contrôlent le temps de réponse et la fluctuation du niveau des eaux souterraines dans les aquifères cristallins régionaux par rapport à la topographie, aux dépôts de sédiments, aux précipitations et à la fonte des neiges. À cet égard, la compartimentation de l'aquifère cristallin en domaines structuraux est nécessaire, afin de prendre en compte l'hétérogénéité de l'aquifère cristallin par rapport aux différents réseaux de fractures existants dans le massif rocheux. Des investigations de terrain ont été menées dans la région de Lanaudière, Québec, Canada, où la roche cristalline sous-jacente affleure à plusieurs endroits, permettant un accès aux affleurements pour l'échantillonnage des fractures. De plus, quatre forages non équipés, forés dans la roche cristalline, étaient disponibles pour l'échantillonnage des fractures. Habituellement, l'échantillonnage de fractures comprend la collecte de plusieurs échantillons de fractures, qui impliquent de nombreux groupes de fractures. Le regroupement des échantillons de fractures en domaines structuraux est généralement utile pour les géologues, les hydrogéologues et les géomécaniciens dans la mesure où une région de roches fracturées est subdivisée en sous-régions ayant un comportement similaire en termes de propriétés hydromécaniques. L'une des méthodes couramment utilisées pour regrouper les échantillons de fractures en domaines structuraux est celle de Mahtab and Yegulalp, considérant l'orientation des clusters de fractures et ignorant plusieurs paramètres de fractures, tels que l'espacement, l'ouverture et la persistance des fractures, qui sont importants pour la circulation des fluides dans le massif rocheux. Dans cette thèse, nous avons proposé une nouvelle méthode de similarité basée sur les clusters qui considère l'orientation des clusters ainsi que l'ouverture, la persistance et l'espacement des clusters. En outre, une méthode pour la compartimentation d'une zone d'étude donnée en domaines structuraux au moyen de diagrammes de Voronoï a également été proposée. La méthode proposée est plus adaptée que la méthode précédente pour des applications en hydrogéologie et en mécanique des roches, notamment pour les études régionales de la circulation des fluides dans la masse rocheuse. L'étude du temps de réponse et de la variabilité du niveau des eaux souterraines nécessite un réseau de surveillance du niveau des eaux souterraines. L'inclusion de forages privés dans ces réseaux de surveillance peut fournir un moyen peu coûteux d'obtenir un ensemble plus large de données ; cependant, l'utilisation de ces forages est limitée par le fait que le pompage fréquent de ces forages génère des valeurs aberrantes dans les séries temporelles enregistrées. Dans cette thèse, un critère de pente est appliqué pour identifier et éliminer les valeurs aberrantes des séries temporelles du niveau des eaux souterraines provenant de forages privés exploités. Néanmoins, l'élimination des valeurs aberrantes crée un problème de valeurs manquantes, ce qui biaise l'analyse ultérieure des séries temporelles. Ainsi, 14 méthodes d'imputation ont été utilisées pour remplacer les valeurs manquantes. L'approche proposée est appliquée aux séries temporelles du niveau des eaux souterraines provenant d'un réseau de surveillance de 20 forages dans la région de Lanaudière, Québec, Canada. Le critère de pente s'avère très efficace pour identifier les valeurs aberrantes dans les forages privés exploités. Parmi les caractéristiques du modèle de valeurs manquantes, la taille et la position des lacunes dans la série temporelle sont les paramètres les plus importants qui affectent les performances des méthodes d'imputation. Parmi les méthodes d'imputation testées, les interpolations linéaires et de Stineman, ainsi que le filtrage de Kalman ont été les plus efficaces. La présente thèse démontre que les forages privés exploités peuvent être utilisés pour la surveillance des eaux souterraines en éliminant les valeurs aberrantes et en imputant les valeurs manquantes. À l'échelle locale et régionale, le niveau des eaux souterraines est contrôlé par plusieurs facteurs. Les facteurs les plus couramment étudiés sont les contrôles climatiques, géologiques et géomorphologiques sur la variabilité du niveau des eaux souterraines et le temps de réponse, et dans de nombreux cas, un seul facteur de contrôle est pris en compte dans l'analyse. Cependant, de nombreux autres facteurs peuvent affecter la variabilité du niveau des eaux souterraines et le temps de réponse, tels que les propriétés des dépôts de sédiments et les caractéristiques du réseau de fractures dans les aquifères cristallins. Dans cette étude, une approche plus globale est utilisée pour considérer les paramètres climatiques, géomorphologiques et du réseau de fractures comme des facteurs de contrôle potentiels. Au total, 18 paramètres ont été analysés pour déterminer les interrelations, sachant que chaque facteur de contrôle est décrit par plusieurs paramètres. L'étude a analysé un jeu de données de deux ans sur les niveaux d'eau souterraine dans 20 forages réalisés dans la roche cristalline du Bouclier canadien dans la région de Lanaudière, au Québec, Canada Les facteurs liés à la géomorphologie et au réseau de fractures sont liés à la variabilité du niveau des eaux souterraines et à son temps de réponse. Parmi les divers paramètres analysés dans chaque facteur de contrôle, l'épaisseur des sédiments et la pente locale du facteur géomorphologique, ainsi que la persistance moyenne et la conductivité hydraulique équivalente du facteur réseau de fractures, sont les plus étroitement liés à la variabilité du niveau des eaux souterraines et à son temps de réponse. Toutefois, des études complémentaires sont nécessaires pour élucider les processus physiques à l'origine de certaines interrelations entre les paramètres du réseau de fractures et les paramètres de variabilité du niveau des eaux souterraines

Evaluation of the ’Irish Rules’: The Potato Late Blight Forecasting Model and Its Operational Use in the Republic of Ireland

peer-reviewedPotato late blight caused by Phytophthora infestans is one of the most important plant diseases known, requiring high pesticide inputs to prevent disease occurrence. The disease development is highly dependent on weather conditions, and as such, several forecasting schemes have been developed worldwide which seek to reduce the inputs required to control the disease. The Irish Rules, developed in the 1950s and calibrated to accommodate the meteorological network, the characteristics of potato production and the P. infestans population at the time, is still operationally utilized by the national meteorological agency, Met Éireann. However, numerous changes in the composition and dynamics of the pathosystem and the risks of production/economic consequences associated with potato late blight outbreaks have occurred since the inception of the Irish Rules model. Additionally, model and decision thresholds appear to have been selected ad hoc and without a clear criteria. We developed a systematic methodology to evaluate the model using the empirical receiver operating curve (ROC) analysis and the response surface methodology for the interpretation of the results. The methodology, written in the R language, is provided as an open, accessible and reproducible platform to facilitate the ongoing seasonal re-evaluation of the Irish Rules and corresponding decision thresholds. Following this initial analysis, based on the available data, we recommend the reduction of the thresholds for relative humidity and an initial period duration from 90% and 12 h to 88% and 10 h, respectively. Contrary to recent reports, we found that the risk of blight epidemics remains low at temperatures below 12 °C. With the availability of more comprehensive outbreak data and with greater insight into the founder population to confirm our findings as robust, the temperature threshold in the model could potentially be increased from 10 °C to 12 °C, providing more opportunities for reductions of pesticide usage. We propose a dynamic operational decision threshold between four and 11 effective blight hours (EBH) set according to frequency of the disease outbreaks in the region of interest. Although the risk estimation according to the new model calibrations is higher, estimated chemical inputs, on average, are lower than the usual grower’s practice. Importantly, the research outlined here provides a robust and reproducible methodological approach to evaluate a semi-empirical plant disease forecasting model

Text as signal. A tutorial with case studies focusing on social media (Twitter)

Sentiment analysis is the automated coding of emotions expressed in text. Sentiment analysis and other types of analyses focusing on the automatic coding of textual documents are increasingly popular in psychology and computer science. However, the potential of treating automatically coded text collected with regular sampling intervals as a signal is currently overlooked. We use the phrase "text as signal" to refer to the application of signal processing techniques to coded textual documents sampled with regularity. In order to illustrate the potential of treating text as signal, we introduce the reader to a variety of such techniques in a tutorial with two case studies in the realm of social media analysis. First, we apply finite response impulse filtering to emotion-coded tweets posted during the US Election Week of 2020 and discuss the visualization of the resulting variation in the filtered signal. We use changepoint detection to highlight the important changes in the emotional signals. Then we examine data interpolation, analysis of periodicity via the fast Fourier transform (FFT), and FFT filtering to personal value-coded tweets from November 2019 to October 2020 and link the variation in the filtered signal to some of the epoch-defining events occurring during this period. Finally, we use block bootstrapping to estimate the variability/uncertainty in the resulting filtered signals. After working through the tutorial, the readers will understand the basics of signal processing to analyze regularly sampled coded text

Within-day variability of pain in youth with juvenile idiopathic arthritis and non-arthritic pain conditions

Purpose: Describe and explain patterns of within-day variability of pain intensity in youth with JIA and non-arthritic pain conditions and within-day relationships between physical activity, mood and pain intensity. Methods: Two complementary studies were conducted. In Study 1 pain intensity data previously collected 3 times per day for 7 days from 112 youth age 8 to 18 years with juvenile idiopathic arthritis (JIA) were examined for within-day patterns using cosinor analysis and generalized estimating equations (GEE). In Study 2, an electronic diary application for the iPod Touch was developed to collect momentary pain and mood data 7 times per day for 4 days from 28 youth age 8 to 17 years with JIA (n=11) or non-arthritic pain conditions (n=17). Physical activity data were collected by accelerometry. GEE analysis was used to examine relationships between pain intensity, physical activity and mood. Results: A cosine pattern of systematic variability in pain intensity was identified in 22.4% of youth in Study 1 (n=85) and 25% in Study 2 (n=28). Age (Study 1: β=0.28, p=0.039), and diagnosis of systemic onset JIA (Study 1: β=2.46, p=0.022) were significant predictors of a cosine pattern of systematic variability. Within-day patterns of pain other than a cosine pattern are identifiable, as time of day (TOD) was a significant predictor of pain on GEE. The relationship between TOD and pain intensity differed by sex and disease subtype (Study 1). On average males had a higher probability of having moderate or severe pain in the morning compared to other times of day. On average females exhibited a U shaped within-day pain pattern with a higher probability of moderate to severe pain in the morning and evening and lower probability in the afternoon. Youth with enthesitis, psoriatic or undifferentiated subtypes of JIA had higher probability of moderate to severe pain in the evening; whereas for all other subtypes this probability was highest in the morning. Pain intensity was related to physical activity level; however, this relationship varied by time of day (Study 2 - combined JIA and non-JIA data). Youth had a higher probability of moderate to severe pain if they were sedentary in the morning, or more physically active in the evening. Higher pain intensity was significantly related to negative mood (β=1.16; p=0.004 [Study 2]) and higher numbers of body locations in pain (β=0.75, p<0.001 [Study 2]). Conclusions: Pain intensity varies by time of day for youth with JIA. This research identifies several within-day patterns that differ by sex and JIA subgroup. Physical activity and mood were associated with within-day fluctuations in pain intensity for youth with JIA and non-arthritic pain conditions. This research provides a foundation for future studies on the clinical relevance of pain variability for predicting treatment response and disease course as well as the development of physical activity interventions for youth with JIA and non-arthritic pain conditions. The Vulnerability Perturbation model of pain is presented for future research on temporal dynamics of pain

Quality assurance of rectal cancer diagnosis and treatment - phase 3 : statistical methods to benchmark centres on a set of quality indicators

In 2004, the Belgian Section for Colorectal Surgery, a section of the Royal Belgian Society for Surgery, decided to start PROCARE (PROject on CAncer of the REctum), a multidisciplinary, profession-driven and decentralized project with as main objectives the reduction of diagnostic and therapeutic variability and improvement of outcome in patients with rectal cancer. All medical specialties involved in the care of rectal cancer established a multidisciplinary steering group in 2005. They agreed to approach the stated goal by means of treatment standardization through guidelines, implementation of these guidelines and quality assurance through registration and feedback. In 2007, the PROCARE guidelines were updated (Procare Phase I, KCE report 69). In 2008, a set of 40 process and outcome quality of care indicators (QCI) was developed and organized into 8 domains of care: general, diagnosis/staging, neoadjuvant treatment, surgery, adjuvant treatment, palliative treatment, follow-up and histopathologic examination. These QCIs were tested on the prospective PROCARE database and on an administrative (claims) database (Procare Phase II, KCE report 81). Afterwards, 4 QCIs were added by the PROCARE group. Centres have been receiving feedback from the PROCARE registry on these QCIs with a description of the distribution of the unadjusted centre-averaged observed measures and the centre’s position therein. To optimize this feedback, centres should ideally be informed of their risk-adjusted outcomes and be given some benchmarks. The PROCARE Phase III study is devoted to developing a methodology to achieve this feedback

Evaluation of an MRI-based screening pathway for prostate cancer

In recent years there has been a wealth of debate regarding prostate cancer screening, with a concurrent increase in new imaging techniques for prostate cancer diagnosis. Imaging has been the technique of choice in lung and breast cancer screening programmes but has not been explored for prostate cancer screening. Herein, this thesis explores the role of magnetic resonance imaging (MRI) as a new approach to screen for prostate cancer. Following an introduction to the current screening landscape, my thesis focuses on the development and validation of a fast MRI, known as a prostagram, that could serve as a viable image-based screening test. Evaluation of this new technique is performed within a prospective, population-based, blinded, cohort study which was conducted at seven primary care practices and two imaging centres. A diverse array of performance characteristics of fast MRI are compared to PSA. These encompass biopsy rates, cancer detection rates, diagnostic accuracy and patient reported experience measures. The second half of this thesis focuses on further optimising the fast MRI protocol for screening and exploring methods of integrating it into an alternative screening pathway. The outcomes point towards a pathway which combines a low threshold PSA and a fast MRI as yielding a more acceptable balance between benefits and harms. This is followed by the development of a risk tool to address the challenges of equivocal MRI lesions. Overall my thesis provides a balanced evaluation of fast MRI as a new screening test and the final chapter highlights outstanding challenges that must be addressed for fast MRI to progress as a legitimate screening modality. There is a requirement for all new screening tests to be evaluated in robust randomised controlled trials and the thesis concludes by setting out a phased research framework for fast MRI to enable a full evaluation over the next decade.Open Acces

Assessment and Redesign of the Synoptic Water Quality Monitoring Network in the Great Smoky Mountains National Park

The purpose of this study was to assess and redesign an existing 83-site synoptic water quality monitoring network in the Great Smoky Mountains National Park. The study involved a spatial analysis of water quality data (pH, ANC, conductivity, chloride, nitrate, sulfate, sodium, and potassium), watershed characteristics (geology, morphology, and vegetation), and collocated site information to determine which sites were redundant and a temporal analysis to determine the effectiveness of the current sampling frequency to detect long-term trends. The spatial analysis employed a simulated annealing algorithm using the variable costs of the network and the results of multivariate data techniques to identify an optimized subset of the existing sampling sites based on a maximization of benefits. A second simulated annealing algorithm was created to identify optimum user-defined monitoring networks of n sites and to validate the results of the first simulated annealing program. The first simulated annealing program identified an optimized network consisting of 67 of the existing 83 sampling sites. The second simulated annealing algorithm bracketed the same 67 sites and also provided a basis for an ordered discontinuation of sampling sites by identifying the best ten-site monitoring network through the best 70-site monitoring network. The temporal analysis employed the “effective” sample method, Sen\u27s slope estimator, Mann-Kendall test for trend, and a boxplot analysis to determine the effectiveness and the power of the current sampling frequency to detect long-term trends. The results showed that the current sampling frequency of four samples per year presents a low statistical power for short historical records. However, increasing the v sampling frequency to more than 12 samples per year creates serial dependence between samples. By combining the results of the spatial and temporal analyses a new network is proposed by dividing the network into primary, secondary, and tertiary sites with sampling frequencies of six and 12 samples per year. Seventeen new sites are also proposed to collect additional data above 3000 feet MSL because the existing number of sampling sites is not proportional to park area in certain elevation ranges

The Epidemiology of Community-Acquired Clostridium Difficile in the Niagara Region, Ontario, Canada, Between September 2011 and December 2013

Clostridium difficile infections (CDIs) have historically been associated with exposure to healthcare settings. In recent years, however, the incidence of community-acquired Clostridium difficile infections (CA-CDI), along with the number of patients requiring hospitalization for it, has been increasing. This research uses a framework grounded in Complex Adaptive Systems (CAS) to reveal new and different epidemiological findings on CA-CDI to indicate novel health equity leverage points. It explores the epidemiology and established risk factors associated with CA-CDI in the Niagara Region, Ontario, and compares them with those of healthcare-associated CDI (HA-CDI) in the same area. The first manuscript evaluates the literature on existing evidence of risk factors for CA-CDI by applying The Joanna Briggs Institute (JBI) Reviewers Manual 2015, Methodology for JBI Scoping Reviews. The review identifies that CA-CDI is seen more often than HA-CDI in younger and female populations. Exposure to antimicrobials is common but not as common as in HA-CDI cases. The scoping review establishes the need for further epidemiological studies on CA-CDI. The second manuscript provides a nonparametric descriptive analysis, comparing CA-CDI and HA-CDI cases in Niagara Health System (NHS) hospitals, based on a retrospective case series design. Hospitalized CA-CDI patients have a lower median age and less exposure to antimicrobials and other medications. Gender proportions are similarly distributed between the two groups. The emerging recommendation is that CA-CDI must be considered as a potential diagnosis in patients admitted to hospital with diarrhea, even in the absence of conventional CDI risk factors. The third and final manuscript evaluates the spatial and genotype features of CA-CDI and HA-CDI. It finds that geographical clustering, temporal patterns, and genotypic features are unique in each category. These studies point to the need for a better understanding of transmission routes between communities and healthcare settings; further research is required to establish community CA-CDI risk factors. Together, these evaluations establish that we must develop a systems approach to explore health problems and respond effectively at a population level. The research and policy environment must be strengthened by modifying current practices, setting priorities, and providing funding for empirical studies and equitable health policies