Numerical Analysis and Scientific Computing Commons^™

Eicompare: Comparing Ecological Inference Estimates Across Ei And Ei:Rc, Loren Collingwood, Kassra Oskooii, Sergio Garcia-Rios, Matt Barreto

The R Journal

Social scientists and statisticians often use aggregate data to predict individual-level behavior because the latter are not always available. Various statistical techniques have been developed to make inferences from one level (e.g., precinct) to another level (e.g., individual voter) that minimize errors associated with ecological inference. While ecological inference has been shown to be highly problematic in a wide array of scientific fields, many political scientists and analysis employ the techniques when studying voting patterns. Indeed, federal voting rights lawsuits now require such an analysis, yet expert reports are not consistent in which type of ecological inference is used. This …

Calculating Biological Module Enrichment Or Depletion And Visualizing Data On Large-Scale Molecular Maps With Acsnminer And Rnavicell Packages, Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Zinovyev, Eric Bonnet

The R Journal

Biological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, the Atlas of Cancer Signaling Network (ACSN) being an example. All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe ACSNMineR for calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSNmolecular pathways gene sets, but can use any gene set encoded as a GMT file, …

Escape From Boxland, Barret Schloerke, Hadley Wickham, Dianne Cook, Heike Hofmann

The R Journal

A library of common geometric shapes can be used to train our brains for understanding data structure in high-dimensional Euclidean space. This article describes the methods for producing cubes, spheres, simplexes, and tori in multiple dimensions. It also describes new ways to define and generate high-dimensional tori. The algorithms are described, critical code chunks are given, and a large collection of generated data are provided. These are available in the R package geozoo, and selected movies and images, are available on the GeoZoo web site (http://schloerke.github.io/geozoo/)

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

CRAN growth

New CRAN task views

New packages in CRAN task views

Easyroc: An Interactive Web-Tool For Roc Curve Analysis Using R Language Environment, Dincer Goksuluk, Selcuk Korkmaz, Gokmen Zararsiz, A Ergun Karaagaoglu

The R Journal

ROC curve analysis is a fundamental tool for evaluating the performance of a marker in a number of research areas, e.g., biomedicine, bioinformatics, engineering etc., and is frequently used for discriminating cases from controls. There are a number of analysis tools which are used to guide researchers through their analysis. Some of these tools are commercial and provide basic methods for ROC curve analysis while others offer advanced analysis techniques and a command-based user interface, such as the R environment. The R environment includes comprehensive tools for ROC curve analysis; however, using a command-based interface might be challenging and time …

Hdm: High-Dimensional Metrics, Victor Chernozhukov, Chris Hansen, Martin Spindler

The R Journal

In this article the package High-dimensional Metrics hdm is introduced. It is a collection of statistical methods for estimation and quantification of uncertainty in high-dimensional approximately sparse models. It focuses on providing confidence intervals and significance testing for (possibly many) low-dimensional subcomponents of the high-dimensional parameter vector. Efficient estimators and uniformly valid confidence intervals for regression coefficients on target variables (e.g., treatment or policy variable) in a high-dimensional approximately sparse regression model, for average treatment effect (ATE) and average treatment effect for the treated (ATET), as well for extensions of these param eters to the endogenous setting are provided. Theory …

Distance Measures For Time Series In R: The Tsdist Package, Usue Mori, Alexander Mendiburu, Jose A. Lozano

The R Journal

The definition of a distance measure between time series is crucial for many time series data mining tasks, such as clustering and classification. For this reason, a vast portfolio of time series distance measures has been published in the past few years. In this paper, the TSdist package is presented, a complete tool which provides a unified framework to calculate the largest variety of time series dissimilarity measures available in R at the moment, to the best of our knowledge. The package implements some popular distance measures which were not previously available in R, and moreover, it also provides wrappers …

Condsurv: An R Package For The Estimation Of The Conditional Survival Function For Ordered Multivariate Failure Time Data, Luis Meira-Machado, Meira-Machado Sestelo

The R Journal

One major goal in clinical applications of time-to-event data is the estimation of survival with censored data. The usual nonparametric estimator of the survival function is the time-honored Kaplan-Meier product-limit estimator. Though this estimator has been implemented in several R packages, the development of the condSURV R package has been motivated by recent contributions that allow the estimation of the survival function for ordered multivariate failure time data. The condSURV package provides three different approaches all based on the Kaplan-Meier estimator. In one of these approaches these quantities are estimated conditionally on current or past covariate measures. Illustration of the …

Measurement Units In R, Edzer Pebesma, Thomas Mailund, James Hiebert

The R Journal

We briefly review SI units, and discuss R packages that deal with measurement units, their compatibility and conversion. Built upon udunits2 and the UNIDATA udunits library, we introduce the package units that provides a class for maintaining unit metadata. When used in expression, it automatically converts units, and simplifies units of results when possible; in case of incompatible units, errors are raised. The class flexibly allows expansion beyond predefined units. Using units may eliminate a whole class of potential scientific programming mistakes. We discuss the potential and limitations of computing with explicit units.

Tigris: An R Package To Access And Work With Geographic Data From The Us Census Bureau, Kyle Walker

The R Journal

TIGER/Line shapefiles from the United States Census Bureau are commonly used for the mapping and analysis of US demographic trends. The tigris package provides a uniform interface for R users to download and work with these shapefiles. Functions in tigris allow R users to request Census geographic datasets using familiar geographic identifiers and return those datasets as objects of class "Spatial*DataFrame". In turn, tigris ensures consistent and high-quality spatial data for R users’ cartographic and spatial analysis projects that involve US Census data. This article provides an overview of the functionality of the tigris package, and concludes with an applied …

Mixtox: An R Package For Mixture Toxicity Assessment, Xiang-Wei Zhu, Jian-Yi Chen

The R Journal

Mixture toxicity assessment is indeed necessary for humans and ecosystems that are continually exposed to a variety of chemical mixtures. This paper describes an R package, called mixtox, which offers a general framework of curve fitting, mixture experimental design, and mixture toxicity prediction for practitioners in toxicology. The unique features of mixtox include: (1) constructing a uniform table for mixture experimental design; and (2) predicting toxicity of a mixture with multiple components based on reference models such as concentration addition, independent action, and generalized concentration addition. We describe the various functions of the package and provide examples to illustrate their …

Water: Tools And Functions To Estimate Actual Evapotranspiration Using Land Surface Energy Balance Models In R, Guillermo Federico Olmedo, Samuel Ortega-Farías, Daniel De La Fuente-Sáiz, David Fonseca- Luego, Fernando Fuentes-Peñailillo

The R Journal

The crop water requirement is a key factor in the agricultural process. It is usually estimated throughout actual evapotranspiration (ETa). This parameter is the key to develop irrigation strategies, to improve water use efficiency and to understand hydrological, climatic, and ecosystem processes. Currently, it is calculated with classical methods, which are difficult to extrapolate, or with land surface energy balance models (LSEB), such as METRIC and SEBAL, which are based on remote sensing data. This paper describes water, an open implementation of LSEB. The package provides several functions to estimate the parameters of the LSEB equation from satellite data …

Domain Identification For Intention Posts On Online Social Media, Thai Le Luong, Quoc Tuan Truong, Hai-Trieu Dang, Xuan Hieu Phan

Research Collection School Of Computing and Information Systems

Today, more and more Internet users are willing to share their feeling, activities, and even their intention about what they plan to do on online social media. We can easily see posts like "I plan to buy an apartment this year", or "We are looking for a tour for 3 people to Nha Trang" on online forums or social networks. Recognizing those user intents on online social media is really useful for targeted advertising. However fully understanding user intents is a complicated and challenging process which includes three major stages: user intent filtering, intent domain identification, and intent parsing and …

Lexicon Knowledge Extraction With Sentiment Polarity Computation, Zhaoxia Wang, Vincent Joo Chuan Tong, Pingcheng Ruan, Fang Li

Research Collection School Of Computing and Information Systems

Sentiment analysis is one of the most popular natural language processing techniques. It aims to identify the sentiment polarity (positive, negative, neutral or mixed) within a given text. The proper lexicon knowledge is very important for the lexicon-based sentiment analysis methods since they hinge on using the polarity of the lexical item to determine a text's sentiment polarity. However, it is quite common that some lexical items appear positive in the text of one domain but appear negative in another. In this paper, we propose an innovative knowledge building algorithm to extract sentiment lexicon knowledge through computing their polarity value …

Finding Causality And Responsibility For Probabilistic Reverse Skyline Query Non-Answers, Yunjun Gao, Qing Liu, Gang Cheng, Linlin Zhou, Baihua Zheng

Research Collection School Of Computing and Information Systems

Causality and responsibility is an essential tool in the database community for providing intuitive explanations for answers/non-answers to queries. Causality denotes the causes for the answers/non-answers to queries, and responsibility represents the degree of a cause which reflects its influence on the answers/non-answers to queries. In this paper, we study the causality and responsibility problem (CRP) for the non-answers to probabilistic reverse skyline queries (PRSQ). We first formalize CRP on PRSQ, and then, we propose an efficient algorithm termed as CP to compute the causality and responsibility for the non-answers to PRSQ. CP first finds candidate causes, and then, it …

Shape Analysis Of Traffic Flow Curves Using A Hybrid Computational Analysis, Wasim Irshad Kayani, Shikhar P. Acharya, Ivan G. Guardiola, Donald C. Wunsch, B. Schumacher, Isaac Wagner-Muns

Engineering Management and Systems Engineering Faculty Research & Creative Works

This paper highlights and validates the use of shape analysis using Mathematical Morphology tools as a means to develop meaningful clustering of historical data. Furthermore, through clustering more appropriate grouping can be accomplished that can result in the better parameterization or estimation of models. This results in more effective prediction model development. Hence, in an effort to highlight this within the research herein, a Back-Propagation Neural Network is used to validate the classification achieved through the employment of MM tools. Specifically, the Granulometric Size Distribution (GSD) is used to achieve clustering of daily traffic flow patterns based solely on their …

Passive Rifting Of Thick Lithosphere In The Southern East African Rift: Evidence From Mantle Transition Zone Discontinuity Topography, Cory A. Reed, Kelly H. Liu, Patrick R. N. Chindandali, Belarmino Massingue, Hassan Mdala, Daniel Mutamina, Youqiang Yu, Stephen S. Gao

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

To investigate the mechanisms for the initiation and early-stage evolution of the nonvolcanic southernmost segments of the East African Rift System (EARS), we installed and operated 35 broadband seismic stations across the Malawi and Luangwa rift zones over a 2 year period from mid-2012 to mid-2014. Stacking of over 1900 high-quality receiver functions provides the first regional-scale image of the 410 and 660 km seismic discontinuities bounding the mantle transition zone (MTZ) within the vicinity of the rift zones. When a 1-D standard Earth model is used for time-depth conversion, a normal MTZ thickness of 250 km is found beneath …

Mantle Structure Beneath The Incipient Okavango Rift Zone In Southern Africa, Youqiang Yu, Kelly H. Liu, Zhouchuan Huang, Dapeng Zhao, Cory A. Reed, Moikwathai Moidaki, Jianshe Lei, Stephen S. Gao

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Numerous investigations of the mature segments of the East African rift system (EARS) have significantly improved our understanding of the structure and processes associated with well-developed continental rifts. In contrast, knowledge of rifting processes at their early stage is still significantly limited. Here we present results from a teleseismic P-wave tomography investigation of the incipient Okavango rift zone (ORZ), which is located at the southwestern terminus of the EARS. P-wave relative travel-time residuals recorded by 17 recently deployed portable seismic stations were manually picked and inverted for three-dimensional upper-mantle and mantle transition-zone tomographic images beneath the ORZ and its adjacent …

Aspect-Based Helpfulness Prediction For Online Product Reviews, Yinfei Yang, Cen Chen, Forrest Sheng Bao

Research Collection School Of Computing and Information Systems

Product reviews greatly influence purchase decisions in online shopping. A common burden of online shopping is that consumers have to search for the right answers through massive reviews, especially on popular products. Hence, estimating and predicting the helpfulness of reviews become important tasks to directly improve shopping experience. In this paper, we propose a new approach to helpfulness prediction by leveraging aspect analysis of reviews. Our hypothesis is that a helpful review will cover many aspects of a product at different emphasis levels. The first step to tackle this problem is to extract proper aspects. Because related products share common …

Editorial: Trust Management For Multimedia Big Data, Zheng Yan, Jun Liu, Deng, Robert H., Francisco Herrera

Research Collection School Of Computing and Information Systems

No abstract provided.