Computer Sciences Commons^™

R Foundation News, Torsten Hothorn

The R Journal

Membership fees and donations received between 2021-07-06 and 2021-12-22.

Donations

Jordan Aharoni (Canada) b-data GmbH (Switzerland) Mark Cachia (Canada) Shalese Fitzgerald (United States) Knut Helge Jensen (Norway) Roger Koenker (United Kingdom) Merck Research Laboratories, Kenilwort (United States) Statistik Aargau, Aarau (Switzerland)

Mgee2: An R Package For Marginal Analysis Of Longitudinal Ordinal Data With Misclassified Responses And Covariates, Yuliang Xu, Shuo Shuo Liu, Grace Y. Yi

The R Journal

Marginal methods have been widely used for analyzing longitudinal ordinal data due to their simplicity in model assumptions, robustness in inference results, and easiness in the implementation. However, they are often inapplicable in the presence of measurement errors in the variables. Under the setup of longitudinal studies with ordinal responses and covariates subject to misclassification, Chen et al. (2014) developed marginal methods for misclassification adjustments using the second-order estimating equations and proposed a two-stage estimation approach when the validation subsample is available. Parameter estimation is conducted through the Newton-Raphson algorithm, and the asymptotic distribution of the estimators is established. While …

Survidm: An R Package For Inference And Prediction In An Illness-Death Model, Gustavo Soutinho, Marta Sestelo, Luís Meira-Machado

The R Journal

Multi-state models are a useful way of describing a process in which an individual moves through a number of finite states in continuous time. The illness-death model plays a central role in the theory and practice of these models, describing the dynamics of healthy subjects who may move to an intermediate "diseased" state before entering into a terminal absorbing state. In these models, one important goal is the modeling of transition rates which is usually done by studying the relationship between covariates and disease evolution. However, biomedical researchers are also interested in reporting other interpretable results in a simple and …

Lg: An R Package For Local Gaussian Approximations, Håkon Otneim

The R Journal

The package lg for the R programming language provides implementations of recent methodological advances on applications of the local Gaussian correlation. This includes the estimation of the local Gaussian correlation itself, multivariate density estimation, conditional density estimation, various tests for independence and conditional independence, as well as a graphical module for creating dependence maps. This paper describes the lg package, its principles, and its practical use.

Analysis Of Corneal Data In R With The Rpaci Package, Darío Ramos-López, Ana D. Maldonado

The R Journal

In ophthalmology, the early detection of keratoconus is still a crucial problem. Placido disk corneal topographers are essential in clinical practice, and many indices for diagnosing corneal irregularities exist. The main goal of this work is to present the R package rPACI, providing several functions to handle and analyze corneal data. This package implements primary indices of corneal irregularity (based on geometrical properties) and compound indices built from the primary ones, either using a generalized linear model or as a Bayesian classifier using a hybrid Bayesian network and performing approximate inference. rPACI aims to make the analysis of corneal …

News From The Forwards Taskforce, Heather Turner

The R Journal

Forwards is an R Foundation taskforce working to widen the participation of underrepresented groups in the R project and in related activities, such as the useR! conference. This report rounds up activities of the taskforce during the second half of 2022.

Drhotnet: An R Package For Detecting Differential Risk Hotspots On A Linear Network, Álvaro Briz-Redón, Francisco Martínez-Ruiz, Francisco Montes

The R Journal

One of the most common applications of spatial data analysis is detecting zones, at a certain scale, where a point-referenced event under study is especially concentrated. The detection of such zones, which are usually referred to as hotspots, is essential in certain fields such as criminology, epidemiology, or traffic safety. Traditionally, hotspot detection procedures have been developed over areal units of analysis. Although working at this spatial scale can be suitable enough for many research or practical purposes, detecting hotspots at a more accurate level (for instance, at the road segment level) may be more convenient sometimes. Furthermore, it is …

We Need Trustworthy R Packages, William Michael Landau

The R Journal

There is a need for rigorous software engineering in R packages, and there is a need for new research to bridge scientific computing with more traditional computing. Automated tools, interdisciplinary graduate courses, code reviews, and a welcoming developer community will continue to democratize best practices. Democratized software engineering will improve the quality, correctness, and integrity of scientific software, and by extension, the disciplines that rely on it

A Guided Tour Of Bayesian Regression, Andrés Ramírez–Hassan, Mateo Graciano-Londoño

The R Journal

This paper presents a Graphical User Interface (GUI) to carry out a Bayesian regression analysis in a very friendly environment without any programming skills (drag and drop). This paper is designed for teaching and applied purposes at an introductory level. Our GUI is based on an interactive web application using shiny and libraries from R. We carry out some applications to highlight the potential of our GUI for applied researchers and practitioners. In addition, the Help option in the main tap panel has an extended version of this paper, where we present the basic theory underlying all regression models that …

Visual Diagnostics For Constrained Optimisation With Application To Guided Tours, H Sherry Zhang, Dianne Cook, Ursula Laa, Nicolas Langrené, Patricia Menéndez

The R Journal

A guided tour helps to visualise high-dimensional data by showing low-dimensional projections along a projection pursuit optimisation path. Projection pursuit is a generalisation of principal component analysis in the sense that different indexes are used to define the interestingness of the projected data. While much work has been done in developing new indexes in the literature, less has been done on understanding the optimisation. Index functions can be noisy, might have multiple local maxima as well as an optimal maximum, and are constrained to generate orthonormal projection frames, which complicates the optimization. In addition, projection pursuit is primarily used for …

A Unifying Framework For Parallel And Distributed Processing In R Using Futures, Henrik Bengtsson

The R Journal

A future is a programming construct designed for concurrent and asynchronous evaluation of code, making it particularly useful for parallel processing. The future package implements the Future API for programming with futures in R. This minimal API provides sufficient constructs for implementing parallel versions of well-established, high-level map-reduce APIs. The future ecosystem supports exception handling, output and condition relaying, parallel random number generation, and automatic identification of globals lowering the threshold to parallelize code. The Future API bridges parallel frontends with parallel backends, following the philosophy that end-users are the ones who choose the parallel backend while the developer focuses …

Compmodels: A Suite Of Computer Model Test Functions For Bayesian Optimization, Tony Pourmohamad

The R Journal

The CompModels package for R provides a suite of computer model test functions that can be used for computer model prediction/emulation, uncertainty quantification, and calibration. Moreover, the CompModels package is especially well suited for the sequential optimization of computer models. The package is a mix of real-world physics problems, known mathematical functions, and black-box functions that have been converted into computer models with the goal of Bayesian (i.e., sequential) optimization in mind. Likewise, the package contains computer models that represent either the constrained or unconstrained optimization case, each with varying levels of difficulty. In this paper, we illustrate the use …

Generalized Linear Randomized Response Modeling Using Glmmrr, Jean-Paul Fox, Konrad Klotzke, Duco Veen

The R Journal

Randomized response (RR) designs are used to collect response data about sensitive behaviors (e.g., criminal behavior, sexual desires). The modeling of RR data is more complex since it requires a description of the RR process. For the class of generalized linear mixed models (GLMMs), the RR process can be represented by an adjusted link function, which relates the expected RR to the linear predictor for most common RR designs. The package GLMMRR includes modified link functions for four different cumulative distributions (i.e., logistic, cumulative normal, Gumbel, Cauchy) for GLMs and GLMMs, where the package lme4 facilitates ML and REML estimation. …

Passo: An R Package For Assessing Partial Association Between Ordinal Variables, Shaobo Li, Xiaorui Zhu, Yuejie Chen, Dungang Liu

The R Journal

Partial association, the dependency between variables after adjusting for a set of covariates, is an important statistical notion for scientific research. However, if the variables of interest are ordered categorical data, the development of statistical methods and software for assessing their partial association is limited. Following the framework established by Liu et al. (2021), we develop an R package PAsso for assessing Partial Associations between ordinal variables. The package provides various functions that allow users to perform a wide spectrum of assessments, including quantification, visualization, and hypothesis testing. In this paper, we discuss the implementation of PAsso in …

An R Package For Non-Normal Multivariate Distributions: Simulation And Probability Calculations From Multivariate Lomax (Pareto Type Ii) And Other Related Distributions, Zhixin Lun, Ravindra Khattree

The R Journal

Convenient and easy-to-use programs are readily available in R to simulate data from and probability calculations for several common multivariate distributions such as normal and t. However, functions for doing so from other less common multivariate distributions, especially those which are asymmetric, are not as readily available, either in R or otherwise. We introduce the R package NonNorMvtDist to generate random numbers from multivariate Lomax distribution, which constitutes a very flexible family of skewed multivariate distributions. Further, by applying certain useful properties of multivariate Lomax distribution, multivariate cases of generalized Lomax, Mardia’s Pareto of Type I, Logistic, Burr, Cook-Johnson’s uniform, …

Studying Users Interactions And Behavior In Social Media Using Natural Language Processing, Sultan Alshamrani

Electronic Theses and Dissertations, 2020-2023

Social media platforms have been growing at a rapid pace, attracting users' engagement with the online content due to their convenience facilitated by many useful features. Such platforms provide users with interactive options such as likes, dislikes as well as a way of expressing their opinions in the form of text (i.e., comments). As more people engage in different social media platforms, such platforms will increase in both size and importance. This growth in social media data is becoming a vital new area for scholars and researchers to explore this new form of communication. The huge data from social media …

Machine Learning Techniques For Topic Detection And Authorship Attribution In Textual Data, Fereshteh Jafariakinabad

Electronic Theses and Dissertations, 2020-2023

The unprecedented expansion of user-generated content in recent years demands more attempts of information filtering in order to extract high-quality information from the huge amount of available data. In this dissertation, we begin with a focus on topic detection from microblog streams, which is the first step toward monitoring and summarizing social data. Then we shift our focus to the authorship attribution task, which is a sub-area of computational stylometry. It is worth mentioning that determining the style of a document is orthogonal to determining its topic, since the document features which capture the style are mainly independent of its …

Hierarchical Control Of Multi-Agent Reinforcement Learning Team In Real-Time Strategy (Rts) Games, Weigui Jair Zhou, Budhitama Subagdja, Ah-Hwee Tan, Darren Wee Sze Ong

Research Collection School Of Computing and Information Systems

Coordinated control of multi-agent teams is an important task in many real-time strategy (RTS) games. In most prior work, micromanagement is the commonly used strategy whereby individual agents operate independently and make their own combat decisions. On the other extreme, some employ a macromanagement strategy whereby all agents are controlled by a single decision model. In this paper, we propose a hierarchical command and control architecture, consisting of a single high-level and multiple low-level reinforcement learning agents operating in a dynamic environment. This hierarchical model enables the low-level unit agents to make individual decisions while taking commands from the high-level …

Channel Integration Services In Online Healthcare Communities, Anqi Zhao, Qian Tang

Research Collection School Of Computing and Information Systems

In online healthcare communities, channel integration services have become the bridge between online and offline channels, enabling patients to easily migrate across channels. Different from pure online services, online-to-offline (On2Off) and offline-to-online (Off2On) channel integration services involve both channels. This study examines the interrelationships between pure online services and channel integration services. Using a panel dataset composed of data from an online healthcare community, we find that pure online services decrease patients’ demand for On2Off integration services but increase their use of Off2On integration services. Our findings suggest that providing healthcare services online can reduce online patients’ needs to visit …

Ai And The Future Of Work: What We Know Today, Steven M. Miller, Thomas H. Davenport

Research Collection School Of Computing and Information Systems

To contribute to a better understanding of the contemporary realities of AI workplace deployments, the authors recently completed 29 case studies of people doing their everyday work with AI-enabled smart machines. Twenty-three of these examples were from North America, mostly in the US. Six were from Southeast Asia, mostly in Singapore. In this essay, we compare our findings on job and workplace impacts to those reported in the MIT Task Force on the Work of the Future report, as we consider that to be the most comprehensive recent study on this topic.

Solving The Vehicle Routing Problem With Simultaneous Pickup And Delivery And Occasional Drivers By Simulated Annealing, Vincent F. Yu, Grace Aloina, Panca Jodiawan, Aldy Gunawan, Tsung-Chi Huang

Research Collection School Of Computing and Information Systems

This research studies the vehicle routing problem with simultaneous pickup and delivery with an occasional driver (VRPSPDOD). VRPSPDOD is a new variant of the vehicle routing problems with simultaneous pickup and delivery (VRPSPD). Different from VRPSPD, in VRPSPDOD, occasional drivers are employed to work with regular vehicles to service customers’ pickup and delivery requests in order to minimize the total cost. We formulate a mixed integer linear programming model for VRPSPD and propose a heuristic algorithm based on simulated annealing (SA) to solve the problem. The results of comprehensive numerical experiments show that the proposed SA performs well in terms …

Building Action Sets In A Deep Reinforcement Learner, Yongzhao Wang, Arunesh Sinha, Sky C.H. Wang, Michael P. Wellman

Research Collection School Of Computing and Information Systems

In many policy-learning applications, the agent may execute a set of actions at each decision stage. Choosing among an exponential number of alternatives poses a computational challenge, and even representing actions naturally expressed as sets can be a tricky design problem. Building upon prior approaches that employ deep neural networks and iterative construction of action sets, we introduce a reward-shaping approach to apportion reward to each atomic action based on its marginal contribution within an action set, thereby providing useful feedback for learning to build these sets. We demonstrate our method in two environments where action spaces are combinatorial. Experiments …

Video Snapshot: Single Image Motion Expansion Via Invertible Motion Embedding, Qianshu Zhu, Chu Han, Guoqiang Han, Tien-Tsin Wong, Shengfeng He

Research Collection School Of Computing and Information Systems

Unlike images, finding the desired video content in a large pool of videos is not easy due to the time cost of loading and watching. Most video streaming and sharing services provide the video preview function for a better browsing experience. In this paper, we aim to generate a video preview from a single image. To this end, we propose two cascaded networks, the motion embedding network and the motion expansion network. The motion embedding network aims to embed the spatio-temporal information into an embedded image, called video snapshot. On the other end, the motion expansion network is proposed to …

Learning Large Neighborhood Search Policy For Integer Programming, Yaoxin Wu, Wen Song, Zhiguang Cao, Jie Zhang

Research Collection School Of Computing and Information Systems

We propose a deep reinforcement learning (RL) method to learn large neighborhood search (LNS) policy for integer programming (IP). The RL policy is trained as the destroy operator to select a subset of variables at each step, which is reoptimized by an IP solver as the repair operator. However, the combinatorial number of variable subsets prevents direct application of typical RL algorithms. To tackle this challenge, we represent all subsets by factorizing them into binary decisions on each variable. We then design a neural network to learn policies for each variable in parallel, trained by a customized actor-critic algorithm. We …

Intelligent Traffic Management: From Practical Stochastic Path Planning To Reinforcement Learning Based City-Wide Traffic Optimization, Kamilia Ahmadi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research focuses on intelligent traffic management including stochastic path planning and city scale traffic optimization. Stochastic path planning focuses on finding paths when edge weights are not fixed and change depending on the time of day/week. Then we focus on minimizing the running time of the overall procedure at query time utilizing precomputation and approximation. The city graph is partitioned into smaller groups of nodes and represented by its exemplar. In query time, source and destination pairs are connected to their respective exemplars and the path between those exemplars is found. After this, we move toward minimizing the city …

Data-Driven Statin Initiation Evaluation And Optimization For Prediabetes Population, Muhenned A. Abdulsahib

Graduate Theses and Dissertations

This dissertation develops quantitative models to support medical decision making of statininitiation considering the uncertainty in disease progression for prediabetes patients. A mathematical model is built to help medical decision-makers take action of statin initiation under uncertainty in future prediabetes progressions. The association between cholesterol drug use, such as statin, and elevating glucose level attracted considerable amounts of attention in the literature. Statin effects on glucose vary with respect to different levels of glucose. The first chapter of this dissertation introduces the problem and an overview of the tools that will be used to solve it. In the second chapter …

Joint Linear And Nonlinear Computation With Data Encryption For Efficient Privacy-Preserving Deep Learning, Qiao Zhang

Electrical & Computer Engineering Theses & Dissertations

Deep Learning (DL) has shown unrivalled performance in many applications such as image classification, speech recognition, anomalous detection, and business analytics. While end users and enterprises own enormous data, DL talents and computing power are mostly gathered in technology giants having cloud servers. Thus, data owners, i.e., the clients, are motivated to outsource their data, along with computationally-intensive tasks, to the server in order to leverage the server’s abundant computation resources and DL talents for developing cost-effective DL solutions. However, trust is required between the server and the client to finish the computation tasks (e.g., conducting inference for the newly-input …

Reinforcement Learning Policy Gradient Methods For Reservoir Operation Management And Control, Sadegh Sadeghi Tabas

All Theses

Changes in demand, various hydrological inputs, and environmental stressors are among issues that water managers and policymakers face on a regular basis. These concerns have sparked interest in applying different techniques to determine reservoir operation policy and improve reservoir release decisions. As the resolution of the analysis rises, it becomes more difficult to effectively represent a real-world system using traditional approaches for determining the best reservoir operation policy. One of the challenges is the “curse of dimensionality,” which occurs when the discretization of the state and action spaces becomes finer or when more state or action variables are taken into …

Interval Estimates: How To Make Them More Adequate And How To Use Them In Economic Analysis And Decision Making, Laura Adriana Berrout-Ramos

Open Access Theses & Dissertations

In many real-life situations, we need to make decisions in situations when we do not have full information about the consequences of different decisions. In particular, instead of the exact values of the relevant quantities, we only know lower and upper bounds on these values – i.e., we know an interval that contains the actual (unknown) value. These interval estimates often come from experts. This fact naturally leads to the following important questions: How should we make decisions under such interval uncertainty? How to gauge the quality of the resulting decisions? And if this quality is not sufficient – because …

Agent Based Modeling Of The Spread Of Social Unrest Based On Infectious Disease Spread Model, Anup Adhikari

School of Computing: Dissertations, Theses, and Student Research

Social unrest activities are the tools for people to show dissatisfaction, and often people are motivated by similar unrest activities in another region. This causes a spread of unrest activities across space and time. In this thesis, we model the spread of social unrest across time and space. The underlying novel methodology is to model the regions as agents that transition from one state to another based on changes in their environment. The methodology involves (1) creating a region vector for each agent based on socio-demographic, cultural, economic, infrastructural, geographic, and environmental (SCEIGE) factors, (2) formulating neighborhood distance function to …