E-Rum2020: How We Turned A Physical Conference Into A Successful Virtual Event,
2020
Vanlog
E-Rum2020: How We Turned A Physical Conference Into A Successful Virtual Event, Mariachiara Fortuna, Francesca Vitalini, Mirko Signorelli, Emanuela Furfaro, Federico Marini, Gert Janssenswillen, Riccardo Porreca, Riccardo L. Rossi, Andrea Guzzo, Roberta Sirovich, Andrea Melloncelli, Lorenzo Salvi, Serena Signorelli, Filippo Chiarello
The R Journal
The European R Users Meeting 2020 (e-Rum2020) was a conference that was held virtually in June 2020. Originally, e-Rum2020 had been planned as a physical event to be held in Milano. However, the spread of the COVID-19 pandemic and the declaration of a nationwide lockdown induced the Organizing Committee to fully rethink the event, and to turn it into a live virtual conference. In this article, we describe the challenges that we encountered during the organization of e-Rum2020, and how wereacted to them. In doing so, we aim to provide future conference organizers with useful information on how to organize …
Miwqs: Multiple Imputation Using Weighted Quantile Sum Regression,
2020
Virginia Commonwealth University
Miwqs: Multiple Imputation Using Weighted Quantile Sum Regression, Paul M. Hargarten, David C. Wheeler
The R Journal
The miWQS package in the Comprehensive R Archive Network (CRAN) utilizes weighted quantile sum regression (WQS) in the multiple imputation (MI) framework. The data analyzed is a set/mixture of continuous and correlated components/chemicals that are reasonable to combine in an index and share a common outcome. These components are also interval-censored between zero and upper thresholds, or detection limits, which may differ among the components. This type of data is found in areas such as chemical epidemiological studies, sociology, and genomics. The miWQS package can be run using complete or incomplete data, which may be placed in the first quantile, …
News From The Forwards Taskforce,
2020
University of Warwick
News From The Forwards Taskforce, Heather Turner
The R Journal
Forwards is an R Foundation taskforce working to widen the participation of under represented 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 2020.
Farmtest: An R Package For Factor-Adjusted Robust Multiple Testing,
2020
Princeton University
Farmtest: An R Package For Factor-Adjusted Robust Multiple Testing, Koushiki Bose, Jianqing Fan, Yuan Ke, Xiaoou Pan, Wen-Xin Zhou
The R Journal
We provide a publicly available library FarmTest in the R programming system. This library implements a factor-adjusted robust multiple testing principle proposed by Fan et al. (2019) for large-scale simultaneous inference on mean effects. We use a multi-factor model to explicitly capture the dependence among a large pool of variables. Three types of factors are considered: observable, latent, and a mixture of observable and latent factors. The non-factor case, which corresponds to standard multiple mean testing under weak dependence, is also included. The library implements a series of adaptive Huber methods integrated with fast data-driven tuning schemes to estimate model …
On The Generation, Structure, And Semantics Of Grammar Patterns In Source Code Identifiers,
2020
Kent State University
On The Generation, Structure, And Semantics Of Grammar Patterns In Source Code Identifiers, Christian D. Newman,, Reem S. Alsuhaibani, Michael J. Decker, Anthony Peruma, Dishant Kaushik, Mohamed Wiem Mkaouer, Emily Hill
Articles
Identifier names are the atoms of program comprehension. Weak identifier names decrease developer productivity and degrade the performance of automated approaches that leverage identifier names in source code analysis; threatening many of the advantages which stand to be gained from advances in artificial intelligence and machine learning. Therefore, it is vital to support developers in naming and renaming identifiers. In this paper, we extend our prior work, which studies the primary method through which names evolve: rename refactorings. In our prior work, we contextualize rename changes by examining commit messages and other refactorings. In this extension, we further consider data …
Changes In R 3.6–4.0,
2020
Czech Technical University
Changes In R 3.6–4.0, Tomas Kalibera, Sebastian Meyer, Kurt Hornik
The R Journal
We give a selection of the most important changes in R 4.0.0 and in the R 3.6 release series. Some statistics on source code commits and bug tracking activities are also provided.
Openland: Software For Quantitative Analysis And Visualization Of Land Use And Cover Change,
2020
Federal University of Mato Grosso
Openland: Software For Quantitative Analysis And Visualization Of Land Use And Cover Change, Reginal Exavier, Peter Zeilhofer
The R Journal
There is an increasing availability of spatially explicit, freely available land use and cover (LUC) time series worldwide. Because of the enormous amount of data this represents, the continuous updates and improvements in spatial and temporal resolution and category differentiation, as well as increasingly dynamic and complex changes made, manual data extraction and analysis is highly time consuming, and making software tools available to automatize LUC data assessment is becoming imperative. This paper presents a software developed in R, which combines LUC raster time series data and their transitions, calculates state-of-the-art LUC change indicators, and creates spatio-temporal visualizations, all in …
Analyzing Basket Trials Under Multisource Exchangeability Assumptions,
2020
Yale University
Analyzing Basket Trials Under Multisource Exchangeability Assumptions, Michael J. Kane, Nan Chen, Alexander M. Kaizer, Xun Jiang, H Amy Xia, Brian P. Hobbs
The R Journal
Basket designs are prospective clinical trials that are devised with the hypothesis that the presence of selected molecular features determine a patient’s subsequent response to a particular “targeted” treatment strategy. Basket trials are designed to enroll multiple clinical subpopulations to which it is assumed that the therapy in question offers beneficial efficacy in the presence of the targeted molecular profile. The treatment, however, may not offer acceptable efficacy to all subpopulations enrolled. Moreover, for rare disease settings, such as oncology wherein these trials have become popular, marginal measures of statistical evidence are difficult to interpret for sparsely enrolled subpopulations. Consequently, …
Motbfs: An R Package For Learning Hybrid Bayesian Networks Using Mixtures Of Truncated Basis Functions,
2020
University of Almería
Motbfs: An R Package For Learning Hybrid Bayesian Networks Using Mixtures Of Truncated Basis Functions, Inmaculada Pérez-Bernabé, Ana D. Maldonado, Antonio Salmerón, Thomas D. Nielsen
The R Journal
This paper introduces MoTBFs, an R package for manipulating mixtures of truncated basis functions. This class of functions allows the representation of joint probability distributions involving discrete and continuous variables simultaneously, and includes mixtures of truncated exponentials and mixtures of polynomials as special cases. The package implements functions for learning the parameters of univariate, multivariate, and conditional distributions, and provides support for parameter learning in Bayesian networks with both discrete and continuous variables. Probabilistic inference using forward sampling is also implemented. Part of the functionality of the MoTBFs package relies on the bnlearn package, which includes functions for learning the …
Kuhn-Tucker And Multiple Discrete-Continuous Extreme Value Model Estimation And Simulation In R: The Rmdcev Package,
2020
University of Saskatchewan
Kuhn-Tucker And Multiple Discrete-Continuous Extreme Value Model Estimation And Simulation In R: The Rmdcev Package, Patrick Lloyd-Smith
The R Journal
This paper introduces the package rmdcev in R for estimation and simulation of KuhnTucker demand models with individual heterogeneity. The models supported by rmdcev are the multiple-discrete continuous extreme value (MDCEV) model and Kuhn-Tucker specification common in the environmental economics literature on recreation demand. Latent class and random parameters specifications can be implemented and the models are fit using maximum likelihood estimation or Bayesian estimation. The rmdcev package also implements demand forecasting and welfare calculation for policy simulation. The purpose of this paper is to describe the model estimation and simulation framework and to demonstrate the functionalities of rmdcev using …
Kspm: A Package For Kernel Semi-Parametric Models,
2020
Montreal university
Kspm: A Package For Kernel Semi-Parametric Models, Catherine Schramm, Sébastien Jacquemont, Karim Oualkacha, Aurélie Labbe, Celia M. T. Greenwood
The R Journal
Kernel semi-parametric models and their equivalence with linear mixed models provide analysts with the flexibility of machine learning methods and a foundation for inference and tests of hypothesis. These models are not impacted by the number of predictor variables, since the kernel trick transforms them to a kernel matrix whose size only depends on the number of subjects. Hence, methods based on this model are appealing and numerous, however only a few R programs are available and none includes a complete set of features. Here, we present the KSPM package to fit the kernel semi-parametric model and its extensions in …
Ordinalclust: An R Package To Analyze Ordinal Data,
2020
Université de Lyon
Ordinalclust: An R Package To Analyze Ordinal Data, Margot Selosse, Julien Jacques, Christophe Biernacki
The R Journal
Ordinal data are used in many domains, especially when measurements are collected from people through observations, tests, or questionnaires. ordinalClust is an innovative R package dedicated to ordinal data that provides tools for modeling, clustering, co-clustering and classifying such data. Ordinal data are modeled using the BOS distribution, which is a model with two meaningful parameters referred to as "position" and "precision". The former indicates the mode of the distribution and the latter describes how scattered the data are around the mode: the user is able to easily interpret the distribution of their data when given these two parameters. The …
A Fast And Scalable Implementation Method For Competing Risks Data With The R Package Fastcmprsk,
2020
University of Southern California
A Fast And Scalable Implementation Method For Competing Risks Data With The R Package Fastcmprsk, Eric S. Kawaguchi, Jenny I. Shen, Gang Li, Marc A. Suchard
The R Journal
Advancements in medical informatics tools and high-throughput biological experimentation make large-scale biomedical data routinely accessible to researchers. Competing risks data are typical in biomedical studies where individuals are at risk to more than one cause (type of event) which can preclude the others from happening. The Fine and Gray (1999) proportional subdistribution hazards model is a popular and well-appreciated model for competing risks data and is currently implemented in a number of statistical software packages. However, current implementations are not computationally scalable for large-scale competing risks data. We have developed an R package, fastcmprsk, that uses a novel forward-backward scan …
Fitzroy: An R Package To Encourage Reproducible Sports Analysis,
2020
University of New South Wales
Fitzroy: An R Package To Encourage Reproducible Sports Analysis, Robert Nguyen, James Day, David Warton, Oscar Lane
The R Journal
The importance of reproducibility, and the related issue of open access to data, has received a lot of recent attention. Momentum on these issues is gathering in the sports analytics community. While Australian Rules football (AFL) is the leading commercial sport in Australia, unlike popular international sports, there has been no mechanism for the public to access comprehensive statistics on players and teams. Expert commentary currently relies heavily on data that isn’t made readily accessible and this produces an unnecessary barrier for the development of an inclusive sports analytics community. We present the R package fitzRoy to provide easy access …
Tulip: A Toolbox For Linear Discriminant Analysis With Penalties,
2020
Florida State University
Tulip: A Toolbox For Linear Discriminant Analysis With Penalties, Yuqing Pan, Qing Mai, Xin Zhang
The R Journal
Linear discriminant analysis (LDA) is a powerful tool in building classifiers with easy computation and interpretation. Recent advancements in science technology have led to the popularity of datasets with high dimensions, high orders and complicated structure. Such datasetes motivate the generalization of LDA in various research directions. The R package TULIP integrates several popular high-dimensional LDA-based methods and provides a comprehensive and user-friendly toolbox for linear, semi-parametric and tensor-variate classification. Functions are included for model fitting, cross validation and prediction. In addition, motivated by datasets with diverse sources of predictors, we further include functions for covariate adjustment. Our package is …
Comparing Multiple Survival Functions With Crossing Hazards In R,
2020
Academia Sinica
Comparing Multiple Survival Functions With Crossing Hazards In R, Hsin-Wen Chang, Pei-Yuan Tsai, Jen-Tse Kao, Guo-You Lan
The R Journal
It is frequently of interest in time-to-event analysis to compare multiple survival functions nonparametrically. However, when the hazard functions cross, tests in existing R packages do not perform well. To address the issue, we introduce the package survELtest, which provides tests for comparing multiple survival functions with possibly crossing hazards. Due to its powerful likelihood ratio formulation, this is the only R package to date that works when the hazard functions cross. We illustrate the use of the procedures in survELtest by applying them to data from randomized clinical trials and simulated datasets. We show that these methods lead …
The Biglasso Package: A Memory- And Computation-Efficient Solver For Lasso Model Fitting With Big Data In R,
2020
University of Iowa
The Biglasso Package: A Memory- And Computation-Efficient Solver For Lasso Model Fitting With Big Data In R, Yaohui Zeng, Patrick Breheny
The R Journal
Penalized regression models such as the lasso have been extensively applied to analyzing high-dimensional data sets. However, due to memory limitations, existing R packages like glmnet and ncvreg are not capable of fitting lasso-type models for ultrahigh-dimensional, multi-gigabyte data sets that are increasingly seen in many areas such as genetics, genomics, biomedical imaging, and high-frequency finance. In this research, we implement an R package called biglasso that tackles this challenge. biglasso utilizes memory-mapped files to store the massive data on the disk, only reading data into memory when necessary during model fitting, and is thus able to handle out-of-core computation …
Argumentation Stance Polarity And Intensity Prediction And Its Application For Argumentation Polarization Modeling And Diverse Social Connection Recommendation,
2020
University of Arkansas, Fayetteville
Argumentation Stance Polarity And Intensity Prediction And Its Application For Argumentation Polarization Modeling And Diverse Social Connection Recommendation, Joseph Winstead Sirrianni
Graduate Theses and Dissertations
Cyber argumentation platforms implement theoretical argumentation structures that promote higher quality argumentation and allow for informative analysis of the discussions. Dr. Liu’s research group has designed and implemented a unique platform called the Intelligent Cyber Argumentation System (ICAS). ICAS structures its discussions into a weighted cyber argumentation graph, which describes the relationships between the different users, their posts in a discussion, the discussion topic, and the various subtopics in a discussion. This platform is unique as it encodes online discussions into weighted cyber argumentation graphs based on the user’s stances toward one another’s arguments and ideas. The resulting weighted cyber …
A Bert-Based Dual Embedding Model For Chinese Idiom Prediction,
2020
Singapore Management University
A Bert-Based Dual Embedding Model For Chinese Idiom Prediction, Minghuan Tan, Jing Jiang
Research Collection School Of Computing and Information Systems
Chinese idioms are special fixed phrases usually derived from ancient stories, whose meanings are oftentimes highly idiomatic and non-compositional. The Chinese idiom prediction task is to select the correct idiom from a set of candidate idioms given a context with a blank. We propose a BERT-based dual embedding model to encode the contextual words as well as to learn dual embeddings of the idioms. Specifically, we first match the embedding of each candidate idiom with the hidden representation corresponding to the blank in the context. We then match the embedding of each candidate idiom with the hidden representations of all …
Actor Concurrency Bugs: A Comprehensive Study On Symptoms, Root Causes, Api Usages, And Differences,
2020
Oakland University
Actor Concurrency Bugs: A Comprehensive Study On Symptoms, Root Causes, Api Usages, And Differences, Mehdi Bagherzadeh, Nicholas Fireman, Anas Shawesh, Raffi Khatchadourian
Publications and Research
Actor concurrency is becoming increasingly important in the development of real-world software systems. Although actor concurrency may be less susceptible to some multithreaded concurrency bugs, such as low-level data races and deadlocks, it comes with its own bugs that may be different. However, the fundamental characteristics of actor concurrency bugs, including their symptoms, root causes, API usages, examples, and differences when they come from different sources are still largely unknown. Actor software development can significantly benefit from a comprehensive qualitative and quantitative understanding of these characteristics, which is the focus of this work, to foster better API documentations, development practices, …
