Computer Sciences Commons^™

Rqgis: Integrating R With Qgis For Statistical Geocomputing, Jannes Muenchow, Patrick Schratz, Alexander Brenning

The R Journal

Integrating R with Geographic Information Systems (GIS) extends R’s statistical capabilities with numerous geoprocessing and data handling tools available in a GIS. QGIS is one of the most popular open-source GIS, and it furthermore integrates other GIS programs such as the System for Automated Geoscientific Analyses (SAGA) GIS and the Geographic Resources Analysis Support System (GRASS) GIS within a single software environment. This and its QGIS Python API makes it a perfect candidate for console-based geoprocessing. By establishing an interface, the R package RQGIS makes it possible to use QGIS as a geoprocessing workhorse from within R. Compared to other …

A Tidy Data Model For Natural Language Processing Using Cleannlp, Taylor Arnold

The R Journal

Recent advances in natural language processing have produced libraries that extract low level features from a collection of raw texts. These features, known as annotations, are usually stored internally in hierarchical, tree-based data structures. This paper proposes a data model to represent annotations as a collection of normalized relational data tables optimized for exploratory data analysis and predictive modeling. The R package cleanNLP, which calls one of two state of the art NLP libraries (CoreNLP or spaCy), is presented as an implementation of this data model. It takes raw text as an input and returns a list of normalized …

R Foundation News, Torsten Hothorn

The R Journal

Donations and members

Donations

Supporting benefactors

Supporting members

Splitting It Up: The Spduration Split-Population Duration Regression Package For Time-Varying Covariates, Andreas Beger, Daniel W. Hill Jr, Nils W. Metternich, Shahryar Minhas, Michael D. Ward

The R Journal

We present an implementation of split-population duration regression in the spduration (Beger et al., 2017) package for R that allows for time-varying covariates. The statistical model accounts for units that are immune to a certain outcome and are not part of the duration process the researcher is primarily interested in. We provide insights for when immune units exist, that can significantly increase the predictive performance compared to standard duration models. The package includes estimation and several post-estimation methods for split-population Weibull and log-logistic models. Weprovide an empirical application to data on military coups.

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.4.3

Afmtoolkit: An R Package For Automated Afm Force-Distance Curves Analysis, Rafael Benítez, Vicente J. Bolós, José-Luis Toca-Herrera

The R Journal

Atomic force microscopy (AFM) is widely used to measure molecular and colloidal inter actions as well as mechanical properties of biomaterials. In this paper the afmToolkit R package is introduced. This package allows the user to automatically batch process AFM force-distance and force-time curves. afmToolkit capabilities range from importing ASCII files and preprocessing the curves (contact point detection, baseline correction...) for finding relevant physical information, such as Young’s modulus, adhesion energies and exponential decay for force relaxation and creep experiments. This package also contains plotting, summary and feature extraction functions. The package also comes with several data sets so the …

Learest: Length And Area Estimation From Data Measured With Additive Error, Mirta Benšić, Petar Taler, Safet Hamedović, Emmanuel Karlo Nyarko, Kristian Sabo

The R Journal

This paper describes an R package LeArEst that can be used for estimating object dimensions from a noisy image. The package is based on a simple parametric model for data that are drawn from uniform distribution contaminated by an additive error. Our package is able to estimate the length of the object of interest on a given straight line that intersects it, as well as to estimate the object area when it is elliptically shaped. The input data may be a numerical vector or an image in JPEG format. In this paper, background statistical models and methods for the package …

Manlymix: An R Package For Manly Mixture Modeling, Xuwen Zhu, Volodymyr Melnykov

The R Journal

Model-based clustering is a popular technique for grouping objects based on a finite mixture model. It has countless applications in different fields of study. The R package ManlyMix implements the Manly mixture model that allows modeling skewness within data groups and performs cluster analysis. ManlyMix is a powerful diagnostics tool that is capable of conducting investigation concerning the normality of variables upon fitting of a Manly forward or backward model. Theoretical foundations as well as description of functions are provided. All features of the package are illustrated with examples in great detail. The analysis of real-life datasets demonstrates the flexibility …

Rpsftm: An R Package For Rank Preserving Structural Failure Time Models, Annabel Allison, Ian R. White, Simon Bond

The R Journal

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999).

The method is randomisation based and uses only the randomised treatment group, …

Simulating Probabilistic Long-Term Effects In Models With Temporal Dependence, Christopher Gandrud, Laron K. Williams

The R Journal

The R package pltesim calculates and depicts probabilistic long-term effects in binary models with temporal dependence variables. The package performs two tasks. First, it calculates the change in the probability of the event occurring given a change in a theoretical variable. Second, it calculates the rolling difference in the future probability of the event for two scenarios: one where the event occurred at a given time and one where the event does not occur. The package is consistent with the recent movement to depict meaningful and easy-to-interpret quantities of interest with the requisite measures of uncertainty. It is the first …

Conference Report: R In Insurance 2017, Nicolas Baradel, Christophe Dutang, Caroline Hillairet

The R Journal

The fifth R in Insurance conference took place at Ecole Nationale de la Statistique et de l’Administration Economique (ENSAE, one of the leading French graduate schools in the fields of statistics, economics, finance and actuarial science) Paris on 8 June 2017. This one-day conference focused once more on the wide range of applications of R in insurance, actuarial science and beyond. The conference programme covered topics including reserving, pricing, loss modelling, the use of R in a production environment and also new statistical methods such as big data analysis.

Bayesian Regression Models For Interval-Censored Data In R, Clifford Anderson-Bergman

The R Journal

The package icenReg provides classic survival regression models for interval-censored data. We present an update to the package that extends the parametric models into the Bayesian framework. Core additions include functionality to define the regression model with the standard regression syntax while providing a custom prior function. Several other utility functions are presented that allow for simplified examination of the posterior distribution.

Simulating Noisy, Nonparametric, And Multivariate Discrete Patterns, Ruby Sharma, Sajal Kumar, Hua Zhong, Mingzhou Song

The R Journal

Requiring no analytical forms, nonparametric discrete patterns are flexible in representing complex relationships among random variables. This makes them increasingly useful for data-driven applications. However, there appears to be no software tools for simulating nonparametric discrete patterns, which prevents objective evaluation of statistical methods that discover discrete relationships from data. We present a simulator to generate nonparametric discrete functions as contingency tables. User can request strictly many-to-one functional patterns. The simulator can also produce contingency tables representing dependent non-functional and independent relationships. An option is provided to apply random noise to contingency tables. We demonstrate the utility of the simulator …

Conference Report: User!2017, Tobias Verbeke

The R Journal

After a very successful 2016 edition in Stanford (US), the useR conference invited the R communitytomeetfromJuly4toJuly7inBrussels(Belgium), heart of Europe. The response was extraordinary: 1175 people (of 54 nationalities) travelled the globe to join for a week of intense exchange and discussion. The conference was held in the Wild Gallery which was– for the occasion– the exclusive territory of R aficionados with many co-hosted events including DSC 2017, RIOT 2017 and an R Foundation meeting.

An important theme throughout the conference was to be welcoming and inclusive. In this respect 25 diversity scholarships were awarded and newbies were welcomed at a …

Rentrez: An R Package For The Ncbi Eutils Api, David J. Winter

The R Journal

The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain mil lions of records describing bibliographic, genetic, genomic, and medical data. Here I present rentrez, a package which provides an R interface to 50 NCBI databases. The package is well-documented, contains an extensive suite of unit tests and has an active user base. The programmatic interface to the NCBI provided by rentrez allows researchers to query databases and download or import particular records into R sessions for subsequent analysis. The complete nature of …

Crtgeedr: An R Package For Doubly Robust Generalized Estimating Equations Estimations In Cluster Randomized Trials With Missing Data, Melanie Prague, Rui Wang, Victor De Gruttola

The R Journal

Semi-parametric approaches based on generalized estimating equations (GEE) are widely used to analyze correlated outcomes in longitudinal settings. In this paper, we present a package CRTgeeDR developed for cluster randomized trials with missing data (CRTs). For use of inverse probability weighting to adjust for missing data in cluster randomized trials, we show that other software lead to biased estimation for non-independence working correlation structure. CRTgeeDR solves this problem. We also extend the ability of existing packages to allow augmented Doubly Robust GEEestimation (DR). Simulation studies demonstrate the consistency of estimators implemented in CRTgeeDR compared to packages such as geepack and …

Bayesbd: An R Package For Bayesian Inference On Image Boundaries, Nicholas Syring, Meng Li

The R Journal

Wepresent the BayesBD package providing Bayesian inference for boundaries of noisy images. The BayesBD package implements flexible Gaussian process priors indexed by the circle to recover the boundary in a binary or Gaussian noised image. The boundary recovered by BayesBD has the practical advantages of guaranteed geometric restrictions and convenient joint inferences under certain assumptions, in addition to its desirable theoretical property of achieving (nearly) minimax optimal rate in a way that is adaptive to the unknown smoothness. The core sampling tasks for our model have linear complexity, and are implemented in C++ for computational efficiency using packages Rcpp and …

Adegraphics: An S4 Lattice-Based Package For The Representation Of Multivariate Data, Aurélie Siberchicot, Alice Julien-Laferrière, Anne-Béatrice Dufour, Jean Thioulouse, Stéphane Dray

The R Journal

The ade4 package provides tools for multivariate analyses. Whereas new statistical methods have been added regularly in the package since its first release in 2002, the graphical functions, that are used to display the main outputs of an analysis, have not benefited from such enhancements. In this context, the adegraphics package, available on CRAN since 2015, is a complete reimplementation of the ade4 graphical functionalities but with large improvements. The package uses the S4 object system (each graph is an object) and is based on the graphical framework provided by lattice and grid. We give a brief description of the …

Arulesviz: Interactive Visualization Of Association Rules With R, Michael Hahsler

The R Journal

Association rule mining is a popular data mining method to discover interesting relation ships between variables in large databases. An extensive toolbox is available in the R-extension package arules. However, mining association rules often results in a vast number of found rules, leaving the analyst with the task to go through a large set of rules to identify interesting ones. Sifting manually through extensive sets of rules is time-consuming and strenuous. Visualization and especially interactive visualization has a long history of making large amounts of data better accessible. The R-extension package arulesViz provides most popular visualization techniques for association …

Queueing: A Package For Analysis Of Queueing Networks And Models In R, Pedro Cañadilla Jiménez, Yolanda Román Montoya

The R Journal

queueing is a package that solves and provides the main performance measures for both basic Markovian queueing models and single and multiclass product-form queueing networks. It can be used both in education and for professional purposes. It provides an intuitive, straightforward wayto build queueing models using S3 methods. The package solves Markovian models of the form M/M/c/K/M/FCFS, open and closed single class Jackson networks, open and closed multiclass networks and mixed networks. Markovian models are used when both the customer inter-arrival time and the server processing time are exponentially distributed. Queueing network solvers are useful for modelling situations in which …

Glmmtmb Balances Speed And Flexibility Among Packages For Zero-Inflated Generalized Linear Mixed Modeling, Mollie E. Brooks, Kasper Kristensen, Koen J. Van Benthem, Arni Magnusson, Casper W. Berg, Anders Nielsen, Hans J. Skaug, Martin Mächler, Benjamin M. Bolker

The R Journal

Count data can be analyzed using generalized linear mixed models when observations are correlated in ways that require random effects. However, count data are often zero-inflated, containing more zeros than would be expected from the typical error distributions. We present a new package, glmmTMB, and compare it to other R packages that fit zero-inflated mixed models. The glmmTMB package fits many types of GLMMs and extensions, including models with continuously distributed responses, but here we focus on count responses. glmmTMB is faster than glmmADMB, MCMCglmm, and brms, and more flexible than INLA and mgcv for zero-inflated …

What Do Developers Search For On The Web?, Xin Xia, Lingfeng Bao, David Lo, Pavneet Singh Kochhar, Ahmed E. Hassan, Zhenchang Xing

Research Collection School Of Computing and Information Systems

Developers commonly make use of a web search engine such as Google to locate online resources to improve their productivity. A better understanding of what developers search for could help us understand their behaviors and the problems that they meet during the software development process. Unfortunately, we have a limited understanding of what developers frequently search for and of the search tasks that they often find challenging. To address this gap, we collected search queries from 60 developers, surveyed 235 software engineers from more than 21 countries across five continents. In particular, we asked our survey participants to rate the …

Software Reengineering: Reverse Engineering With Using 4+1 Architectural Views And Forward Engineering With Mvc Architecture, Shane Mueller

ASA Multidisciplinary Research Symposium

As software complexity is increasing exponentially in our modern era, software architecture becomes increasingly important. The separation of concerns through architecture allows each programmer the opportunity to limit their need of understanding to only the portion of code for which they are responsible for, thus saving large amounts of time.

Sudoku App: Model-Driven Development Of Android Apps Using Ocl?, Yoonsik Cheon, Aditi Barua

Departmental Technical Reports (CS)

Model driven development (MDD) shifts the focus of software development from writing code to building models by developing an application as a series of transformations on models including eventual code generation. Can the key ideas of MDD be applied to the development of Android apps, one of the most popular mobile platforms of today? To answer this question, we perform a small case study of developing an Android app for playing Sudoku puzzles. We use the Object Constraint Language (OCL) as the notation for creating precise models and translate OCL constraints to Android Java code. Our findings are mixed in …

The Impact Of Coverage On Bug Density In A Large Industrial Software Project, Thomas Bach, Artur Andrzejak, Ralf Pannemans, David Lo

Research Collection School Of Computing and Information Systems

Measuring quality of test suites is one of the major challenges of software testing. Code coverage identifies tested and untested parts of code and is frequently used to approximate test suite quality. Multiple previous studies have investigated the relationship between coverage ratio and test suite quality, without a clear consent in the results. In this work we study whether covered code contains a smaller number of future bugs than uncovered code (assuming appropriate scaling). If this correlation holds and bug density is lower in covered code, coverage can be regarded as a meaningful metric to estimate the adequacy of testing. …

On Locating Malicious Code In Piggybacked Android Apps, Li Li, Daoyuan Li, Tegawende F. Bissyande, Jacques Klein, Haipeng Cai, David Lo, Yves Le Traon

Research Collection School Of Computing and Information Systems

To devise efficient approaches and tools for detecting malicious packages in the Android ecosystem, researchers are increasingly required to have a deep understanding of malware. There is thus a need to provide a framework for dissecting malware and locating malicious program fragments within app code in order to build a comprehensive dataset of malicious samples. Towards addressing this need, we propose in this work a tool-based approach called HookRanker, which provides ranked lists of potentially malicious packages based on the way malware behaviour code is triggered. With experiments on a ground truth of piggybacked apps, we are able to automatically …

A Semantics Comparison Workbench For A Concurrent, Asynchronous, Distributed Programming Language, Claudio Corrodi, Alexander Heußner, Christopher M. Poskitt

Research Collection School Of Computing and Information Systems

A number of high-level languages and libraries have been proposed that offer novel and simple to use abstractions for concurrent, asynchronous, and distributed programming. The execution models that realise them, however, often change over time---whether to improve performance, or to extend them to new language features---potentially affecting behavioural and safety properties of existing programs. This is exemplified by SCOOP, a message-passing approach to concurrent object-oriented programming that has seen multiple changes proposed and implemented, with demonstrable consequences for an idiomatic usage of its core abstraction. We propose a semantics comparison workbench for SCOOP with fully and semi-automatic tools for analysing …

Defaultification Refactoring: A Tool For Automatically Converting Java Methods To Default, Raffi Khatchadourian, Hidehiko Masuhara

Publications and Research

Enabling interfaces to declare (instance) method implementations, Java 8 default methods can be used as a substitute for the ubiquitous skeletal implementation software design pattern. Performing this transformation on legacy software manually, though, may be non-trivial. The refactoring requires analyzing complex type hierarchies, resolving multiple implementation inheritance issues, reconciling differences between class and interface methods, and analyzing tie-breakers (dispatch precedence) with overriding class methods. All of this is necessary to preserve type-correctness and confirm semantics preservation. We demonstrate an automated refactoring tool called Migrate Skeletal Implementation to Interface for transforming legacy Java code to use the new default construct. The …

Wrangle Your Data Like A Pro With The Data Processing Power Of Python, Geoffrey P. Timms, Jeremy M. Brown

Charleston Library Conference

Management, delivery, and marketing of library resources and collections necessitate interaction with a plethora of data from many sources and in many forms. Accessing and transforming data into meaningful information or different formats used in library automation can be time consuming, but a working knowledge of a programming language can improve efficiency in many facets of librarianship. From processing lists to creating extensible markup language (XML), from editing machine-readable cataloging (MARC) records before upload to automating statistical reports, the Python programming language and third-party application programming interfaces (APIs) can be used to accomplish both behind-the-scenes tasks and end-user facing projects. …

Distributed Evolution Of Spiking Neuron Models On Apache Mahout For Time Series Analysis, Andrew Palumbo

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.