Programming Languages and Compilers 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

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 …

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 …

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 …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. Bioconductor 3.6 was released on 31 October, 2017. It is compatible with R 3.4.3 and consists of 1473 software packages, 326 experiment data packages, and 911 up-to-date annotation packages. The release announcement includes descriptions of 100 new software packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands