Programming Languages and Compilers Commons^™

Visualizing Morphogenesis With The Processing Programming Language, Avik Patel, Amar Bains, Richard Millet, Tamira Elul

Faculty Publications & Research of the TUC College of Osteopathic Medicine

We used Processing, a visual artists’ programming language developed at MIT Media Lab, to simulate cellular mechanisms of morphogenesis – the generation of form and shape in embryonic tissues. Based on observations of in vivo time-lapse image sequences, we created animations of neural cell motility responsible for elongating the spinal cord, and of optic axon branching dynamics that establish primary visual connectivity. These visual models underscore the significance of the computational decomposition of cellular dynamics underlying morphogenesis.

Stochastic Invariants For Probabilistic Termination, Krishnendu Chatterjee, Petr Novotný, Dorde Zikelic

Research Collection School Of Computing and Information Systems

Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability 1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability, and this problem has not been addressed yet. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider …

Exploratory Analysis Of Discourses Between Students Engaged In A Debugging Task, Ma. Mercedes T. Rodrigo

Department of Information Systems & Computer Science Faculty Publications

This paper determined if and how high-performing and low-performing students differed in the language that they used as they collaborated on a debugging task. 180 students worked in pairs to debug 12 small programs with known errors. Students were segregated into high and low achievement levels based on the number of bugs they found. Chat transcripts from the pairs were analyzed using the Linguistic Inquiry and Word Count (LIWC) software. We found that high- and low-performing students only varied in terms of their use of words that implied discrepancy and sadness.

Designing An Intervention For Novice Programmers Based On Meaningful Gamification: An Expert Evaluation, Jenilyn L. Agapito, Ma. Mercedes T. Rodrigo

Department of Information Systems & Computer Science Faculty Publications

Gamification is defined as the addition of game-like elements and mechanics to non-game contexts to encourage certain desired behaviors. It is becoming a popular classroom intervention used in computer science instruction, including CS1, the first course computer science students take. It is being operationalized to enhance students' learning experience and achievement. However, existing studies have mostly implemented reward-based game elements which have resulted to contrasting behaviors among the students. Meaningful gamification, characterized as the use of game design elements to encourage users build internal motivation to behave in a certain way, is contended to be a more effective approach. The …

Automated Refactoring Of Legacy Java Software To Default Methods, Raffi Khatchadourian, Hidehiko Masuhara

Publications and Research

Java 8 default methods, which allow interfaces to contain (instance) method implementations, are useful for the skeletal implementation software design pattern. However, it is not easy to transform existing software to exploit default methods as it 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 to preserve type-correctness and confirm semantics preservation. In this paper, we present an efficient, fully-automated, type constraint-based refactoring approach that assists developers in taking advantage of enhanced interfaces for their legacy Java software. The approach features an extensive …

Long And Short-Range Air Navigation On Spherical Earth, Nihad E. Daidzic

International Journal of Aviation, Aeronautics, and Aerospace

Global range air navigation implies non-stop flight between any two airports on Earth. Such effort would require airplanes with the operational air range of at least 12,500 NM which is about 40-60% longer than anything existing in commercial air transport today. Air transportation economy requires flying shortest distance, which in the case of spherical Earth are Orthodrome arcs. Rhumb-line navigation has little practical use in long-range flights, but has been presented for historical reasons and for comparison. Database of about 50 major international airports from every corner of the world has been designed and used in testing and route validation. …

The R Journal (December 2016) 8(2): Complete Issue, The R Foundation

The R Journal

Editorial, Michael Lawrence

Contributed Research Articles

multipleNCC: Inverse Probability Weighting of Nested Case-Control Data, Nathalie C. Støer and Sven Ove Samuelsen

QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis, Christopher M. Moore, Christopher R. Stieha, Ben C. Nolting, Maria K. Cameron, and Karen C. Abbott

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy, Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, and Daniele Ramazzotti

diverse: An R Package to Analyze Diversity in Complex Systems, Miguel R. Guevara, Dominik Hartmann, and Marcelo Mendoza

Simulating Correlated Binary and Multinomial Responses under Marginal Model Specification: …

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 …

Normal Tolerance Interval Procedures In The Tolerance Package, Derek S. Young

The R Journal

Statistical tolerance intervals are used for a broad range of applications, such as quality control, engineering design tests, environmental monitoring, and bioequivalence testing. tolerance is the only R package devoted to procedures for tolerance intervals and regions. Perhaps the most commonly-employed functions of the package involve normal tolerance intervals. A number of new procedures for this setting have been included in recent versions of tolerance. In this paper, we discuss and illustrate the functions that implement these normal tolerance interval procedures, one of which is a new, novel type of operating characteristic curve.

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 3.4 was released on 18 October, 2016. It is com patible with R 3.3 and consists of 1296 software packages, 309 experiment data packages, and 933 up-to-date annotation packages. The release announcement includes descriptions of 101 new packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

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 …

Multiplencc: Inverse Probability Weighting Of Nested Case-Control Data, Nathalie C. Støer, Sven Ove Samuelsen

The R Journal

Reuse of controls from nested case-control designs can increase efficiency in many situations, for instance with competing risks or in other multiple endpoints situations. The matching between cases and controls must be broken when controls are to be used for other endpoints. A weighted analysis can then be performed to take care of the biased sampling from the cohort. We present the R package multipleNCC for reuse of controls in nested case-control studies by inverse probability weighting of the partial likelihood. The package handles right-censored, left-truncated and additionally matched data, and varying numbers of sampled controls and the whole analysis …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.3.2 patched

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

CRAN growth

New CRAN task views

New packages in CRAN task views

Micompr: An R Package For Multivariate Independent Comparison Of Observations, Nuno Fachada, João Rodrigues, Vitor V. Lopes, Rui C. Martins, Agostinho C. Rosa

The R Journal

The R package micompr implements a procedure for assessing if two or more multivariate samples are drawn from the same distribution. The procedure uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. This technique is independent of the distributional properties of samples and automatically selects features that best explain their differences. The procedure is appropriate for comparing samples of time series, images, spectrometric measures or similar high-dimension multivariate observations

Nmfgpu4r: Gpu-Accelerated Computation Of The Non-Negative Matrix Factorization (Nmf) Using Cuda Capable Hardware, Sven Koitka, Christoph M. Friedrich

The R Journal

In this work, a novel package called nmfgpu4R is presented, which offers the computation of Non-negative Matrix Factorization (NMF) on Compute Unified Device Architecture (CUDA) platforms within the R environment. Benchmarks show a remarkable speed-up in terms of time per iteration by utilizing the parallelization capabilities of modern graphics cards. Therefore the application of NMFgets more attractive for real-world sized problems because the time to compute a factorization is reduced by an order of magnitude.

Quantreg.Nonpar: An R Package For Performing Nonparametric Series Quantile Regression, Michael Lipsitz, Alexandre Belloni, Victor Chernozhukov, Iván Fernández-Val

The R Journal

The R package quantreg.nonpar implements nonparametric quantile regression methods to estimate and make inference on partially linear quantile models. quantreg.nonpar obtains point estimates of the conditional quantile function and its derivatives based on series approximations to the nonparametric part of the model. It also provides point-wise and uniform confidence intervals over a region of covariate values and/or quantile indices for the same functions using analytical and resampling methods. This paper serves as an introduction to the package and displays basic functionality of the functions contained within.

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, …

An Introduction To Principal Surrogate Evaluation With The Pseval Package, Michael C. Sachs, Erin E. Gabriel

The R Journal

We describe a new package called pseval that implements the core methods for the evaluation of principal surrogates in a single clinical trial. It provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation methods are provided, including print, summary, plot, and testing. We summarize the main statistical methods that are implemented in the package and illustrate its use from the perspective …

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/)