John Rischard Rice is one of the founders of mathematical software as a distinct scholarly community. Trained in mathematics he spent four decades in Purdue University’s Department of Computer Sciences. During the 1970s, he convened a series of seminal conferences on the topic and established ACM Transactions on Mathematical Software, which he edited for many years. Rice led development of the ...

In this paper we take advantage of the concepts developed for centralized module management, such as dynamic loading and unloading of modules, and show how they can be used to support the development and operation of distributed applications. We do so through R-OSGi, a distributed middleware platform that extends the centralized, industrystandard OSGi specification to support distributed module...

We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data. The fslr package performs operations on 'nifti' image objects in R using command-line functions from FSL, and returns R objects back to the user. fslr allows users to develop image processing and analysis...

Survival analysis is widely applied in many fields such as biology, medicine, and public health. A typical analysis of survival data involves the modeling of time-to-event data, such as the time until death. To find Survival probabilities of the given observations censored or not, use Kaplan-Meier methods of estimation. But this method gives survival probabilities at any specific time. So this ...

We describe the Rocker project, which provides a widely-used suite of Docker images with customized R environments for particular tasks. We discuss how this suite is organized, and how these tools can increase portability, scaling, reproducibility, and convenience of R users and developers.

An important component of quality control for statistical graphics software is the ability not only to test that code runs without errors, but also to test that code produces the right result. The simple way to test for the correct result in graphical output is to test whether a test file differs from a control file; this is effective in determining whether a difference exists. However, the tes...

The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii) analytical codes and (iii) dissemination. In this paper, different documentation formats and online repositories are introduced. To integrate and manage the r...

The T-R Trees software system is a set of software tools for the graphical and programmatic manipulation of expressive and structural hierarchies in music composition. It is loosely based on the hierarchies described in Fred Lerdahl and Ray Jackendoof’s landmark book A Generative Theory of Tonal Music—weighted grouping and prolongational reduction trees (also called tension-relaxation or T-R tr...