The Rockerverse: Packages and Applications for Containerisation with R

Nüst, Daniel; Eddelbuettel, Dirk; Bennett, D. Scott; Cannoodt, Robrecht; Clark, Dav; Daróczi, Gergely; Edmondson, Mark; Fay, Colin; Hughes, Ellis; Kjeldgaard, Lars; Lopp, Sean; Marwick, Ben; Nolis, Heather; Nolis, Jacqueline; Ooi, Hong; Ram, Karthik; Ross, Noam; Shepherd, Lori; Sólymos, Péter; Swetnam, Tyson L.; Turaga, Nitesh; Petegem, Charlotte Van; Williams, Jason; Willis, Craig; Xiao, Nan

doi:10.32614/rj-2020-007

Cited by 8 publications

(8 citation statements)

References 44 publications

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“… Use Docker to document your runtime environment in a machine-readable way, and to ensure others can recreate your computational environment with all the necessary dependencies. For instance, the Rocker Project 36 ( https://www.rocker-project.org ) provides widely used Docker images for R across different applications. Test your code in a clean environment before sharing or publishing it, as it could help you identify dependencies and missing files.…”

Section: Best Practices and Recommendationsmentioning

confidence: 99%

A large-scale study on research code quality and execution

et al. 2022

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This article presents a study on the quality and execution of research code from publicly-available replication datasets at the Harvard Dataverse repository. Research code is typically created by a group of scientists and published together with academic papers to facilitate research transparency and reproducibility. For this study, we define ten questions to address aspects impacting research reproducibility and reuse. First, we retrieve and analyze more than 2000 replication datasets with over 9000 unique R files published from 2010 to 2020. Second, we execute the code in a clean runtime environment to assess its ease of reuse. Common coding errors were identified, and some of them were solved with automatic code cleaning to aid code execution. We find that 74% of R files failed to complete without error in the initial execution, while 56% failed when code cleaning was applied, showing that many errors can be prevented with good coding practices. We also analyze the replication datasets from journals’ collections and discuss the impact of the journal policy strictness on the code re-execution rate. Finally, based on our results, we propose a set of recommendations for code dissemination aimed at researchers, journals, and repositories.

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Section: Best Practices and Recommendationsmentioning

confidence: 99%

A large-scale study on research code quality and execution

et al. 2022

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“…The R package renv (Ushey, 2020) was used to manage R package dependencies, and will install the required the packages and versions used here. We also provide a docker container which captures a compatible computational environment for running the scripts (Nüst, Eddelbuettel, Bennett, Cannoodt, Clark, Daróczi, ... Petegem, 2020). All task outcomes (apart from the Go/No-Go d') were normalized.…”

Section: Discussionmentioning

confidence: 99%

Collecting big data with small screens: Group tests of children’s cognition with touchscreen tablets are reliable and valid

et al. 2020

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Collecting experimental cognitive data with young children usually requires undertaking one-on-one assessments, which can be both expensive and time-consuming. In addition, there is increasing acknowledgement of the importance of collecting larger samples for improving statistical power Button et al. (Nature Reviews Neuroscience 14(5), 365–376, 2013), and reproducing exploratory findings Open Science Collaboration (Science, 349(6251), aac4716–aac4716 2015). One way both of these goals can be achieved more easily, even with a small team of researchers, is to utilize group testing. In this paper, we evaluate the results from a novel tablet application developed for the Resilience in Education and Development (RED) Study. The RED-app includes 12 cognitive tasks designed for groups of children aged 7 to 13 to independently complete during a 1-h school lesson. The quality of the data collected was high despite the lack of one-on-one engagement with participants. Most outcomes from the tablet showed moderate or high reliability, estimated using internal consistency metrics. Tablet-measured cognitive abilities also explained more than 50% of variance in teacher-rated academic achievement. Overall, the results suggest that tablet-based, group cognitive assessments of children are an efficient, reliable, and valid method of collecting the large datasets that modern psychology requires. We have open-sourced the scripts and materials used to make the application, so that they can be adapted and used by others.

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“…Rocker project, which provides a widely-used suite of Docker images with customized R environments for particular tasks [13]. Dockerfile and Docker are the favourite approaches for cooperation between roles in an organization such as developers and IT drivers and between participants in knowledge sharing [14].…”

Section: 2: Containerizationmentioning

confidence: 99%

A Lightweight Portable Multithreaded Client-Server Docker Containers

Alsaffar¹,

Alezzy²

2022

Technium

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In terms of diversity in operating systems, environments, and platforms, and with limited host infrastructure resources to hold all operating systems and platforms, the need arises to design applications that run in many or we can say in all operating systems and platforms. This paper deals with designing and implementing a lightweight multithreaded client-server application appears as a separate Docker container. Both client and server containers are based on alpine Linux and developed using Python programming language. The execution unit in the containers is Python program files. As a case study, the server acts as a Wikipedia server and it can serve many clients simultaneously. The Docker will build the containers depending on a writing Dockerfile for each container and push them to the registry (docker hub). When pulled the image of the containers from the registry account, then it could be run the container on a host. The proposed containerized multithreaded client-server model will become a portable with limited capabilities other than using Virtualization. Resources and cost requirements to achieve portability is evaluated for both virtualization and containerization paradigms. The results showed the superiority of containerization over the virtualization in both resources and cost requirements.

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The Rockerverse: Packages and Applications for Containerisation with R

Cited by 8 publications

References 44 publications

A large-scale study on research code quality and execution

A large-scale study on research code quality and execution

Collecting big data with small screens: Group tests of children’s cognition with touchscreen tablets are reliable and valid

A Lightweight Portable Multithreaded Client-Server Docker Containers

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