Posts about reproducible paper (old posts, page 4)

Analysis of Open Data and Computational Reproducibility in Registered Reports in Psychology

Ongoing technological developments have made it easier than ever before for scientists to share their data, materials, and analysis code. Sharing data and analysis code makes it easier for other researchers to re-use or check published research. These benefits will only emerge if researchers can reproduce the analysis reported in published articles, and if data is annotated well enough so that it is clear what all variables mean. Because most researchers have not been trained in computational reproducibility, it is important to evaluate current practices to identify practices that can be improved. We examined data and code sharing, as well as computational reproducibility of the main results without contacting the original authors, for Registered Reports published in the in psychological literature between 2014 and 2018. Of the 62 articles that met our inclusion criteria data was available for 40 articles, and analysis scripts for 43 articles. For the 35 articles that shared both data and code and performed analyses in SPSS, R, or JASP, we could run the scripts for 30 articles, and reproduce the main results for 19 articles. Although the percentage of articles that shared both data and code (61%) and articles that could be computationally reproduced (54%) was relatively high compared to other studies, there is clear room for improvement. We provide practices recommendations based on our observations, and link to examples of good research practices in the papers we reproduced.

Automatic generation of provenance metadataduring execution of scientific workflows

Data processing in data intensive scientific fields likebioinformatics is automated to a great extent. Among others,automation is achieved with workflow engines that execute anexplicitly stated sequence of computations. Scientists can usethese workflows through science gateways or they develop themby their own. In both cases they may have to preprocess their raw data and also may want to further process the workflowoutput. The scientist has to take care about provenance of thewhole data processing pipeline. This is not a trivial task dueto the diverse set of computational tools and environments usedduring the transformation of raw data to the final results. Thuswe created a metadata schema to provide provenance for dataprocessing pipelines and implemented a tool that creates this metadata during the execution of typical scientific computations.

Empirical examination of the replicability of associations between brain structure and psychological variables

Linking interindividual differences in psychological phenotype to variations in brain structure is an old dream for psychology and a crucial question for cognitive neurosciences. Yet, replicability of the previously-reported ‘structural brain behavior’ (SBB)-associations has been questioned, recently. Here, we conducted an empirical investigation, assessing replicability of SBB among heathy adults. For a wide range of psychological measures, the replicability of associations with gray matter volume was assessed. Our results revealed that among healthy individuals 1) finding an association between performance at standard psychological tests and brain morphology is relatively unlikely 2) significant associations, found using an exploratory approach, have overestimated effect sizes and 3) can hardly be replicated in an independent sample. After considering factors such as sample size and comparing our findings with more replicable SBB-associations in a clinical cohort and replicable associations between brain structure and non-psychological phenotype, we discuss the potential causes and consequences of these findings.

Methodological Reporting Behavior, Sample Sizes, and Statistical Power in Studies of Event- Related Potentials: Barriers to Reproducibility and Replicability

Methodological reporting guidelines for studies of event-related potentials (ERPs) were updated in Psychophysiology in 2014. These guidelines facilitate the communication of key methodological parameters (e.g., preprocessing steps). Failing to report key parameters represents a barrier to replication efforts, and difficultly with replicability increases in the presence of small sample sizes and low statistical power. We assessed whether guidelines are followed and estimated the average sample size and power in recent research. Reporting behavior, sample sizes, and statistical designs were coded for 150 randomly-sampled articles from five high-impact journals that frequently publish ERP studies from 2011 to 2017. An average of 63% of guidelines were reported, and reporting behavior was similar across journals, suggesting that gaps in reporting is a shortcoming of the field rather than any specific journal. Publication of the guidelines paper had no impact on reporting behavior, suggesting that editors and peer reviewers are not enforcing these recommendations. The average sample size per group was 21. Statistical power was conservatively estimated as .72-.98 for a large effect size, .35-.73 for a medium effect, and .10-.18 for a small effect. These findings indicate that failing to report key guidelines is ubiquitous and that ERP studies are only powered to detect large effects. Such low power and insufficient following of reporting guidelines represent substantial barriers to replication efforts. The methodological transparency and replicability of studies can be improved by the open sharing of processing code and experimental tasks and by a priori sample size calculations to ensure adequately powered studies.

A Large-scale Study about Quality and Reproducibility of Jupyter Notebooks

Jupyter Notebooks have been widely adopted by many different communities, both in science and industry. They support the creation of literate programming documents that combine code, text, and execution results with visualizations and all sorts of rich media. The self-documenting aspects andthe ability to reproduce results have been touted as significant benefits of notebooks. At the same time, there has been growing criticism that the way notebooks are being used leads to unexpected behavior, encourage poor coding practices, and that their results can be hard to reproduce. To understand good and bad practices used in the development of real notebooks, we studied 1.4 million notebooks from GitHub. We present a detailed analysis of their characteristics that impact reproducibility. We also propose a set of best practices that can improve the rate of reproducibility and discuss open challenges that require further research and development.

Towards minimum reporting standards for life scientists

Transparency in reporting benefits scientific communication on many levels. While specific needs and expectations vary across fields, the effective use of research findings relies on the availability of core information about research materials, data, and analysis. In December 2017, a working group of journal editors and experts in reproducibility convened to create the “minimum standards” working group. This working group aims to devise a set of minimum expectations that journals could ask their authors to meet, and will draw from the collective experience of journals implementing a range of different approaches designed to enhance reporting and reproducibility (e.g. STAR Methods), existing life science checklists (e.g. the Nature Research reporting summary), and the results of recent meta-research studying the efficacy of such interventions (e.g. Macleod et al. 2017; Han et al. 2017).