Posts about reproducible paper (old posts, page 13)

noWorkflow: a Tool for Collecting, Analyzing, and Managing Provenance from Python Scripts

We present noWorkflow, an open-source tool that systematically and transparently collects provenance from Python scripts, including data about the script execution and how the script evolves over time. During the demo, we will show how noWorkflow collects and manages provenance, as well as how it supports the analysis of computational experiments.We will also encourage attendees to use noWorkflow for their own scripts.

Using ReproZip for Reproducibility and Library Services

Achieving research reproducibility is challenging in many ways: there are social and cultural obstacles as well as a constantly changing technical landscape that makes replicating and reproducing research difficult. Users face challenges in reproducing research across different operating systems, in using different versions of software across long projects and among collaborations, and in using publicly available work. The dependencies required to reproduce the computational environments in which research happens can be exceptionally hard to track – in many cases, these dependencies are hidden or nested too deeply to discover, and thus impossible to install on a new machine, which means adoption remains low. In this paper, we present ReproZip, an open source tool to help overcome the technical difficulties involved in preserving and replicating research, applications, databases, software, and more. We examine the current use cases of ReproZip, ranging from digital humanities to machine learning. We also explore potential library use cases for ReproZip, particularly in digital libraries and archives, liaison librarianship, and other library services. We believe that libraries and archives can leverage ReproZip to deliver more robust reproducibility services, repository services, as well as enhanced discoverability and preservation of research materials, applications, software, and computational environments.

Reproducibility Librarianship

Over the past few years, research reproducibility has been increasingly highlighted as a multifaceted challenge across many disciplines. There are socio-cultural obstacles as well as a constantly changing technical landscape that make replicating and reproducing research extremely difficult. Researchers face challenges in reproducing research across different operating systems and different versions of software, to name just a few of the many technical barriers. The prioritization of citation counts and journal prestige has undermined incentives to make research reproducible. While libraries have been building support around research data management and digital scholarship, reproducibility is an emerging area that has yet to be systematically addressed. To respond to this, New York University (NYU) created the position of Librarian for Research Data Management and Reproducibility (RDM & R), a dual appointment between the Center for Data Science (CDS) and the Division of Libraries. This report will outline the role of the RDM & R librarian, paying close attention to the collaboration between the CDS and Libraries to bring reproducible research practices into the norm.

The Reproducibility Of Research And The Misinterpretation Of P Values

We wish to answer this question: If you observe a "significant" P value after doing a single unbiased experiment, what is the probability that your result is a false positive? The weak evidence provided by P values between 0.01 and 0.05 is explored by exact calculations of false positive rates. When you observe P = 0.05, the odds in favour of there being a real effect (given by the likelihood ratio) are about 3:1. This is far weaker evidence than the odds of 19 to 1 that might, wrongly, be inferred from the P value. And if you want to limit the false positive rate to 5%, you would have to assume that you were 87% sure that there was a real effect before the experiment was done. If you observe P = 0.001 in a well-powered experiment, it gives a likelihood ratio of almost 100:1 odds on there being a real effect. That would usually be regarded as conclusive, But the false positive rate would still be 8% if the prior probability of a real effect was only 0.1. And, in this case, if you wanted to achieve a false positive rate of 5% you would need to observe P = 0.00045. It is recommended that P values should be supplemented by specifying the prior probability that would be needed to produce a specified (e.g. 5%) false positive rate. It may also be helpful to specify the minimum false positive rate associated with the observed P value. And that the terms "significant" and "non-significant" should never be used. Despite decades of warnings, many areas of science still insist on labelling a result of P < 0.05 as "significant". This practice must account for a substantial part of the lack of reproducibility in some areas of science. And this is before you get to the many other well-known problems, like multiple comparisons, lack of randomisation and P-hacking. Science is endangered by statistical misunderstanding, and by university presidents and research funders who impose perverse incentives on scientists.

Reproducibility in Machine Learning-Based Studies: An Example of Text Mining

Reproducibility is an essential requirement for computational studies including those based on machine learning techniques. However, many machine learning studies are either not reproducible or are difficult to reproduce. In this paper, we consider what information about text mining studies is crucial to successful reproduction of such studies. We identify a set of factors that affect reproducibility based on our experience of attempting to reproduce six studies proposing text mining techniques for the automation of the citation screening stage in the systematic review process. Subsequently, the reproducibility of 30 studies was evaluated based on the presence or otherwise of information relating to the factors. While the studies provide useful reports of their results, they lack information on access to the dataset in the form and order as used in the original study (as against raw data), the software environment used, randomization control and the implementation of proposed techniques. In order to increase the chances of being reproduced, researchers should ensure that details about and/or access to information about these factors are provided in their reports.

trackr: A Framework for Enhancing Discoverability and Reproducibility of Data Visualizations and Other Artifacts in R

Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their own. We present the trackr framework for organizing, automatically annotating, discovering, and retrieving results. We identify sources of automatically extractable metadata for computational results, and we define an extensible system for organizing, annotating, and searching for results based on these and other metadata. We present an opensource implementation of these concepts for plots, computational artifacts, and woven dynamic reports generated in the R statistical computing language.