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  • Revisiting the zonally asymmetric extratropical circulation of the Southern Hemisphere spring using complex empirical orthogonal functions

    Authors: Elio Campitelli, Leandro Díaz, Carolina Vera
    DOI: 10.1007/s00382-023-06780-0
    Submitted by eliocamp      
      Mean reproducibility score:   1.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    I used a lot of different tools and strategies to make this paper easily reproducible at different levels. There's Docker container for the highest level of reproducibility, and package versions are managed with renv. The data used in the paper is hosted on Zenodo to avoid long queue times when downloading from the Climate Data Store and future-proof for when it goes away and checksumed before using it.

    Tags: R Docker climate
  • A multi-level analysis of data quality for formal software citation

    Authors: David Schindler, Tazin Hossain, Sascha Spors, Frank Krüger
    DOI: https://doi.org/10.48550/arXiv.2306.17535
    Submitted by frank.krueger    
      Mean reproducibility score:   9.0/10   |   Number of reviews:   2
    Why should we attempt to reproduce this paper?

    We spend a lot of time to make our analyses reproducible. A review would allow us to collect some information on whether we are successful with it.

  • What do analyses of city size distributions have in common?

    Authors: Clémentine Cottineau
    DOI: 10.1007/s11192-021-04256-8
    Submitted by clementinecottineau      
      Mean reproducibility score:   8.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    This article was meant to be entirely reproducible, with the data and code published alongside the article. It is however not embedded within a container (e.g. Docker). Will it past the reproducibility test tomorrow? next year? I'm curious.

  • Living HTA: Automating Health Technology Assessment with R

    Authors: Robert A. Smith, Paul P. Schneider, Wael Mohammed
    DOI: 10.12688/wellcomeopenres.17933.1
    Submitted by rasmith3    

    Why should we attempt to reproduce this paper?

    We think this is an interesting paper for anyone who wants to learn to build an API with the R package plumber. This is a novel method in health economics, but we believe will help improve the transparency of modelling methods in our field.

  • Does ethnic density influence community participation in mass participation physical activity events?

    Authors: Robert A. Smith, Paul P. Schneider, Alice Bullas, Steve Haake, Helen Quirk, Rami Cosulich1, Elizabeth Goyder
    DOI: 10.12688/wellcomeopenres.15657.2
    Submitted by rasmith3    
      Mean reproducibility score:   9.2/10   |   Number of reviews:   5
    Why should we attempt to reproduce this paper?

    The code and data are both on GitHub. The paper has been published in Wellcome Open Research and has been replicated by multiple other authors.

  • Investigating the replicability of preclinical cancer biology

    Authors: Timothy M Errington, Maya Mathur, Courtney K Soderberg, Alexandria Denis, Nicole Perfito, Elizabeth Iorns, Brian A Nosek
    DOI: 10.7554/eLife.71601
    Submitted by samuelpawel      

    Why should we attempt to reproduce this paper?

    This papers represents an important milestone in meta-science, as it is one of the first large-scale replication projects outside the social sciences.

  • Laser-assisted propagation of a relativistic electron bunch in air

    Authors: R M G M Trines, A P L Robinson, J R Wilkinson, J N Kirk, D S Hills, R M Deas, S Morris, T Goffrey, K Bennett, T D Arber
    DOI: 10.1088/1361-6587/ac0b9d
    Submitted by Stuart_Morris      

    Why should we attempt to reproduce this paper?

    Most electron beam physics is considered in the context of a vacuum, but there are applications to long-range electron beam transmission in air. As particle acceleration sources become more compact, we may have the chance to take particle beams out to the real world. The example provided in the paper describes that of x-ray backscatter detectors, where significantly stronger signals could be achieved by scanning objects with electron beams. This paper forms the basis for a potential new mode of particle-beam research, and it is important to ensure the reproducibility of this work for groups who wish to explore the applications of this new technology.

  • Thermodynamics of stacking disorder in ice nuclei

    Authors: David Quigley
    DOI: 10.1063/1.4896376
    Submitted by dquigley      
      Mean reproducibility score:   3.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    The results of this paper have been used in multiple subsequent studies as a benchmark against which other methods of performing the same calculation have been tested. Other groups have challenged the results as suffering from finite size effects, in particular the calculations on mixtures of cubic and hexagonal ice. Should there be time during in the event, participants could check this by performing calculations on larger unit cells. Each individual calculation should converge adequately within 96 hours making it amenable to a HPC ReproHack. Given modern HPC hardware many such calculations could be run concurrently on a single HPC node.

  • Highly efficient conversion of laser energy to hard X-rays in high intensity laser-solid simulations

    Authors: S. Morris, A. Robinson, C. Ridgers
    DOI: 10.1063/5.0055398
    Submitted by Stuart_Morris      

    Why should we attempt to reproduce this paper?

    There are many applications to multi-MeV X-rays. Their penetrative properties make them good for scanning dense objects for industry, and their ionising properties can destroy tumours in radiotherapy. They are also around the energy of nuclear transitions, so they can trigger nuclear reactions to break down nuclear waste into medical isotopes, or to reveal smuggled nuclear-materials for port security. Laser-driven X-ray generation offers a compact and efficient way to create a bright source of X-rays, without having to construct a large synchrotron. To fully utilise this capability, work on optimising the target design and understanding the underlying X-ray mechanisms are essential. The hybrid-PIC code is in a unique position to model the full interaction, so its ease-of-use and reproducibility are crucial for this field to develop.

  • REMoDNaV: robust eye-movement classification for dynamic stimulation

    Authors: Asim H. Dar, Adina S. Wagner, Michael Hanke
    DOI: https://doi.org/10.3758/s13428-020-01428-x
    Submitted by adswa    
      Mean reproducibility score:   7.0/10   |   Number of reviews:   3
    Why should we attempt to reproduce this paper?

    In theory, reproducing this paper should only require a clone of a public Git repository, and the execution of a Makefile (detailed in the README of the paper repository at https://github.com/psychoinformatics-de/paper-remodnav). We've set up our paper to be dynamically generated, retrieving and installing the relevant data and software automatically, and we've even created a tutorial about it, so that others can reuse the same setup for their work. Nevertheless, we've for example never tried it out across different operating systems - who knows whether it works on Windows? We'd love to share the tips and tricks we found to work, and even more love feedback on how to improve this further.

  • Optimizing the Use of Carbonate Standards to Minimize Uncertainties in Clumped Isotope Data

    Authors: Ilja J. Kocken, Inigo A. Müller, Martin Ziegler
    DOI: 10.1029/2019GC008545
    Submitted by japhir      

    Why should we attempt to reproduce this paper?

    Even though the approach in the paper focuses on a specific measurement (clumped isotopes) and how to optimize which and how many standards we use, I hope that the problem is general enough that insight can translate to any kind of measurement that relies on machine calibration. I've committed to writing a literate program (plain text interspersed with code chunks) to explain what is going on and to make the simulations one step at a time. I really hope that this is understandable to future collaborators and scientists in my field, but I have not had any code review internally and I also didn't receive any feedback on it from the reviewers. I would love to see if what in my mind represents "reproducible code" is actually reproducible, and to learn what I can improve for future projects!

  • No Effect of Nature Representations on State Anxiety, Actual and Perceived Noise

    Authors: Korbmacher, M., & Wright, L.
    DOI: 10.31234/osf.io/8gtyq
    Submitted by hub-admin    
      Mean reproducibility score:   5.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    Basic analyses, which are easy to understand and reproduce + the paper contains multiple imputation, which can be interesting; ALL materials are available

    Tags: R
  • Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial

    Authors: Berlanga-Taylor, A. J., Plant, K., Dahl, A., Lau, E., Hill, M., Sims, D., Heger, A., et al.
    Submitted by hub-admin  
    Number of reviews:   1
    Why should we attempt to reproduce this paper?

    It was a null findings paper that disappointed many people. Could I have made a mistake in the coding?; I'm interested in using it as an example of reproducible research and learning from ReproHack. It's nerve wracking to submit for inspection from others so I also want to overcome that fear and be able to lead my students by example. I'll be available via the Slack group or other forms for communication as suggested by organisers. Please note it's only the gene expression and related data that's available on ArrayExpress.

    Tags: Python R
  • Analytic reproducibility in articles receiving open data badges at the journal Psychological Science: An observational study

    Authors: Hardwicke, T. E., Bohn, M., MacDonald, K., Hembacher, E., Nuijten, M. B., Peloquin, B. N., deMayo, B., Long, B., Yoon, E. J., & Frank, M. C.
    DOI: 10.1098/rsos.201494
    Submitted by hub-admin    
      Mean reproducibility score:   9.7/10   |   Number of reviews:   3
    Why should we attempt to reproduce this paper?

    This is perhaps an interesting 'meta' example for ReproHack as in this study we attempted to reproduce analyses reporrted in 25 published articles. So it seems even more important that our own analyses are reproducible! We tried our best to adhere to best practices in this regard, so we would be very keen to know if anyone has problems reproducing our analyses and/or learning how we can make the process easier. A couple of things to note: 1. In addition to the links to the data and analysis scripts provided above, we also have a Code Ocean container for this article (https://doi.org/10.24433/CO.1796004.v3), which should theoretically allow you to reproduce the analyses with the click of a single button (we hope!). 2. In addition to the main research analyses (for which I've provided links above), we also have data, scripts, and Code Ocean containers for each of the reprodubility attempts for the 25 articles we looked at. I don't know if you will also want to look at this level of the analyses, but if you do then take a look at Supplementary Information section E here: https://royalsocietypublishing.org/doi/suppl/10.1098/rsos.201494 For each reproducibility attempt, there is a short 'vignette' describing the outcome, and a link to data/scripts on the OSF and a Code Ocean container.

    Tags: R
  • The role of conidia in the dispersal of Ascochyta rabiei

    Authors: Khaliq, I., Fanning, J., Melloy, P. et al.
    DOI: 10.1007/s10658-020-02126-2
    Submitted by hub-admin    

    Why should we attempt to reproduce this paper?

    I suggested a few papers last year. I’m hoping that we’ve improved our reproducibility with this one, this year. We’ve done our best to package it up both in Docker and as an R package. I’d be curious to know what the best way to reproduce it is found to be. Working through vignettes or spinning up a Docker instance. Which is the preferred method?

    Tags: R Docker
  • Unveiling the diversity of spatial data infrastructures in Latin America: evidence from an exploratory inquiry

    Authors: Luis M. Vilches-Blázquez & Daniela Ballari
    DOI: 10.1080/15230406.2020.1772113
    Submitted by hub-admin    
      Mean reproducibility score:   10.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    It is kind of an easy reproducible code. It reads the data, makes few descriptive statistical analysis and plots figures using ggplot2.

    Tags: R
  • Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos

    Authors: Bellon, M. R., Mastretta-Yanes, A., Ponce-Mendoza, A., Ortiz-Santamaría, D., Oliveros-Galindo, O., Perales, H., … Sarukhán, J.
    DOI: 10.1098/rspb.2018.1049
    Submitted by hub-admin    
      Mean reproducibility score:   6.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    Cleaning the databases used for this study was one of the most challenging aspects of it, so making it public is the best way to make the more out of it. We made an effort to document all analyses and data wrangling steps. We are interested to know if it is truly reproducible so that we can follow this same scheme for further projects, or adjust accordingly.

    Tags: R
  • pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage

    Authors: Bonaretti S, Gold GE, Beaupre GS
    DOI: 10.1371/journal.pone.0226501
    Submitted by hub-admin    
      Mean reproducibility score:   6.5/10   |   Number of reviews:   2
    Why should we attempt to reproduce this paper?

    The paper describes pyKNEEr, a python package for open and reproducible research on femoral knee cartilage using Jupyter notebooks as a user interface. I created this paper with the specific intent to make both the workflows it describes and the paper itself open and reproducible, following guidelines from authorities in the field. Therefore, two things in the paper can be reproduced: 1) workflow results: Table 2 contains links to all the Jupyter notebooks used to calculate the results. Computations are long and might require a server, so if you want to run them locally, I recommend using only 2 or 3 images as inputs for the computations. Also, the paper should be sufficient, but if you need further introductory info, there are a documentation website: https://sbonaretti.github.io/pyKNEEr/ and a "how to" video: https://youtu.be/7WPf5KFtYi8 2) paper graphs: In the captions of figures 1, 4, and 5 you can find links to data repository, code (a Jupyter notebook), and the computational environment (binder) to fully reproduce the graph. These computations can be easily run locally and require a few seconds. All Jupyter notebooks automatically download data from Zenodo and provide dependencies, which should make reproducibility easier.

  • A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma

    Authors: Piqué, D.G., Montagna, C., Greally, J.M. et al.
    Submitted by hub-admin    
      Mean reproducibility score:   4.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    This paper provides a novel approach to identifying oncogenes based on RNA overexpression in subsets of tumor relative to adjacent normal tissue. Showing that this study can be reproduced would aid other researchers who are attempting to identify oncogenes in other cancer types using the same methodology.

    Tags: R
  • Good Me Bad Me: Prioritization of the Good-Self During Perceptual Decision-Making

    Authors: Hu, C.-P., Lan, Y., Macrae, C. N., & Sui, J.
    DOI: 10.1525/collabra.301
    Submitted by hub-admin    
      Mean reproducibility score:   7.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    It'll a great helpful to independently check the scientific record I've published, so that errors, if there are any, could be corrected. Also, I will learn how to share the data in a more accessible to other if you could give me feedback.

    Tags: Python R Matlab

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