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

    Authors: Clémentine Cottineau
    DOI: 10.1007/s11192-021-04256-8
    Submitted by clementinecottineau      

    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:   10.0/10   |   Number of reviews:   2
    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.

  • Droplet impact onto a spring-supported plate: analysis and simulations

    Authors: Michael J. Negus, Matthew R. Moore, James M. Oliver, Radu Cimpeanu
    DOI: https://doi.org/10.1007/s10665-021-10107-5
    Submitted by MNegus      
      Mean reproducibility score:   8.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    The direct numerical simulations (DNS) for this paper were conducted using Basilisk (http://basilisk.fr/). As Basilisk is a free software program written in C, it can be readily installed on any Linux machine, and it should be straightforward to then run the driver code to re-produce the DNS from this paper. Given this, the numerical solutions presented in this paper are a result of many high-fidelity simulations, which each took approximately 24 CPU hours running between 4 to 8 cores. Hence the difficulty in reproducing the results should mainly be in the amount of computational resources it would take, so HPC resources will be required. The DNS in this paper were used to validate the presented analytical solutions, as well as extend the results to a longer timescale. Reproducing these numerical results will build confidence in these results, ensuring that they are independent of the system architecture they were produced on.

  • 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:   9.5/10   |   Number of reviews:   2
    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
  • Mental Health and Social Contact During the COVID-19 Pandemic: An Ecological Momentary Assessment Study

    Authors: Eiko I. Fried, Faidra Papanikolaou, Sacha Epskamp
    DOI: 10.31234/osf.io/36xkp
    Submitted by hub-admin    
      Mean reproducibility score:   8.0/10   |   Number of reviews:   3
    Why should we attempt to reproduce this paper?

    Currently submitted paper on COVID19 on mental health. Unique clinical data (time series during the pandemic onset) & methods, hopefully fun to work on. Possibly too boring / easy to reproduce given my data & code? Not sure.

    Tags: R
  • Where should new parkrun events be located? Modelling the potential impact of 200 new events on socio-economic inequalities in access and participation

    Authors: Schneider PP, Smith RA, Bullas AM, Bayley T, Haake SS, Brennan A, Goyder E
    Submitted by hub-admin    
      Mean reproducibility score:   7.0/10   |   Number of reviews:   3
    Why should we attempt to reproduce this paper?

    If all went right, the analysis should be fully reproducible without the need to make any adjustments. The paper aims to find optimal locations for new parkruns, but we were not 100% sure how 'optimal' should be defined. We provide a few examples, but the code was meant to be flexible enough to allow potential decision makers to specify their own, alternative objectives. The spatial data set is also quite interesting and fun to play around with. Cave: The full analysis takes a while to run (~30+ min) and might require >= 8gb ram.

  • Modality switch effects emerge early and increase throughout conceptual processing: Evidence from ERPs

    Authors: Bernabeu, P., Willems, R. M., & Louwerse, M. M.
    Submitted by hub-admin    

    Why should we attempt to reproduce this paper?

    Open data and reproducibility was important in this project.

    Tags: R
  • Evaluation of the ‘Irish Rules’: The Potato Late Blight Forecasting Model and Its Operational Use in the Republic of Ireland

    Authors: Cucak, M., Sparks, A., Moral, R.D.A., Kildea, S., Lambkin, K. and Fealy, R.
    Submitted by hub-admin  
    Number of reviews:   2
    Why should we attempt to reproduce this paper?

    It is a rare find of full reproducibility in the field of plant disease epidemiology.

    Tags: R
  • Explicit (but not implicit) environmentalist identity predicts pro-environmental behavior and policy preferences

    Authors: Brick, C., & Lai, C. K.
    DOI: 10.1016/j.jenvp.2018.07.003
    Submitted by hub-admin    
      Mean reproducibility score:   6.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    The results of the individual studies (4) could be interpreted in support for the hypothesis, but the meta-analysis suggested that implicit identification was not a useful predictor overall. This conclusion is an important goalpost for future work.