Papers



Submit a Paper!

Browse ReproHack papers

  • 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.

  • Machine learning a model for RNA structure prediction

    Authors: Nicola Calonaci, Alisha Jones, Francesca Cuturello, Michael Sattler, Giovanni Bussi
    DOI: 10.1093/nargab/lqaa090
    Submitted by giovannibussi      

    Why should we attempt to reproduce this paper?

    The method is trained on the data that were available, but it is meant to be re-trainable as soon as new data are published. It would be great to be really sure that even someone else will be able to do it. In case we receive any feedback, we would be really happy to improve our Github repository so as to make the reproduction easier!

  • 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!

  • 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.

  • Open Trade Statistics

    Authors: Pachá (Mauricio Vargas Sepúlveda)
    Submitted by hub-admin    

    Why should we attempt to reproduce this paper?

    The focus of the project is reproducibility. Here we show the differences to access data compared to similar initiatives: https://ropensci.org/blog/2019/05/09/tradestatistics/. Also, similar projects have obscure parts, while our exposes the code from raw data downloading to dashboard creation.

    Tags: R Shiny

Search for papers

Filter by tags

Python R GDAL GEOS GIS Shiny PROJ Galaxies Astronomy HPC Databases Binder Social Science Stata make Computer Science Jupyter Notebook tidyverse emacs literate earth sciences clumped isotopes org-mode geology eyetracking LaTeX Git ArcGIS Docker Drake SVN knitr C Matlab Mathematica Meta-analysis swig miniconda tensorflow keras Pandas SQL neuroscience robotics deep learning planner reiforcement learning Plasma physics Hybrid-PIC EPOCH Laser Gamma-ray X-ray radiation Petawatt Fortran plasma PIC physics Monte Carlo Atomistic Simulation LAMMPS Electron Transport DFT descriptors interatomic potentials machine learning Molecular Dynamics Python scripting AIRSS structure prediction density functional theory high-throughput machine-learning RNA bioinformatics CFD Fluid Dynamics OpenFOAM C++ DNS Mathematics Droplets Basilisk Particle-In-Cell psychology Stan Finance SAS Replication crisis Economics Malaria consumer behavior number estimation mental arithmetic psychophysics Archaeology Precipitation Epidemiology Parkrun Health Health Economics HTA plumber science of science Zipf networks city size distribution urbanism literature review Preference Visual Questionnaire Mann-Whitney Correlation Conceptual replication Cognitive psychology Multinomial processing tree (MPT) modeling #urbanism #R k-means cluster analysis city-regions Urban Knowledge Systems Topic modelling Planning Support Systems Software Citation Quarto snakemake Numerical modelling Ocean climate physical oceanography apptainer oceanography R package structural equation modeling bayes factor Forest Simulations Models of forest dynamics All tags Clear tags

Key

  Associated with an event
  Available for general review
  Public reviews welcome