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.
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.
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.
This paper presents a fine example of high-throughput computational materials screening studies, mainly focusing on the carbon nanoclusters of different sizes. In the paper, a set of diverse empirical and machine-learned interatomic potentials, which are commonly used to simulate carbonaceous materials, is benchmarked against the higher-level density functional theory (DFT) data, using a range of diverse structural features as the comparison criteria. Trying to reproduce the data presented here (even if you only consider a subset of the interaction potentials) will help you devise an understanding as to how you could approach a high-throughput structure prediction problem. Even though we concentrate here on isolated/finite nanoclusters, AIRSS (and other similar approaches like USPEX, CALYPSO, GMIN, etc.,) can also be used to predict crystal structures of different class of materials with applications in energy storage, catalysis, hydrogen storage, and so on.
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.
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.