This paper is fully reproducible; we provide the protocol that the different modelers used, the data produced from these models, the observed data, and the code to run the analysis that led to the results of the paper, figures, and text. I have not come across any other paper in forestry that is as fully reproducible as our paper, so it might also be a rare example in this field and hopefully a motivation to others to do so. Please notice that we do not provide the models that were used to run the simulations, as these are the results used (or data collection), but we do provide the data resulting from these simulations.
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.
The current code is written in Torch, which is no longer actively maintained. Since deep learning in nanophotonics is an area of active interest (e.g. for the design of new metamaterials), it is important to update the code to use a more modern deep learning library such as tensorflow/keras
I tried hard to make this paper as reproducible as possible, but as techniques and dependencies become more complex, it is hard to make it 100% clear. Any form of feedback is more than welcome.
I guess it could be a cool learning experience. The paper is written with knitr, uses a seed, is part of the R package it describes, was openly written using version control (SVN, R-Forge) and is available in an open access journal (@up_jors).
