All relevant raw data is available on OSF at doi.org/10.17605/OSF.IO/E58WS under a GPL3 license.
First, fork the GitHub repo onto your Desktop. Then, download the data from OSF such that you maintain the same folder structure as already present on OSF. Make sure that your computer runs the latest version of R and RStudio. Install the rtransparent package by running devtools::install_github('serghiou/rtransparent). You should now be able to run the code - RStudio will let you know if any of the packages is missing and prompt you to install it.
The repo is structured across 4 sub-sections in the order that they were done: the manual adjudication subsection, the development of the tool (this code is found in the rtransparent repo), the evaluation of the tool and the use of the tool to assess all open access articles on PubMed Central. Each subsection is subdivided into 2 directories. The data directory contains all data and can be found on OSF and the code directory contains all code.
Please do let us know if you have any questions and especially if you discover any bugs! You can do so by openning an Issue on GitHub or by sending an email to stelios.serghiou@gmail.com.