kinfitr: Reproducible PET Pharmacokinetic Modelling in R

Quantification of Positron Emission Tomography (PET) data is performed using pharmacokinetic models. There exist many models for describing this data, each of which may describe the data better or worse depending on the specific application, and there are both theoretical, practical and empirical reasons to select any one model over another. As such, effective PET modelling requires a high degree of flexibility, while effective communication of all steps taken through scientific publications is not always feasible. Reproducible research practices address these concerns, in that researchers share analysis code, and data if possible, such that all steps are recorded, allowing an independent researcher to reproduce the results and assess their veracity. In this article, I present kinfitr: a software package for performing kinetic modelling using the open-source R language, in a reproducible manner. The R community has a strong culture of reproducible research, and the language consists of numerous tools which allow both effective and easy sharing and communication of analysis code. The package is written in such a way as to allow the analyst the freedom to use and rapidly exchange between approaches, and to assess goodness of fit, with 14 different kinetic models currently implemented using a consistent syntax, as well as tools for working with the data. By providing open-source tools for kinetic modelling, including documentation and examples, it is hoped that this will extend access to methodology for research groups lacking software engineering expertise, as well as simplify and thereby encourage transparent and reproducible reporting.