How is R cited in research outputs? Structure, impacts, and citation standard

This paper addresses software citation by analyzing how R and its packages are cited in a sample of PLoS papers. A codebook is developed to support a content analysis of the full-text papers. Our results indicate that the software R and its packages are inconsistently cited, as is the case with other scientific software. The inconsistency derives partly from the variety of citation standards currently used for software, and partly from fact that these standards are not well followed by authors on multiple levels. This work sheds light on the future development of software citation standards, especially given the present landscape of conflicting citation practices. Moreover, our approach furnishes a possible blueprint for dealing with the granularity of software entities in scientific citation: we consider citations of the core R software environment, of specific R packages, and of individual functions.