An empirical exploration of the diversified R ecosystem

Referee: [Abstract / user-discipline results] Abstract and the section presenting user-discipline results: the claim that the main academic user groups come from agricultural, biological, environmental, and medical sciences rests on disciplinary classification of papers citing R, yet no description is given of how disciplines were assigned, how citation records were filtered or deduplicated, or how selection biases (field-specific citation norms, non-publishing users) were addressed. This directly undermines the central user-base claim.

Authors: We acknowledge that the manuscript provides no description of the disciplinary classification method, citation filtering, deduplication, or bias mitigation steps. In the revised manuscript we will insert a new subsection under Methods that specifies the classification scheme (journal subject categories from the source database), the exact filtering and deduplication rules applied to the citation records, the date range of the data pull, and an explicit discussion of limitations arising from field-specific citation practices and the exclusion of non-publishing users. revision: yes

Referee: [Data sources and methods] The section on data sources and methods: the manuscript states conclusions from CRAN metadata and citation data but supplies no details on data acquisition dates, cleaning steps, statistical procedures, error handling, or controls for citation inflation and incomplete coverage. Without these, the support for all empirical claims cannot be evaluated.

Authors: We agree that the absence of these details prevents proper evaluation. The revised Methods section will report the precise acquisition dates for both CRAN metadata and the bibliometric records, all cleaning and preprocessing steps performed, any statistical procedures used, error-handling rules, and a dedicated paragraph addressing potential citation inflation and coverage gaps in the source databases. revision: yes

Referee: [Collaboration patterns] The collaboration-patterns analysis: the same citation-derived data source is used to examine developer collaborations and their effects, amplifying the risk that any unaddressed measurement biases in the bibliometric layer propagate to the collaboration conclusions.

Authors: We note that the collaboration analysis primarily draws on CRAN package maintainer and contributor metadata rather than citation records; however, the referee is correct that any bibliometric component could introduce bias. In revision we will (i) clearly separate the data sources used for each analysis, (ii) add explicit caveats about possible propagation of measurement error, and (iii) include a brief sensitivity check where feasible. We therefore mark this revision as partial because full elimination of all bibliometric bias may not be possible with the available data. revision: partial