If I use R for a plot, or a simple bit of regression, or anova, or even cross-validation. I don't reference it in a paper. I only cite it if there is a package designed for a particular type of data (e.g. a Bioconductor package) or something a bit more esoteric (e.g. apcluster). About 95% of the work is data munging and - sorry Hadley - I don't cite dplyr, purrr, magrittr etc...
However I have notice that in clinical trial or small social science papers simple analyses of this type are often cited as being done in SPSS or SAS. I think this just reflects the fact that non specialist data analysts are more likely to cite SAS or SPSS for simple procedures such as graphs or anova as an appeal to authority.
So I reckon the data may reflect a trend but tells us little about the true levels.