Hi,
I hope you are doing well!

I have a question. I and my colleagues wrote a paper by using R language and 
its packages. We also used some tutorials. We have words count limitation for 
our paper. In early version of paper, I cited all packages in the reference 
list of paper (my paper will be published in an academic journal). After that, 
we had to keep references to tutorials in the reference list and remove 
reference to R and its packages (I strictly should fit paper to 2000 words). We 
created an online appendix and listed all packages which we used. Some packages 
are related to paper. For example, when i used command 'citation()'  in R 
console for package "tidytext", R informed me that i should cite such package 
as this:


Silge, J., & Robinson, D. (2016). tidytext: Text Mining and Analysis Using Tidy 
Data Principles in R. JOSS, 1(3). https://doi.org/10.21105/joss.00037

Now, all packages and their related papers are not in the reference list of 
paper, but they will be available in an online appendix in the journal website. 
Is such practice OK or should I cite all packages in the reference list?
I attached online appendix. We will submit our paper to a journal soon.
Should I cite papers which are related to packages in the reference list? if I 
do not cite, i will face with permission problem regard to usage of package?

Many thanks!
With best regards,


Dr. Mehdi Dadkhah


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