Add references

[VisruthSK]

Add appropriate citations for functions.

[jgabry]

Here are some suggestions:

• sample: https://jmlr.org/papers/volume15/hoffman14a/hoffman14a.pdf and maybe https://arxiv.org/pdf/1701.02434 (in the appendix it has a more recent description of Stan's version of NUTS)
• pathfinder: https://jmlr.org/beta/papers/v23/21-0889.html
• variational: https://jmlr.org/papers/volume18/16-107/16-107.pdf

For all of them (including optimize and laplace methods) we could also cite the Stan manual because it has sections describing each of the algorithms. https://mc-stan.org/docs/reference-manual/ has an Algorithms section with subsections/chapters for each algorithm.

[jgabry]

cmdstanr also has a loo method that calls the loo package, but I'm not sure if we should add citations for all the loo papers in the doc for the loo method, or just point to the loo package which has all of them. I guess same question for the summary method which calls the posterior package and includes diagnostics from the papers related to the posterior package.

[VisruthSK]

I think we should include the citations from loo/posterior--for stanflow, if a user only uses cmdstanr I don't see why the R packages should be cited instead of their methods, so in that vein I think the docs should have the method citations

[jgabry]

@avehtari Do you have anything else you think we should cite beyond my suggestions above?

[avehtari]

@jgabry your suggestions are fine