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If you would like to refer to Dynare in a research article, the recommended way is to cite the present manual, as follows:
Stéphane Adjemian, Houtan Bastani, Michel Juillard, Ferhat Mihoubi, George Perendia, Marco Ratto and Sébastien Villemot (2011), “Dynare: Reference Manual, Version 4,” Dynare Working Papers, 1, CEPREMAP
Note that citing the Dynare Reference Manual in your research is a good way to help the Dynare project.
If you want to give a URL, use the address of the Dynare website: http://www.dynare.org.
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