To cite the pmd package in publications use:

Yu M, Olkowicz M, Pawliszyn J (2019). “Structure/reaction directed analysis for LC-MS based untargeted analysis.” Analytica Chimica Acta, 1050, 16 - 24. ISSN 0003-2670, doi: 10.1016/j.aca.2018.10.062, https://www.sciencedirect.com/science/article/pii/S0003267018313047.

Yu M, Petrick L (2020). “Untargeted high-resolution paired mass distance data mining for retrieving general chemical relationships.” Communications Chemistry, 3, 157. ISSN 2399-3669, doi: 10.1038/s42004-020-00403-z, https://doi.org/10.1038/s42004-020-00403-z.

Some functions (e.g. getmd use xcms party algorithms, see manpages and related packages for respective citations.

Corresponding BibTeX entries:

  @Article{,
    title = {Structure/reaction directed analysis for LC-MS based
      untargeted analysis},
    journal = {Analytica Chimica Acta},
    volume = {1050},
    pages = {16 - 24},
    year = {2019},
    issn = {0003-2670},
    doi = {10.1016/j.aca.2018.10.062},
    url =
      {https://www.sciencedirect.com/science/article/pii/S0003267018313047},
    author = {Miao Yu and Mariola Olkowicz and Janusz Pawliszyn},
  }

  @Article{,
    title = {Untargeted high-resolution paired mass distance data
      mining for retrieving general chemical relationships},
    journal = {Communications Chemistry},
    volume = {3},
    pages = {157},
    year = {2020},
    issn = {2399-3669},
    doi = {10.1038/s42004-020-00403-z},
    url = {https://doi.org/10.1038/s42004-020-00403-z},
    author = {Miao Yu and Lauren Petrick},
  }