To cite simplePHENOTYPES in publications use:

Fernandes, S.B., and Lipka, A.E. (2020). simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes. BMC Bioinformatics 21(1):491. https://doi.org/10.1186/s12859-020-03804-y

When controlling the genetic correlation in the pleiotropy architecture (the `cor` argument), also cite:

Prado et al. (in preparation). Exact control of the genetic correlation in multi-trait phenotype simulation.

When simulating variance QTL (the vqtl() layer), also cite:

Murphy, M.D., Fernandes, S.B., Morota, G. et al. (2022). Assessment of two statistical approaches for variance genome-wide association studies in plants. Heredity 129, 93-102. https://doi.org/10.1038/s41437-022-00541-1

When using the crossing pipelines (cross/selfcross/double_haploid), also cite the isqg framework they are ported from:

Toledo, F.H., Perez-Rodriguez, P., Crossa, J. and Burgueno, J. (2019). isqg: A Binary Framework for in Silico Quantitative Genetics. G3 Genes|Genomes|Genetics 9(8), 2425-2428. https://doi.org/10.1534/g3.119.400373

Corresponding BibTeX entries:

  @Article{,
    title = {simplePHENOTYPES: SIMulation of pleiotropic, linked and
      epistatic phenotypes},
    author = {Samuel B. Fernandes and Alexander E. Lipka},
    journal = {BMC Bioinformatics},
    year = {2020},
    volume = {21},
    number = {1},
    pages = {491},
    doi = {10.1186/s12859-020-03804-y},
  }

  @Unpublished{,
    title = {Exact control of the genetic correlation in multi-trait
      phenotype simulation},
    author = {Prado {et al.}},
    year = {in preparation},
    note = {Manuscript in preparation},
  }

  @Article{,
    title = {Assessment of two statistical approaches for variance
      genome-wide association studies in plants},
    author = {Matthew D. Murphy and Samuel B. Fernandes and Gota Morota
      and Alexander E. Lipka},
    journal = {Heredity},
    year = {2022},
    volume = {129},
    pages = {93--102},
    doi = {10.1038/s41437-022-00541-1},
  }

  @Article{,
    title = {isqg: A Binary Framework for in Silico Quantitative
      Genetics},
    author = {Fernando H. Toledo and Paulino Perez-Rodriguez and Jose
      Crossa and Juan Burgueno},
    journal = {G3 Genes|Genomes|Genetics},
    year = {2019},
    volume = {9},
    number = {8},
    pages = {2425--2428},
    doi = {10.1534/g3.119.400373},
  }