In published work that uses or mentions nimbleEcology, please cite the package (Goldstein et al. 2020), including the version used. When using cases of dCJS, dHMM and/or dDHMM, please also cite Turek et al. (2016). When using cases of dOcc and/or dDynOcc, please also cite Ponisio et al. (2020). When using cases of dNmixture, please also cite Goldstein and de Valpine (2022).

Goldstein B, Turek D, Ponisio L, de Valpine P (2024). “nimbleEcology: Distributions for Ecological Models in nimble.” R package version 0.5.0, https://cran.r-project.org/package=nimbleEcology.

Turek D, de Valpine P, Paciorek C (2016). “Efficient Markov chain Monte Carlo sampling for hierarchical hidden Markov models.” Environmental and Ecological Statistics, 23, 549-564. doi:10.1007/s10651-016-0353-z.

Ponisio L, de Valpine P, Michaud N, Turek D (2020). “One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE.” Ecology and Evolution, 10, 2385–2416. doi:10.1002/ece3.6053.

Goldstein B, de Valpine P (2022). “Comparing N-mixture Models and GLMMs for Relative Abundance Estimation in a Citizen Science Dataset.” Scientific Reports, 12, 12276. doi:10.1038/s41598-022-16368-z.

Corresponding BibTeX entries:

  @Misc{,
    title = {{nimbleEcology}: Distributions for Ecological Models in
      {nimble}},
    author = {Benjamin R. Goldstein and Daniel Turek and Lauren Ponisio
      and Perry {de Valpine}},
    url = {https://cran.r-project.org/package=nimbleEcology},
    year = {2024},
    version = {0.5.0},
    note = {{R} package version 0.5.0},
  }

  @Article{,
    title = {Efficient Markov chain Monte Carlo sampling for
      hierarchical hidden Markov models},
    journal = {Environmental and Ecological Statistics},
    volume = {23},
    pages = {549-564},
    year = {2016},
    author = {D. Turek and P. {de Valpine} and C.J. Paciorek},
    doi = {10.1007/s10651-016-0353-z},
  }

  @Article{,
    title = {One size does not fit all: Customizing MCMC methods for
      hierarchical models using {NIMBLE}},
    journal = {Ecology and Evolution},
    volume = {10},
    pages = {2385–2416},
    year = {2020},
    author = {L. Ponisio and P. {de Valpine} and N. Michaud and D.
      Turek},
    doi = {10.1002/ece3.6053},
  }

  @Article{,
    title = {Comparing {N-mixture} Models and {GLMMs} for Relative
      Abundance Estimation in a Citizen Science Dataset},
    journal = {Scientific Reports},
    volume = {12},
    pages = {12276},
    year = {2022},
    author = {B.R. Goldstein and P. {de Valpine}},
    doi = {10.1038/s41598-022-16368-z},
  }