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., P. de Valpine, and C.J. Paciorek. 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., P. de Valpine, N. Michaud, and D. Turek. 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.R., and P. de Valpine. 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},
  }