Citations

Author

Steffi LaZerte

Published

September 23, 2024

Packages

You probably only need to cite

  • mcgv for gam models
  • DHARMa for model diagnostics
  • MASS for negative binomial GLM models
  • possibly the tidyverse for general data manipulation

but you should keep track of the packages used and their versions (see General Info, but note that if an workflow step was updated separately, see the most up-to-date package versions under that pages “General Info”).

Note: There are several papers for citing mgcv, but they recommend the 2017 book for an overview, which I think makes the most sense.

mgcv (for GAMs)

Wood S (2017). Generalized Additive Models: An Introduction with R, 2 edition. Chapman and Hall/CRC.

DHARMa (for model checks)

Hartig F (2022). DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models. R package version 0.4.6, https://CRAN.R-project.org/package=DHARMa.

MASS (for negative binomial GLM)

Venables WN, Ripley BD (2002). Modern Applied Statistics with S, Fourth edition. Springer, New York. ISBN 0-387-95457-0, https://www.stats.ox.ac.uk/pub/MASS4/.

tidyverse (for general data management and figures)

Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686 https://doi.org/10.21105/joss.01686.

Reproducibility

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       Ubuntu 22.04.4 LTS
 system   x86_64, linux-gnu
 ui       X11
 language en_CA:en
 collate  en_CA.UTF-8
 ctype    en_CA.UTF-8
 tz       America/Winnipeg
 date     2024-07-10
 pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 ! package     * version date (UTC) lib source
 P cachem        1.1.0   2024-05-16 [?] CRAN (R 4.4.0)
 P cli           3.6.2   2023-12-11 [?] CRAN (R 4.4.0)
 P devtools      2.4.5   2022-10-11 [?] CRAN (R 4.4.0)
 P digest        0.6.35  2024-03-11 [?] CRAN (R 4.4.0)
 P ellipsis      0.3.2   2021-04-29 [?] CRAN (R 4.4.0)
 P evaluate      0.23    2023-11-01 [?] CRAN (R 4.4.0)
 P fastmap       1.2.0   2024-05-15 [?] CRAN (R 4.4.0)
 P fs            1.6.4   2024-04-25 [?] CRAN (R 4.4.0)
 P glue          1.7.0   2024-01-09 [?] CRAN (R 4.4.0)
 P htmltools     0.5.8.1 2024-04-04 [?] CRAN (R 4.4.0)
 P htmlwidgets   1.6.4   2023-12-06 [?] CRAN (R 4.4.0)
 P httpuv        1.6.15  2024-03-26 [?] CRAN (R 4.4.0)
 P jsonlite      1.8.8   2023-12-04 [?] CRAN (R 4.4.0)
 P knitr         1.47    2024-05-29 [?] CRAN (R 4.4.0)
 P later         1.3.2   2023-12-06 [?] CRAN (R 4.4.0)
 P lifecycle     1.0.4   2023-11-07 [?] CRAN (R 4.4.0)
 P magrittr      2.0.3   2022-03-30 [?] CRAN (R 4.4.0)
 P memoise       2.0.1   2021-11-26 [?] CRAN (R 4.4.0)
 P mime          0.12    2021-09-28 [?] CRAN (R 4.4.0)
 P miniUI        0.1.1.1 2018-05-18 [?] CRAN (R 4.4.0)
 P pkgbuild      1.4.4   2024-03-17 [?] CRAN (R 4.4.0)
 P pkgload       1.3.4   2024-01-16 [?] CRAN (R 4.4.0)
 P profvis       0.3.8   2023-05-02 [?] CRAN (R 4.4.0)
 P promises      1.3.0   2024-04-05 [?] CRAN (R 4.4.0)
 P purrr         1.0.2   2023-08-10 [?] CRAN (R 4.4.0)
 P R6            2.5.1   2021-08-19 [?] CRAN (R 4.4.0)
 P Rcpp          1.0.12  2024-01-09 [?] CRAN (R 4.4.0)
 P remotes       2.5.0   2024-03-17 [?] CRAN (R 4.4.0)
   renv          1.0.7   2024-04-11 [1] CRAN (R 4.4.0)
 P rlang         1.1.3   2024-01-10 [?] CRAN (R 4.4.0)
 P rmarkdown     2.27    2024-05-17 [?] CRAN (R 4.4.0)
 P rstudioapi    0.16.0  2024-03-24 [?] CRAN (R 4.4.0)
 P sessioninfo   1.2.2   2021-12-06 [?] CRAN (R 4.4.0)
 P shiny         1.8.1.1 2024-04-02 [?] CRAN (R 4.4.0)
 P stringi       1.8.4   2024-05-06 [?] CRAN (R 4.4.0)
 P stringr       1.5.1   2023-11-14 [?] CRAN (R 4.4.0)
 P urlchecker    1.0.1   2021-11-30 [?] CRAN (R 4.4.0)
 P usethis       2.2.3   2024-02-19 [?] CRAN (R 4.4.0)
 P vctrs         0.6.5   2023-12-01 [?] CRAN (R 4.4.0)
 P xfun          0.44    2024-05-15 [?] CRAN (R 4.4.0)
 P xtable        1.8-4   2019-04-21 [?] CRAN (R 4.4.0)
 P yaml          2.3.8   2023-12-11 [?] CRAN (R 4.4.0)

 [1] /home/steffi/Projects/vulture_migration/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
 [2] /home/steffi/.cache/R/renv/sandbox/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu/9a444a72

 P ── Loaded and on-disk path mismatch.

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