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.
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/.
Reproducibility
─ 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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