Last updated: 2025-05-25

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Knit directory: SaniVult/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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  • base (R Core Team 2021)
  • workflowr (Blischak, Carbonetto, and Stephens 2019)
  • rmarkdown (Xie, Dervieux, and Riederer 2020)
  • checkpoint (Ooi, de Vries, and Microsoft 2021)
  • coda (Plummer et al. 2006)
  • data.table (Dowle and Srinivasan 2021)
  • ggmcmc (Fernández-i-Marín 2016)
  • ggsci (Xiao 2018)
  • grateful (Rodríguez-Sánchez and Hutchins 2020)
  • mvtnorm (Genz and Bretz 2009)
  • pacman (Rinker and Kurkiewicz 2018)
  • patchwork (Pedersen 2020)
  • runjags (Denwood 2016)
  • tidyverse (Wickham et al. 2019)
  • truncnorm (Mersmann et al. 2018)
  • viridis (Garnier et al. 2021)
  • xtable (Dahl et al. 2019)
  • dplyr (Wickham et al. 2021)
  • ggpubr (Kassambara 2020)
  • plyr (Wickham 2011)
  • readr (Wickham and Hester 2021)
  • reshape2 (Wickham 2007)
  • tibble (Müller and Wickham 2021)

References

Blischak, John D, Peter Carbonetto, and Matthew Stephens. 2019. “Creating and Sharing Reproducible Research Code the Workflowr Way [Version 1; Peer Review: 3 Approved].” F1000Research 8 (1749). https://doi.org/10.12688/f1000research.20843.1.
Dahl, David B., David Scott, Charles Roosen, Arni Magnusson, and Jonathan Swinton. 2019. Xtable: Export Tables to LaTeX or HTML. https://CRAN.R-project.org/package=xtable.
Denwood, Matthew J. 2016. “runjags: An R Package Providing Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS.” Journal of Statistical Software 71 (9): 1–25. https://doi.org/10.18637/jss.v071.i09.
Dowle, Matt, and Arun Srinivasan. 2021. Data.table: Extension of ‘Data.frame‘. https://CRAN.R-project.org/package=data.table.
Fernández-i-Marín, Xavier. 2016. “ggmcmc: Analysis of MCMC Samples and Bayesian Inference.” Journal of Statistical Software 70 (9): 1–20. https://doi.org/10.18637/jss.v070.i09.
Garnier, Simon, Ross, Noam, Rudis, Robert, Camargo, et al. 2021. viridis - Colorblind-Friendly Color Maps for r. https://doi.org/10.5281/zenodo.4679424.
Genz, Alan, and Frank Bretz. 2009. Computation of Multivariate Normal and t Probabilities. Lecture Notes in Statistics. Heidelberg: Springer-Verlag.
Kassambara, Alboukadel. 2020. Ggpubr: ’Ggplot2’ Based Publication Ready Plots. https://CRAN.R-project.org/package=ggpubr.
Mersmann, Olaf, Heike Trautmann, Detlef Steuer, and Björn Bornkamp. 2018. Truncnorm: Truncated Normal Distribution. https://CRAN.R-project.org/package=truncnorm.
Müller, Kirill, and Hadley Wickham. 2021. Tibble: Simple Data Frames. https://CRAN.R-project.org/package=tibble.
Ooi, Hong, Andrie de Vries, and Microsoft. 2021. Checkpoint: Install Packages from Snapshots on the Checkpoint Server for Reproducibility. https://CRAN.R-project.org/package=checkpoint.
Pedersen, Thomas Lin. 2020. Patchwork: The Composer of Plots. https://CRAN.R-project.org/package=patchwork.
Plummer, Martyn, Nicky Best, Kate Cowles, and Karen Vines. 2006. “CODA: Convergence Diagnosis and Output Analysis for MCMC.” R News 6 (1): 7–11. https://journal.r-project.org/archive/.
R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Rinker, Tyler W., and Dason Kurkiewicz. 2018. pacman: Package Management for R. Buffalo, New York. http://github.com/trinker/pacman.
Rodríguez-Sánchez, Francisco, and Shaurita D. Hutchins. 2020. Grateful: Facilitate Citation of r Packages. https://github.com/Pakillo/grateful.
Wickham, Hadley. 2007. “Reshaping Data with the reshape Package.” Journal of Statistical Software 21 (12): 1–20. http://www.jstatsoft.org/v21/i12/.
———. 2011. “The Split-Apply-Combine Strategy for Data Analysis.” Journal of Statistical Software 40 (1): 1–29. http://www.jstatsoft.org/v40/i01/.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.
Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2021. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
Wickham, Hadley, and Jim Hester. 2021. Readr: Read Rectangular Text Data. https://CRAN.R-project.org/package=readr.
Xiao, Nan. 2018. Ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for ’Ggplot2’. https://CRAN.R-project.org/package=ggsci.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.