Section 17 R packages



The data analysis, construction of graphics and visualisation of the 2018 Veterinary Laboratory Service data have been conducted by using the R programming language [R Core Team (2013) and the RStudio integrated development environment. Eddelbuettel and Balamuta (2019), with their pinp package have provided the template for this report, which is originally based on the PNAS2 article style. Most of the charts were plotted with the package ggplot2 (Wickham et al. 2018) and the tables constructed with kableExtra (Zhu 2018) and finalfit (Harrison, Drake, and Ots 2019).

The webpage (HTML) version of the Disease Surveillance Report has also been compiled in RStudio by applying the package bookdown (Xie 2018). An extensive use of rmarkdow andLaTeX languages were also utilised with both packages, pinp and bookdown, for formatting and typesetting.

Many other packages were also used in the preparation of this report, as shown below.

References

R Core Team. 2013. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/.

Eddelbuettel, Dirk, and James Balamuta. 2019. Pinp: ’Pinp’ Is Not ’Pnas’. https://CRAN.R-project.org/package=pinp.

Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, and Kara Woo. 2018. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.

Zhu, Hao. 2018. KableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax. https://CRAN.R-project.org/package=kableExtra.

Harrison, Ewen, Tom Drake, and Riinu Ots. 2019. Finalfit: Quickly Create Elegant Regression Results Tables and Plots When Modelling. https://CRAN.R-project.org/package=finalfit.

Xie, Yihui. 2018. Bookdown: Authoring Books and Technical Documents with R Markdown. https://CRAN.R-project.org/package=bookdown.

  1. Proceedings of the National Academy of Sciences of the United States of America.↩

 

A cooperative effort between the VLS and the SAT Section of the DAFM