This book is based on R Markdown and bookdown (https://github.com/rstudio/bookdown).
A copy of the book in bookdown::pdf_book format can be generated by typing in Rstudio bookdown::render_book('index.Rmd', 'bookdown::pdf_book').
The references are kept in the book.bib file. They are generated from TeXMed - a BibTeX interface for PubMed at https://www.bioinformatics.org/texmed/. The references take the form of
@Article{10.1111/2041-210x.12628, Authors= {Yu, G. and Smith, D.K. and Guan, H.Z. and Guan, Y. and Lam, T.}, Title={ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data}, Journal="Methods in Ecology and Evolution", Year="2016", Volume="28", Pages={28-36}, doi={10.1111/2041-210x.12628} }
The files were uploaded to github using git bash
Some issues have occurred between when the files were written in 2020 with bookdown version 0.21 and change in knitr. The file is_abs_path() was removed from knitr 1.34 has been removed in the latest version of knitr. This was resolved by downloading knitr version 1.33 from Archives and installing the tar.gz files.
#initiating repository
git remote add origin https://github.com/GNtem2/HealthcareRBook.git
git push -u origin master
#removing files from github
git git rm --cached 04-application.Rmd
git commit -m "remove old 04-application.Rmd"
git push -u origin master
#adding files to github
git add *.Rmd
git commit -m "updating bookdown with new chapters and data"
git push -u origin master