I have uploaded the new PDF file to the plone site. There are still some formatting problems, especially the R output text would go beyond the right side of the text body — too wide. I have reduced the font size two degrees (using footnote size), but they are still too wide. I wonder if I should just not include it, or increase the width of the body. I read through some posts online that suggested using the default width because it’s the optimal for reading.
I will start working on the first part and then add in the bibliography to complete this document. I also need to finish the two appendices.
I’ve added comments via acrobat to the pdf and uploaded it to the plone site. Let me know if you have questions!