RMarkdownWord

Creating output for collaborators/customers:

• Word document with background and methods
• Excel file with sheets for all tables
• PDF file with all figures

R Markdown

• Dynamic documents created by script
• can create HTML, PDF, LaTeX, and Word
• apparently under active development, surpring changes once in a while

In RStudio:

File->New File->R Markdown

Will ask for some basic information and type (can be changed later!)

Creates a prefilled document with examples

OR

load your template xxx.Rmd

Change content to your needs

Click on the clew of yarn with needles and knit your docx

This saves your script!!

• Plain text
  • here you put things like methods, explanations …
  • basic formatting like bold, italics, list etc
  • can contain (small) parts of R code, output will be integrated in text
• Code chunks
  • like ordinary scripts
  • defined by 3backticks{r} for begin and 3backticks for end
  • header may contain name (strongly suggested) and options

• Within chunk, commands can be run the usual way
• Ctrl-A Ctrl-Enter will NOT work (runs plain text as well)
• You may run a complete chunk (Ctrl-Alt-C) or all chunks (Ctrl-Alt-R)
• Reindenting code (Ctrl-A Ctrl-I) will change plain text and global header (BEWARE!)

• Can be set for each chunk in header:

  {r import, echo=FALSE,warning=FALSE, results='hide',message=FALSE}

• Can be set globally

  opts_chunk$set(message=F,warning=F,comment=NA,echo=F, dpi=300,fig.width=plotsize*1.5, fig.height=plotsize*1.2)

• I tend to suppress source code echoing in reports

1. Create Word file with R Markdown
2. Change formats (e.g. A4, margins)
3. Add header / footer …
4. Save
5. Use as template:

output:

  word_document:

      reference_docx: template.docx

• Currently, I loose formatting for headers :-(

• testing of different table packages
• solving template problem
• dynamic page orientation (landscape)
• testing grids with ggplots
• defining output folder