12.5 Output figures in the HTML5 format.11.17 Customize the printing of objects in chunks (*).11.16 Step-by-step plots with low-level plotting functions (*).11.13 Add attributes to text output blocks (*).11.12 Remove leading hashes in text output.11.11 Output text as raw Markdown content (*).11.9 Collapse text output blocks into source blocks.11.7 Hide code, text output, messages, or plots.11.5 Cache a code chunk for multiple output formats.11.3 Multiple graphical output formats for the same plot.10.3 Other packages for creating tables.10.2.4 Scaling down wide tables in LaTeX.10.1.9 Generate multiple tables from a for-loop (*).8.2 The two-way workflow between R Markdown and Word.7.14 Improve accessibility of HTML pages.7.10 Include the content of an existing HTML file (*).7.8 Embed arbitrary files in the HTML output file.7.7 Embed the Rmd source file in the HTML output file.7.5 Fold all code blocks but show some initially.6.10 Use a custom Pandoc LaTeX template (*).6.7 Render documents containing Unicode characters.5.6.1 Show a verbatim inline expression.5.1.1 Using an R function to write raw HTML or LaTeX code.4.20 Manipulate Markdown via Pandoc Lua filters (*).4.19 Put together all code in the appendix (*).4.18 Omit a heading in the table of contents.4.15.3 Other packages for making diagrams.4.14 Create an animation from multiple R plots.4.12 Preserve a large number of line breaks.4.11 Combine words into a comma-separated phrase.4.5.4 Include appendix after bibliography (*).4.5.3 Add all items to the bibliography.4.5.2 Add an item to a bibliography without using it.4.3 Access the document metadata in R code.3.2 Write Markdown in the RStudio visual editor.2.3 What can we change to change the results?.1.2 Install LaTeX (TinyTeX) for PDF reports.1.1 Use a Pandoc version not bundled with the RStudio IDE.\usepackage[scale=1,angle=0,opacity=1,contents= after the bibliography so that the appendix would use the same mark from the beginning. I ended up using this solution after adding and modifying the colors, changing the size and position. My first search showed that it was possible, but I didn’t want to load the tikz package. One thing I liked from other thesis is the ability to have on the printed edition a little mark on the side of the page to find a section. The book_filename if present on index.Rmd is overwritten by what is on _bookdown.yml but be careful also on what goes to _bookdown.yml and on the specific format on _output.yml. Lot and lof indicate if list of tables (lot) and list of figures (lof) should be included on the pdf output. The bindingoffset adds some space to make it easier reading. Geometry Defines the margins, consider that on books the central zone will not be readable. Papersize this chooses the available space and greatly affects the position of figures and tables, which can float on the text according to LaTeX algorithm. It is useful for printing where the reader doesn’t have the option to click a link but might be interested in knowing more.įontfamily and fontsize decide which font and size will be used. Links-as-notes Instead of having hyperlinks have them included as notes. Link-citations Add a link to the citation? Split_by in the html format how to move to the next section. Papersize: a4 # The printed size of the thesis # links-as-notes: true # Only activate for actual printing The once I included are: split_by: chapter Many latex instructions go to the index.Rmd file. Well, without further delay let’s dive in things I learned: That’s why I tweaked the default format inspired by the recent thesis defended on my group. On my case I didn’t have any template and the university guidelines are not long, (have two compulsory pages at the beginning and have 5 sections). If yours is there, or if you want to learn how are they you can have a look at the files. It is the most important format as ultimately is what I’m going to use for printing.įirst of all you should know there is a package thesisdown with a few templates for some universities. Most of the experiences and advise I’ll share here are based on my experiences to improve the pdf format. I made the thesis in web and pdf format (and epub) to make more available the thesis. On this post I am documenting the experiences I had writing my PhD thesis with bookdown.
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