While there seems to be quite a bit of discussion about this (here, here, here), it is not clear how one could remove the section heading auto_identifiers (the "#" that appears after a slide's section header; h1,h2,etc.) from a Xaringan theme in Rmarkdown.
Can this be done within the YAML? (markdown: kramdown seems to have an auto_ids: false addition to the header as shown here)
Can this be done in a custom.css by editing .h1 etc.?
Similar to this post:
If the headers are specified as:
# header1 {#header1id}
## header2
### header3
The resulting HTML:
<h1 id="header1id">header1</h1>
<h2 id="header2">header2</header2>
<h3 id="header3">header3</header3>
But I would prefer:
<h1 id="header1id">header1</h1>
<h2>header2</h2>
<h3>header3</h3>
Obviously, using the html directly works (e.g., <h1>header1</h1>), but it would be great to be able to use the markdown # headers.
For completeness, an example YAML within a Rmarkdown.Rmd Xaringan template:
---
title: "Please Remove the # Anchors"
author: "Begin Er"
date: "Now"
output:
xaringan::moon_reader:
css: [default, metropolis, metropolis-fonts]
nature:
beforeInit: "macros.js"
highlightStyle: github
highlightLines: true
countIncrementalSlides: false
ratio: "16:9"
---
Thanks!
Related
I am trying to update my portfolio website with new Quarto-generated HTML files rather than my older RMarkdown-generated HTML files. I have rendered these updated files and they look great!
However, when I have uploaded this HTML to my GitHub Pages website, using htmlpreview, I get a very different picture...
Keep in mind that htmlpreview works perfectly well for my RMarkdown-renderd documents:
Here is my YAML for the Quarto document if it is of help:
author: "Brian Lookabaugh"
toc: true
number-sections: true
format:
html:
code-background: true
I think using self-contained: true would solve your case, since you would need a standalone HTML file.
author: "Brian Lookabaugh"
toc: true
number-sections: true
format:
html:
self-contained: true
code-background: true
For reference, see this page from Quarto Docs.
Iw as working on a gitbook using bookdown in R several months ago. Today, I resumed my work again, but when I rendered the book the font of the output changed dramatically. It vanishes! I don't remember having changed anything on the TAML of the book. This is how it looks now. Right after the word WELCOME, the text becomes lighter and lighter until it literally disappears. It has a sort of vanishing effect that I have no idea how I got.
Thank you for your help.
Best,
this is my _output.yml
bookdown::gitbook:
config:
toc:
collapse: section
scroll_highlight: yes
before: |
<li>PovcalNet Internal Guidelines</li>
after: |
<li>Published with bookdown</li>
download: ["pdf", "epub"]
toolbar:
position: fixed
edit : null
search: yes
fontsettings:
theme: white
family: sans
size: 2
sharing:
facebook: no
github: no
twitter: no
linkedin: no
weibo: no
instapaper: no
vk: no
info: yes
bookdown::pdf_book:
includes:
in_header: preamble.tex
latex_engine: xelatex
citation_package: natbib
keep_tex: yes
bookdown::epub_book:
stylesheet: style.css
And this is my _bookdown.yml
book_filename: "Povcalnet_internal_guidelines"
repo: https://github.com/xxxxxx/Povcalnet_internal_guidelines/
output_dir: "docs"
delete_merged_file: true
language:
label:
fig: "Figure "
tab: "Table "
ui:
edit: "Edit"
chapter_name: "Chapter "
rmd_files: [
"index.Rmd",
"intro.Rmd",
"Folder_structure.Rmd",
"Collaboration_in_Git.Rmd",
"DM_Group_data.Rmd",
"Handover.Rmd",
"references.Rmd",
]
before_chapter_script: "_common.R"
And, I am rendering the book using the following instruction,
bookdown::render_book("index.Rmd", "bookdown::gitbook")
I found the problem. Basically, in one of my .Rmd files I create a diagram using the DiagrammeR package. When one of my colleagues removed the diagram, the issue was gone, but we had no diagram. However, I created a separate .mmd (mermaid) file and updated both packages glue and DiagrammeR. All of this solved the problem.
thanks.
The example below (i.e. saved as a file index.rmd ) has the same code chunk to display an image above and below the top level heading, but the image doesn't appear above the top level heading. This occurs if there is a file _output.yml with only this entry bookdown::gitbook: in the same directory.
That line seems to enforce a table of contents (which I want) and that appears to strip out anything (image or text) before the first top level heading by default (which I don't want) - so can this behaviour be modified?
---
site: bookdown::bookdown_site
---
```{r echo=FALSE, message=FALSE, warning=FALSE}
library(imager)
im <- load.image(system.file('extdata/Leonardo_Birds.jpg',package='imager'))
plot(im, axes=FALSE)
```
# R Markdown
```{r echo=FALSE, message=FALSE, warning=FALSE}
library(imager)
im <- load.image(system.file('extdata/Leonardo_Birds.jpg',package='imager'))
plot(im, axes=FALSE)
```
What follows is workaround to your Options 2 and 3, using Markdown and CSS to style images and HTML+CSS to style text; also, using base64 image (transparent gif) generator as an space separator between elements.
Beware of whitespaces! (at the end of each line - place two white spaces and hit ENTER)
Does one of these approaches/hacks work for you? If not, it would be better to delete the answer, it may be misleading to others.
---
title: |
{width=300px}|
|:-:|
{width=300px style="display: block; margin:0 auto"}
{width=300px height=90px align=left}
{width=300px height=90px align=center}
{width=300px height=90px align=right}
{width=150px}
R Markdown Title
<center>R Markdown Title</center>
<p style="text-align: right;">R Markdown Title</p>
{width=150px}
author: "Author Name"
date: "08/03/2020"
---
Using Markdown table to "style" images |-| (left-aligned), |:-:| (centered) and |-:| (right-aligned) will work well with simple RMarkdown outputs.
I realised that you have an image under # top level heading positioned at the very top of the page - with top:0px. causing image duplication and, possibly, hover problem:
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:0px;height:100px;" />
replace with:
{width=50px style="display: block; margin:0 auto;"}
and see what will happen.
---
title: |
{width=300px style="display: block; margin:0 auto;"}
{width=50px}
R Markdown Title
{width=50px}
output:
html_document: default
---
# I'm a top level heading {-}
{width=50px style="display: block; margin:0 auto;"}
Note, you need to replace the image with a local image if you want to show the image in the rstudio viewer.
The image will be visible in the html file created when you knit, if you open in a browser connected to the internet.
```{r echo=FALSE, message=FALSE, warning=FALSE}
plot(cars)
```
EDIT:
Let's try to find a common ground, A Minimal Book Example, github here.
Adjustments made in index.Rmd:
---
title: |
{height=300px}
author: "Author Name"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
---
# Prerequisites
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
index.Rmd output:
Adjustments made in Chapter: Introduction (01-intro.Rmd):
# Introduction {#intro}
{height=240px}
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \#ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \#ref(methods).
01-intro.Rmd output:
With this solution we are "masking" a top level heading (# Introduction) with .png image, which will appear in the Table of Content as text.
Disadvantage: besides the obvious hack, image width must be at least equal or wider than top level heading title.
Note: 3 options are provided here, and none of them are perfect. The perfect solution may rely on modifications to the bookdown package?
Option 1:
Use includes with before_body like this in your _output.yml file (suggested here):
bookdown::gitbook:
css: assets/style.css
includes:
before_body: assets/big-image.html
after_body: assets/footer.html
Disadvantages:
i) Requires making a html file just to insert an image.
ii) If using a web-based image, won't show in Rstudio viewer.
iii) If using a local image, path can get mixed up and won't show in online web html rendering
iv) Includes image at the top of each chapter of bookdown if using before_body: my_image.html. Alternative option in_header: my_image.html does not seem compatible with the sidebar index.
Option 2
Insert image via yaml in index.rmd, using the solution under Tip 3 Add a Logo in your title/header/footer at this blog post
---
title: |
My title
Disadvantages:
i) When you hover over the image, it displays a copy of the image in a slightly different location (Can this "Hover" behaviour be disabled?)
ii) If using a web-based image, won't show in Rstudio viewer.
iii) If using a local image, path can get mixed up and won't show in online web html rendering
Option 3
The code below borrowed from here (which you can place below the top level heading) presumably goes direct through the knitting process and inserts itself in the final html. The issue is that the image doesn't make room for itself and ends up over the first text. Is there some simple html/css to sort this out?
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:0px;height:100px;" />
Disadvantages:
i) Image doesn't make room for itself and ends up over the first text. You can get around this with a hack by coding extra space (trial and error) through the yaml title like this:
title: |
.
.
.
.
site: bookdown::bookdown_site
EDIT
This is superseded by Radovan's accepted answer.
This was the best answer, taking option 3 from my previous answer, and combining a code approach to making the relevant space from Radovan's answer.
You will still have problems if you want to include a title in the YAML (I don't need this, as my title is in the image).
Also, on first loading the page, it presents nicely, but image is not seen if you go to the top of the document using the table of contents (the inheader approach used by this bookdown shows a better behaviour, but appears at the top of every chapter, which is not desired).
---
title: |
{height=300px}
output:
html_document: default
---
# I'm a top level heading {-}
<img src="https://i.imgur.com/GiViTbA.png" style="position:absolute;top:50px;height:300px;align:center;" />
Note, you need to replace the image with a local image if you want to show the image in the rstudio viewer.
The image will be visible in the html file created when you knit, if you open in a browser connected to the internet.
```{r echo=FALSE, message=FALSE, warning=FALSE}
plot(cars)
```
The problem of hovering the image duplicating the image can be fixed by removing the line below from the css file that is generated at \libs\gitbook-2.6.7\css\style.css
.book .book-header h1 a:hover{color:inherit;text-decoration:none}#media (max-width:1000px){.book .book-header h1{display:none}}
as a result, this code below places the image right above the title:
---
title: |
{width=400px style="display: block; margin:0 auto; align:center;" }
<center>GEOG380 Basic Stats with R</center>
---
I am trying to build a book, with 9 chapters. I am using the bookdown::bookdown_site package for that, which I have included in the YAML header in index.Rmd. But when I knit the book, using bookdown::tufte_book2, the pdf file generate the text inside the chunks with different font colors.
When I try to run each chapter individually, using "tufte_handout", the outcome is as expected. Main text and inside chunk text is monochrome and TimesNewRoman.
In rStudio, before build the book, I have tried in Sweave/Program defaults to use both Latex Engines, "xeLaTex" and "pdfLaTex"
YAML header in index.Rmd
---
title: "Operations Research Using R<br />"
author: "Timothy R. Anderson"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
monofont: Times New Roman
highlight: monochrome
documentclass: book
bibliography: ["Master4Bookdowns.bib"]
---
YAML header in each individual ChapterX.Rmd file:
---
title: 'Chapter 3: More LP Models'
header-includes:
- \usepackage{longtable}
- \usepackage{caption}
monofont: Times New Roman
output:
tufte::tufte_handout:
citation_package: natbib
latex_engine: xelatex
toc: TRUE
number_sections: true
highlight: monochrome
tufte::tufte_html: default
tufte::tufte_book:
citation_package: natbib
latex_engine: xelatex
highlight: monochrome
---
I expect all document with the same font type and monochrome.
Since bookdown::tufte_book2 is not specified in your main YAML header, I assume you have an _output.yml file that defines the output format. In that case, you have to add highlicht: monochrome there, i.e.:
bookdown::tufte_book2:
highlight: monochrome
[other options]
I'm writing a document in R Markdown and I'd like it to include a footer on every page when I knit a PDF document. Does anyone have any idea on how to do this?
Yes, this question has been asked and answered here: Adding headers and footers using Pandoc. You just need to sneak a little LaTeX into the YAML header of your markdown document.
This markdown header does the trick:
---
title: "Test"
author: "Author Name"
header-includes:
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhead[CO,CE]{This is fancy header}
- \fancyfoot[CO,CE]{And this is a fancy footer}
- \fancyfoot[LE,RO]{\thepage}
output: pdf_document
---
Works for me with an Rmd file in RStudio Version 0.98.1030 for Windows.
Another option would be to use the argument includes provided by rmarkdown::pdf_document() (documentation). This allows you to keep the footer in a separate file. If your footer is defined in footer.tex, the header of your R Markdown file would look like this:
---
output:
pdf_document:
includes:
after_body: footer.tex
---
This also assumes that footer.tex is in the same directory as the R Markdown file.
Update: The file footer.tex can contain any valid LaTeX that you want to be inserted at the end of your PDF document. For example, footer.tex could contain the following:
This \textbf{text} will appear at the end of the document.
To manage the height of the footer, you can use the following:
date: '`r paste("Date:",Sys.Date())`'
output:
pdf_document:
latex_engine: xelatex
header-includes:
- \setlength{\footskip}{-50pt} # set the footer size
Keep Coding!