I am using rmarkdown and knitr
I have two questions:
Q1: I am not sure why the figure caption does not appear when I build my rmarkdown document.
Here is an example. I get the figure there but with not the figure caption!
---
title: "Untitled"
author: "XXXX"
date: "9 September 2016"
output: pdf_document
---
## R Markdown
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
Q2: I am developing an R-package using RStudio. I am able to create an html_vignette using the code below. However, I am not sure why I am not able to create a PDF vignette when I change the output to output: rmarkdown::pdf_vignette? The latter gives an error:
Error: 'pdf_vignette' is not an exported object from 'namespace:rmarkdown'
Execution halted
---
title: "TITLE XXX"
author: "AMT"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{package-intro}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
I am new to this area, so if somebody can explain that would be great.
Related
I'm using R markdown to make a beamer presentation.
When I try to include an error message output from R on the slide it goes off the page.
Here is my code:
---
title: "Untitled"
author: "John Smith"
date: '2022-04-29'
output: beamer_presentation
---
This error message goes off the page
```{r cars, echo = TRUE, error=TRUE}
summary(carrrrrrrrrrrrrrrrs)
```
And, this is what the slides look like:
How do I keep the code on the page, either by putting it on multiple lines or reducing font size?
You can use the same technique as in Change representation (background-color & frame) of chunks in RMarkdown (with Beamer-Presentations) to redefine the verbatim environment in such a way that it uses the listings package. The listings package then allows you to both add line breaks and adjust the font size to your liking:
---
title: "Untitled"
author: "John Smith"
date: '2022-04-29'
output:
beamer_presentation:
keep_tex: true
header-includes:
- \let\verbatim\undefined
- \let\verbatimend\undefined
- \usepackage{listings}
- \lstnewenvironment{verbatim}{\lstset{breaklines=true,basicstyle=\ttfamily\footnotesize}}{}
---
This error message goes off the page
```{r cars, echo = TRUE, error=TRUE}
summary(carrrrrrrrrrrrrrrrs)
```
I cannot compile to a pdf-beamer from a very simple minimal example (below), with no packages.
I click - Knit - Knit to pdf
(Note this is not a duplicate of previous posts, because those all involved using Kable; I am not using it; fresh restart not calling any packages here)
I tried with and without classoption: table
Knit to html works just fine.
Restarted Rstudio; no improvement
---
title: "Untitled"
author: "Test"
date: "20 novembre 2018"
classoption: table
output:
beamer_presentation:
keep_tex: yes
---
# Test nothing
blah
```
Throws error: ! LaTeX Error: Option clash for package xcolor.
I want it to compile a beamer pdf slide show, of course.
I've put the log file here
My default.beamer (stored at /Users/yosemite/.pandoc/templates/default.beamer I think) is linked HERE
I wrote my own titlepage and it is loaded via an include in the R-markdown file. However, this conflicts with the pandoc title. I am trying to find settings in the R markdown yaml header such that pandoc does not insert the following code snipped into the tex-file.
% Create subtitle command for use in maketitle
\newcommand{\subtitle}[1]{
\posttitle{
\begin{center}\large#1\end{center}
}
}
\setlength{\droptitle}{-2em}
\title{}
\pretitle{\vspace{\droptitle}}
\posttitle{}
\author{}
\preauthor{}\postauthor{}
\date{}
\predate{}\postdate{}
There is no clear indication in the pandoc documents or the r markdown guidelines how to disable the title generation. Any help would be appreciated.
Update: In particular, I am looking for solutions that allow me to keep creating my title page with the \maketitle command. That is why I focussed on this particular code snipped that I want to get rid of.
I also use my own title page with rmarkdown documents for latex/pdf outputs. To remove the title, you can add the following command in a text file called with in_header :
\AtBeginDocument{\let\maketitle\relax}
A reproductible example with the header.tex file built directly within the Rmd document:
---
title: "RMarkdown No title Test"
author: "StatnMap"
date: "July 30, 2017"
output:
pdf_document:
includes:
in_header: header.tex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r rm_title_page, echo=FALSE}
head <- cat('
\\AtBeginDocument{\\let\\maketitle\\relax}
', file = "header.tex")
```
# Title 1
**Some text**
# Title 2
**Some text**
Using compact-title: false in the YAML works.
---
title: "This title is not compact"
author: "Test"
date: "2019 May 10"
output: pdf_document
compact-title: false
---
I had the same problem today. Here's what I did. (Maybe I'll update the solution when I come up with something better.)
The solution is dumb but useful. I can't set an arbitrary space between the lines now, because I used \newline.
---
title: "\\huge My Smart Title"
author: "\\newline \\Large My Smart Author"
date: "\\newline \\Large 2018-12-25"
output:
pdf_document:
includes:
in_header: preamble.tex
latex_engine: xelatex
---
Below are the outputs before and after the solution.
BEFORE:
AFTER:
Note:
You may be confused about the different sizes of the "author" and the "date" in the two pictures above, if you don't know that the fontsize of the "author" and the "date" is \large instead of \Large by default.
END
I'm trying to run inline R code in the YAML front matter before getting rmarkdown to run the file. However it isn't working for me. Here's an example:
---
title: "**Title**"
classoption: xcolor=dvipsnames
output:
beamer_presentation:
slide_level: 2
pandoc_args: [
"--bibliography", "`r paste('path/to/bib')`"
]
---
<!-- slide 1 -->
## Intro ##
Which throws an error:
pandoc-citeproc: could not find `r paste('path/to/bib')`
This is a simple example, but highlights my main problem. How do I get rmarkdown to run the inline R code in the YAML front matter?
It is a similar problem to these questions:
Manipulate RMarkdown metadata from within R code chunks
YAML current date in rmarkdown
This is how I solved this. I knit from RStudio. Curiously, I had to use one solution for the date and csl fields and a different solution for the bibliography field. !expr did not work in the date or csl lines (for me). And quoted r code didn't work in the bibliography line (for me). I have the bibliography and csl files in a package (inst/docs folder). rmarkdown files, which are not part of that package, use those.
---
title: "Title"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: html_document
bibliography: !expr system.file("docs", "my.bib", package = "MyPackage")
csl: '`r system.file("docs", "my.csl", package = "MyPackage")`'
---
# Introduction
Yada yada [#MyRef04].
# References
my.bib is the BibTex file with MyRef04. csl is the style file
This is a situation where one person maintains a package which has data, code, bibliography, etc. Others, potentially unknown to the package writer, install that package from GitHub and write or run rmarkdown files that use the package. The users almost certainly do not use Git or GitHub and I don't want them to have to download any extra files after installing the package from GitHub.
Update: After posting the above, I happened to install markdown from GitHub because I needed something in the development version. With version ‘1.7.5’ of rmarkdown on GitHub you can use r code in the bibliography line:
---
title: "Title"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: html_document
bibliography: '`r system.file("docs", "my.bib", package = "MyPackage")`'
csl: '`r system.file("docs", "my.csl", package = "MyPackage")`'
---
To install rmarkdown from GitHub
library(devtools)
install_github("rstudio/rmarkdown")
So I found a round about way of getting what I wanted. Rmarkdown I don't think allows R expressions/commands in the YAML, probably for a good reason. What I ended up doing was putting all the output yaml commands in a file called _output.Ryaml like so:
beamer_presentation:
slide_level: 2
includes:
in_header: "src/preamble.tex"
pandoc_args: [
"--bibliography", "`r paste('path/to/bib')`",
"--variable", "classoption:xcolor=dvipsnames",
"--variable", "fontsize:9pt"
]
Then in the main slides.Rmd file, was something like:
---
title: "**Title**"
author: Luke
---
<!-- slide 1 -->
## Intro ##
Then, I can generate the slides using the R code (which I put into a Makefile):
knitr::knit('_output.Ryaml', '_output.yaml')
rmarkdown::render('slides.Rmd')
unlink('_output.yaml')
Seems to be working well enough. If anyone's got a better idea, let me know!
I am attempting to create an rmarkdown document. I have finally figured out a way to approach this, although it has taken quite some time. The last thing I would like to be able to do is to add an image to the title page of my pdf document.
The trouble I have is that my title page is defined by the top section of YAML. Below is the contents of my example.Rmd file. I use the Knit PDF button in RStudio to turn it into a PDF.
---
title: "This is a my document"
author: "Prepared by: Dan Wilson"
date: '`r paste("Date:",Sys.Date())`'
mainfont: Roboto Light
fontsize: 12pt
documentclass: report
output:
pdf_document:
latex_engine: xelatex
highlight: tango
---
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r, echo=FALSE}
plot(cars)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
If anyone has some tips that would allow me to put an image (logo.png) above my title that would be great.
Based on the previous solution, the following code does not require an auxiliary header.tex file. All contents are contained in the .Rmd file. The LaTeX commands are instead defined in a header-includes block in the YAML header. More info can be found here.
Replace my_graphic.png below with your local graphic file.
---
title: "A title page image should be above me"
header-includes:
- \usepackage{titling}
- \pretitle{\begin{center}\LARGE\includegraphics[width=12cm]{my_graphic.png}\\[\bigskipamount]}
- \posttitle{\end{center}}
output:
pdf_document:
toc: true
---
\newpage
# Section 1
Some text.
I was able to solve this using LaTeX package titling
---
title: "Untitled"
author: "Name"
date: "September 19, 2015"
output:
pdf_document:
includes:
in_header: header.tex
---
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r, echo=FALSE}
plot(cars)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
Where the header.tex should include the following code:
\usepackage{titling}
\pretitle{%
\begin{center}
\LARGE
\includegraphics[width=4cm,height=6cm]{logo.png}\\[\bigskipamount]
}
\posttitle{\end{center}}
and replace logo.png with the image you would like to use and make sure the file is in the root directory of your Rmd file. You can change image width and height to your needs. For more information on available options go to titling
For a beamer presentation you can do it like this:
title: "Title"
subtitle: "Subtitle"
author: "author"
date: "date"
header-includes:
- \titlegraphic{\centering \includegraphics[width=12cm]{titlepic.png}}
output:
beamer_presentation:
latex_engine: xelatex
theme: "metropolis"
highlight: "espresso"
classoption: "aspectratio=169"
The titlegraphic will be placed below your title text
For beamer presentation if you want an image at the bottom you can kind of cheat and add the image where the date line should be. Then if you want to insert date you can add institution (which is before date). the ![] should be tabbed (4 spaces from the far left of the page)
date: |
{width=3in}