Cross reference and caption not working in Rmd file - r

Can anyone help me understand how to write my header so that the figure caption and cross reference works?
I am practicing making captions and cross references to a simple plot in my Rmd file. I understand that to do so, I should add to my header: "output: bookend::pdf_document2" and "fig_caption = yes". Then, to a chunk called myfigure, I should add "fig.cap = "\label{fig:myfigure} My caption". To cross reference this figure I should write in the text "#ref(fig:myfigure)". My code is below. It won't knit because the formatting of the header is wrong.
---
title: "knit"
author: "Chase Hommeyer"
date: "4/1/2019"
output: bookdown::pdf_document2
toc: true
fig_caption: yes
---
```{r myfigure, fig.cap = "\\label{fig:myfigure} My caption"}
plot(pressure)
```
My plot is called \#ref(fig:myfigure).
Then, I tried deleting the whitespace before toc and fig_caption, and it knit, but no caption appeared, and the text literally printed "#ref(fig:myfigure)" instead of a cross reference. The header I tried is here:
---
title: "knit"
author: "Chase Hommeyer"
date: "4/1/2019"
output: bookdown::pdf_document2
toc: true
fig_caption: yes
---
I also tried adding "pdf_document:" to the header, but the same issue of no caption and the cross reference being literally "#ref(fig:myfigure)". This header I tried is here:
---
title: "knit"
author: "Chase Hommeyer"
date: "4/1/2019"
output: bookdown::pdf_document2
pdf_document:
toc: true
fig_caption: yes
---
Can anyone help me understand how to write my header so that it works?

use \ref{fig:myfigure} instead of \\#ref(fig:myfigure)
See RStudio Community Post

You have a wrong YAML header and some wrong understanding of referencing. I used this RMD file:
---
title: "knit"
author: "Chase Hommeyer"
date: "4/1/2019"
output:
bookdown::pdf_document2:
toc: true
fig_caption: yes
---
```{r myfigure, fig.cap = "My caption"}
plot(pressure)
```
My plot is called Figure \#ref(fig:myfigure).
First, break the line after output in the header. The whitespaces are very important in the YAML header!
Then, read the bookdown manual:
The label of a figure environment is generated from the label of the code chunk, e.g., if the chunk label is foo, the figure label will be fig:foo (the prefix fig: is added before foo). To reference a figure, use the syntax, where label is the figure label, e.g., fig:foo.
To reference your plot with the chunk name "myfigure", just write \#ref(fig:myfigure). The caption of the figure can be set via fig.cap in the chunk options.

Related

RMarkdown: Customize Color and Font Size of (automated) Citations

I am fairly new to RMarkdown and trying to apply some LaTeX logic here. Currently, I am creating a PDF presentation with RMarkdown (beamer_presentation). Is it possible to change the font size and color of automatic citations ([#shortname]) so that e.g., all citations appear slightly smaller than the normal text and in gray?
In LaTeX beamer presentations, I managed to re-define the cite command and apply this. I was not yet able to recreate this in RMarkdown however.
When I was trying to manually (I'd much prefer automatic a solution) change the font color of citations \textcolor{gray}{[e.g., #shortname]} (also $\textcolor{gray}{[e.g., #shortname]}$), I received this error message:
I was unable to find any missing LaTeX packages from the error log slides.log. ! Missing $ inserted. $ l.182 \end{frame} Try to find the following text in slides.Rmd: \end{frame}
You may need to add $ $ around a certain inline R expression r in slides.Rmd (see the above hint). See https://github.com/rstudio/rmarkdown/issues/385 for more info.
The link in the error message did not help me either.
I am grateful for your help! I'll include a MWE below.
Till
---
title: "A title"
author: "Till"
date: 25.07.2022
output:
beamer_presentation:
incremental: true # bullet points on multiple pages
toc: false # add generated page listing sections
slide_level: 2 # depth level for render content
latex_engine: lualatex
keep_tex: TRUE
bibliography: literature.bib
csl: american-sociological-association.csl
header-includes: \usepackage{xcolor}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(tinytex.verbose = TRUE) # for debugging
```
# First Section
## Example Slide
- Some text which will be followed by a citation \textcolor{gray}{[e.g., #shortname]}
- Some more text, now without a citation
The literature.bib file could look somewhat like this:
#article{shortname,
title = {citation title},
journaltitle = {Journal},
shortjournal = {Journal},
author = {Lastname, Firstname},
date = {2022},
}
The problem with your \textcolor approach is that you can't use markdown syntax in the argument of a latex macro. You can avoid this problem by using \begingroup \color{gray} [e.g., #shortname] \endgroup:
---
title: "A title"
author: "Till"
date: 25.07.2022
output:
beamer_presentation:
incremental: true # bullet points on multiple pages
toc: false # add generated page listing sections
slide_level: 2 # depth level for render content
latex_engine: lualatex
keep_tex: TRUE
bibliography: literature.bib
csl: american-sociological-association.csl
header-includes: \usepackage{xcolor}
---
#```{r setup, include=FALSE}
# I did not know how to include R-Chunks in the code block withouth breaking the formatting, so just remove the Hashtags before the three ticks and this endless comment
knitr::opts_chunk$set(echo = TRUE)
options(tinytex.verbose = TRUE) # for debugging
#```
# First Section
## Example Slide
- Some text which will be followed by a citation \begingroup \tiny\color{gray} [e.g., #shortname] \endgroup
- Some more text, now without a citation

bookdown - how to get figure title above figure and figure notes below figure when using word_document2

I am trying to switch from LaTeX to RMarkdown+bookdown when writing a paper that includes tables and figures. One main motivation is to be able to create both Word documents and PDF documents.
For word_document2, how can I add a figure title/caption above the figure as well as figure notes below the same figure?
Here is how I would do it in LaTeX (and it would be convenient to continue using LaTeX as I am transferring everything over from LaTeX to RMarkdown).
\begin{figure}
\caption{Figure Title...}
\label{figure_label}
\vspace*{.2cm}
\includegraphics[width=7in]{figure_name.png}\\
\caption*{Figure Notes...}
\end{figure}
More broadly, is it possible to use LaTeX code with word_document2?
Note that my preamble currently looks like:
---
title: "..."
author: "..."
date: "10/14/2021"
output:
bookdown::word_document2:
number_sections: false
bookdown::pdf_document2:
number_sections: false
header-includes:
- \usepackage{floatrow}
- \floatsetup[figure]{capposition=top}
citation_package: default
bibliography: ../references.bib
always_allow_html: true
---
And I am currently able to get the caption above the figure, but just for the pdf_document2 (see Caption above figure using knitr (LaTeX/PDF)):
```{r figure-label, fig.cap="Figure Title", fig.width=6, fig.height=3.7, fig.align="center"}
...
This doesn't seem to work when creating the Word document.
yihui says in his documentation¹ we can use the officedown² package to influence word layouts. It has the Plot- option topcaption: you can set it to true as shown below.
[¹] https://bookdown.org/yihui/rmarkdown-cookbook/word-officedown.html
[²] https://cran.r-project.org/web/packages/officedown/index.html
---
title: "..."
author: "..."
date: "10/14/2021"
output:
officedown::rdocx_document:
plots:
style: Normal
align: center
topcaption: true
bookdown::pdf_document2:
number_sections: false
header-includes:
- \usepackage{floatrow}
- \floatsetup[figure]{capposition=top}
citation_package: default
---
```{r figure-label, fig.cap="Top Caption", fig.width=6, fig.height=3.7}
plot(rnorm(1000,300,32))
library(officedown)
``
this should give you a docx with figure captions on top.

How to remove compact title from R markdown to latex conversion?

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

Figure name in caption using RMarkdown

I am writing my first .rmd report using RMarkdown and then I knit it to pdf file. As I write it in my national language, I would like to have figures captions in my language too. The problem is that the default caption format is "Figure 1: My caption". I would like to change this generative "Figure 1:" part but I couldn't find how. Any help will be appreciated.
Try specifying the language in the YAML header of an rmarkdown document (documentation link):
---
title: "Crop Analysis Q3 2013"
output: pdf_document
fontsize: 11pt
geometry: margin=1in
lang: german
---
The language code will be processed by the babel LaTeX package (at least in the case of pdflatex).
I found out that it is possible to do using LaTeX:
---
title: "My raport"
output:
pdf_document:
fig_caption: yes
header-includes:
- \usepackage{caption}
---
\def\figurename{MyFigureName}
Still: is there any simpler way?
It should work like this:
---
output:
pdf_document:
fig_caption: true
---
```{r figWithCaption, echo=F, fig.cap="My Figure Caption"}
plot(cars) # your figure
```

How to add table of contents in Rmarkdown?

I am using RStudio for writing markdown documents and want to add Table of Contents (TOC) at top of the documents so that the user could click the relevant section for reading. There were some relevant examples on rpubs but now I can't seem to find them. Please note that I don't use pandoc and am quite new to Rmd & knitr. Is there any way to add TOCs without using pandoc? If using pandoc is must then which functions are relevant?
EDIT
Here's a small sample page:
---
title: "Sample Document"
output:
html_document:
toc: true
theme: united
---
Header 1
---------------
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>.
## Header 2
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)
```
### Header 3
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
I tried running this in RStudio v 0.98.864 and it worked! but sadly it didn't work on 0.98.501 and 0.98.507. I am working on my thesis in 0.98.501 and after updating RStudio, some of my analyses didn't work. So, I reverted back to 0.98.501.
What should I do now? I really want TOCs but without harming the outputs of other analyses.
The syntax is
---
title: "Sample Document"
output:
html_document:
toc: true
theme: united
---
in the documentation. Make sure this is at the beginning of your document. Also make sure your document actually has headers otherwise R can't tell what you want in the table of contents.
Syntax with more options:
---
title: "Planets"
author: "Manoj Kumar"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
html_document:
toc: true # table of content true
toc_depth: 3 # upto three depths of headings (specified by #, ## and ###)
number_sections: true ## if you want number sections at each table header
theme: united # many options for theme, this one is my favorite.
highlight: tango # specifies the syntax highlighting style
css: my.css # you can add your custom css, should be in same folder
---
If you are using pdf_document, you might want to add table of contents in a new page, which toc: true does not allow. It puts the table of contents right after the document title, author and date--because it is in yaml.
If you want to have it in a new page, you have to use some latex language. Here is what I did.
---
title: \vspace{3.5in}"Title"
author: "Name"
date: "`r Sys.Date()`"
output:
pdf_document:
fig_caption: true
number_sections: true
---
\newpage # adds new page after title
\tableofcontents # adds table of contents
\listoffigures
\listoftables
\newpage
So, after yaml (the chunk between ---), I added a new page using \newpage, then a table of contents using \tableofcontents, a list of figures using \listoffigures, a list of tables \listoftables, and a new page before everything else.
Note, \vspace{3in} in the title adds vertical space of 3 inch from the top before printing yaml (title, etc.).
Read more here: https://www.sharelatex.com/learn/Table_of_contents

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