I feel like this is a straight forward thing, but everything I find doesn't quite get me what I want. I'm using rmarkdown and knitting to a latex .pdf. I'd like to have my in-text citations have round () parenthesis instead of the block ones. The yaml below uses a references.bib file to correctly import the references. Is there anything I can do to easily change my parenthesis to round?
---
title: "Title"
author: "Author"
date: "16/03/2020"
output:
pdf_document:
fig_caption: yes
citation_package: natbib
bibliography: references.bib
editor_options:
chunk_output_type: console
---
I've used an approach here, but it returns an error:
Error in yaml::yaml.load(..., eval.expr = TRUE) :
Parser error: while parsing a block mapping at line 6, column 5 did not
find expected key at line 7, column 30`
---
title: "Title"
author: "Author"
date: "16/03/2020"
output:
pdf_document:
fig_caption: yes
bibliography: references.bib
editor_options:
chunk_output_type: console
\usepackage[round]{natbib}
---
Any ideas? Thanks for your suggestions / ideas...
The problem with your attempt to include \usepackage[round]{natbib} in the rmarkdown header is that rmarkdown seems not clever enough to parse commands with optional arguments. One can trick it by hiding the command in a .tex file
---
title: "Title"
author: "Author"
date: "16/03/2020"
output:
pdf_document:
fig_caption: yes
includes:
in_header: preamble.tex
bibliography: references.bib
---
test [#knuth]
with preamble.tex
\usepackage[round]{natbib}
https://rstudio.cloud/project/1061588
Using the header-includes: option should fix the issue.
---
title: "Title"
author: "Author"
date: "16/03/2020"
output:
pdf_document:
fig_caption: yes
citation_package: natbib
bibliography: references.bib
editor_options:
chunk_output_type: console
header-includes:
- \usepackage[round]{natbib}
---
Related
For a project, I would like the knitr-output when choosing for a HTML to enable code folding, but to hide all code when knitting a word document.
My current RMarkdown YAML:
---
title: "Title"
author: "me"
output:
bookdown::html_document2:
code_folding: hide
number_sections: false
word_document:
reference_docx: reference.docx
# Option to hide code in word document?
pdf_document:
latex_engine: xelatex
bibliography: references.bib
link-citations: yes
editor_options:
markdown:
wrap: 72
linestretch: 2
lang: en
---
Is there an option for the word_document YAML-tag to make this possible? Or another workaround or package? If you set echo=FALSE or include=FALSE in the R chuncks, then this also omits the code in the HTML document. Looked around in RMarkdown documentation and different forums, but can't find a way to achieve this.
One option would be to use knitr::is_html_output to check whether you are rendering to HTML or not. This could then be used to conditionally set echo=FALSE for non-HTML output:
---
title: "Title"
author: "me"
output:
word_document:
# Option to hide code in word document?
#reference_docx: reference.docx
bookdown::html_document2:
code_folding: hide
number_sections: false
pdf_document:
latex_engine: xelatex
---
```{r include=FALSE}
if (!knitr::is_html_output()) knitr::opts_chunk$set(echo=FALSE)
```
```{r}
library(ggplot2)
ggplot(mtcars, aes(hp, mpg)) +
geom_point()
```
Word Output
HTML Output
I am knitting a pdf file from Rmd.. My working dir includes the .Rmd file and pdf output. Knitr sends all figures to the figure folder because I set the figure path to fig.path <- "figure/". But when I knit the pdf file, it gives me an error: ! LaTeX Error: File `figure/figure-1' not found. although all figures are in the figure folder. Something is wrong with my directories but I cannot figure out what exactly.
Here is my setting:
---
title: "Paper"
subtitle: "\\textsc{Online Paper}"
df_print: paged
author: "Anonymous"
output:
pdf_document:
extra_dependencies: flafter
includes:
# in_header: Helper/header.tex
latex_engine: xelatex
number_sections: yes
link-citations: yes
html_document:
df_print: paged
# bibliography: Helper/bibtex.bib
biblio-style: apa6
link-citations: yes
linkcolor: blue
urlcolor: blue
---
I am using rticles::elsevier_article to write a manuscript. I am not able to add the linenumber properly. What I did:
header-includes:
- \usepackage{lineno}
- \linenumbers
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article
But, in this case when having equations the line numbers are not added, and neither the sections where the equations are embedded. Any suggestion?
Seems like your YAML is malformatted. Better to do it like this:
bookdown::pdf_book:
base_format: rticles::elsevier_article
includes:
in_header: "preamble.tex"
Then add additional LaTeX header lines to preamble.tex:
\usepackage{booktabs}
\usepackage{lineno}
\linenumbers
Example
index.Rmd
---
title: "A Minimal Book Example"
author: "You"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article
includes:
in_header: "preamble.tex"
abstract: "This is your awesome abstract"
---
# Introduction
```{r, results='asis'}
cat(
stringi::stri_rand_lipsum(1)
)
```
(The code chunk requires the stringi package to be installed.)
How do I use \label and \ref to link sections in rmarkdown when outputting to pdf please. I have tried various permutations from https://bookdown.org/yihui/bookdown/cross-references.html and https://bookdown.org/yihui/rmarkdown-cookbook/cross-ref.html with no success.
One attempt
---
title: "Untitled"
output: pdf_document
---
See Section \#ref(sec:label).
# Section One (\#sec:label)
which gives
You can modify your document as follows:
---
title: "Untitled 1"
date: "28 de junio de 2020"
link-citations: yes
output:
pdf_document:
includes:
keep_tex: yes
number_sections: yes
toc_depth: 2
---
\section{This is the first section} \label{section1}
You will be some in \ref{section1}
Then you can see how numbers appear, just add \label{} to your sections and use \ref{} to call. Also, I suggest using \section{}, and modify YAML as I included. Hoping this can help.
I'm not getting a pdf output from my rnotebook.
My header in my "index.Rmd" is:
---
title: "some title"
author: "me"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "Notes on a Leasing Company busines risk and opportunities."
---
I'm rendering the book in the console with the following code:
bookdown::render_book("index.rmd", output_format = "bookdown::pdf_book")
Output is:
Error: Functions that produce HTML output found in document targeting latex output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:
always_allow_html: yes
Note however that the HTML output will not be visible in non-HTML formats.
How do I go about changing the output type?
My file "_output.yml" file is:
toc:
before: |
<li>A Minimal Book Example</li>
after: |
<li>Published with bookdown</li>
download: ["pdf", "epub"]
bookdown::pdf_book:
includes:
in_header: preamble.tex
latex_engine: xelatex
citation_package: natbib
keep_tex: yes
bookdown::epub_book: default