Input data
I prepared an example Rmd file with references to figure, table and equation, setting as an output 'bookdown::pdf_document2'. It compiles without errors to PDF.
I placed it on dropbox:
https://www.dropbox.com/sh/zmu0a4wq95ywssv/AAD-nHlkDiLknLk2NVR4Xup3a?dl=0
Question
Now I wish to set as an output format 'rticles::elsevier_article'
How can I do that?
Issue
When I change output line from:
bookdown::pdf_document2
to
rticles::elsevier_article
I'm receiving an error message.
Even if I remove other parameters from output:
I still receive an error message:
! Undefined control sequence.
Accented characters when input "as is" do not appear to behave well with elsevier_article. See suggestions below.
Bare-bones document
Here is a bare-bones document using rticles::elsevier_article:
---
title: "Sample document"
author:
- name: "Mateusz Kędzior"
affiliation: Some Institute of Technology
email: Mateusz#example.com
footnote: Corresponding Author
- name: Żąćł Źęń
csl: https://www.zotero.org/styles/geoderma
output:
rticles::elsevier_article:
citation_package: natbib
keep_tex: yes
number_sections: yes
toc: no
keywords: keywordA, keywordB
abstract: This is a sample abstract \newline This is the second line of abstract.
---
Hello world.
which renders with no complaints:
Reference with accents
Now, we wish to add a reference with accents. We follow the answer here: https://tex.stackexchange.com/questions/57743/how-to-write-%C3%A4-and-other-umlauts-and-accented-letters-in-bibliography. I imported your bibliography into Zotero, and then exported the item with a "Central European (ISO)" encoding (not UTF-8) to obtain
#article{kedzior_this_2018,
title = {This is sample title only {\k A} {\L }},
volume = {99},
url = {http://megooglethat.com/},
journal = {Some journal},
author = {K{\k e}dzior, Mateusz and {\'Z}{\k e}{\'n}, {\.Z}{\k a}{\'c}{\l }},
year = {2018},
keywords = {keywordC},
pages = {21 -- 31}
}
The R Markdown document now becomes
---
title: "Sample document"
author:
- name: "Mateusz Kędzior"
affiliation: Some Institute of Technology
email: Mateusz#example.com
footnote: Corresponding Author
- name: Żąćł Źęń
csl: https://www.zotero.org/styles/geoderma
output:
rticles::elsevier_article:
citation_package: natbib
keep_tex: yes
number_sections: yes
toc: no
biblio-files: bibliography2.bib
keywords: keywordA, keywordB
abstract: This is a sample abstract \newline This is the second line of abstract.
---
## Citations and references
Let me cite an article: [#kedzior_this_2018]
# References
I then knited this in RStudio, but realised that I had to get the tex output and rebuild it (outside of RStudio) to get the desired output
Other problems
For accented characters in figure captions, encode them accordingly (as with the bibliography). You may find http://w2.syronex.com/jmr/latex-symbols-converter helpful. In addition, to the best of my knowledge bookdown style cross-referencing does not work with rticles. If you have follow-up questions, you may get more helpful answers if you break your question down into smaller chunks.
I've added a bit of updated material to the commenthttps://github.com/rstudio/rticles/issues/92#issuecomment-402784283 where it states (may be updated):
output:
bookdown::pdf_document2:
base_format: rticles::elsevier_article
number_sections: yes
such that the way I've had this work is using pdf_book versus pdf_document2:
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article
number_sections: yes
This allows for figure and table referencing within an rticles document.
Related
I am rather experienced with R but new to markdown and especially bookdown. I wonder how to render a single chapter and merge it with the existing book without re-building the whole book. The reason why I am asking is that I am creating a book that contains parameterised chapters and each chapter runs very long (1-2 hours). All in all, it will be hundreds of chapters with the same analysis, but different input data and would time-wise add up. I am aware of the knit-and-merge approach, in fact, that's the reason why I chose bookdown, but somehow it is not working as expected.
I am honestly also a little bit confused by the different rendering possibilities. There is the built-book button, the knit button, serve_book(), render_book(), preview_chapter(), ... I figured that one should avoid using the knit button in bookdown and that serve_book() will automatically compile changes. My approach so far is entering serve_book() into console, where it renders the whole book, then I create a new chapter, hit save and it runs the chunks of only that chapter (exactly what I want!) and the single HTML file of the new chapter appears. However, it doesn't show them when I look at the book via the index.html file.
I am only interested in an HTML book and do not need any other output formats.
In order to recreate the problem, I am just using the bookdown example and adding chapters to it.
_bookdown.yaml
book_filename: "book_name"
new_session: yes #true
before_chapter_script: _common.R
delete_merged_file: true
language:
ui:
chapter_name: "Chapter "
_output.html
bookdown::bs4_book:
css: style.css
theme:
primary: "#10395B"
#repo: https://github.com/rstudio/bookdown-demo
bookdown::pdf_book:
includes:
in_header: preamble.tex
latex_engine: xelatex
citation_package: natbib
keep_tex: yes
bookdown::epub_book: default
_index.yaml
---
title: |
{width=200px}|
|-|
||
author: "Name"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
#output: bookdown::bs4_book
documentclass: book
bibliography: [book.bib, packages.bib]
# url: your book url like https://bookdown.org/yihui/bookdown
# cover-image: path to the social sharing image like images/cover.jpg
description: |
This is a minimal example of using the bookdown package to write a book.
The HTML output format for this example is bookdown::bs4_book,
set in the _output.yml file.
biblio-style: apalike
csl: chicago-fullnote-bibliography.csl
---
# About {-}
I would appreciate any help!
Thanks in advance :)
I am writing a report with R Markdown in which I include references. The problem is that R markdown automatically places references at the end of the report. I would like to place an Appendix after the references, is there a way to do it? I saw that it is possible with a child document but I would like to have everything in a unique .Rmd file.
Below is a reproducible example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
\cite{greenwood_financial_1989}
<!-- where I would like the references to be -->
# Appendix
bla bla
and here is the content of the references.bib file:
#article{greenwood_financial_1989,
title = {Financial Development, Growth and the Distribution of Income},
url = {https://www.nber.org/papers/w3189},
number = {3189},
journaltitle = {NBER Working Paper Series},
date = {1989},
author = {Greenwood, Jeremy and Jovanovic, Boyan}
}
Any idea ?
This is explained in the R Markdown Cookbook (section 3.5.4). We can force the bibliography to be printed at a particular place with:
# References
<div id="refs"></div>
# Appendix
Note that:
this works if we cite the papers with #id_of_paper (which is the recommended way in R Markdown) but not with \cite{id_of_paper}.
this does not work if we use citation_package: biblatex in YAML
Here's my adapted example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
#greenwood_financial_1989
# References
<div id="refs"></div>
# Appendix
bla bla
If using
citation_package: biblatex
you can include the bibliography at an arbitrary point using
\printbibliography
This does not, of itself, stop pandoc adding a (further) end-of-document bibliography, but since pandoc ignores latex in non-latex output, we can suppress that by redefining \printbibliography on the fly to do nothing.
So try this, for a references section preceding an Appendix:
# References
<div id="refs"></div>
\printbibliography[heading=none]
\def\printbibliography{}
# Appendix 1
Appendix goes here, and is not followed by a bibliography.
I am writing a report with R Markdown in which I include references. The problem is that R markdown automatically includes references at the end of the report (without calling them with \printbibliography for example) and the section title is "References". I am writing in French so I would like the title to be "Références", but more generally is there any way to modify the title of that section?
Below is reproducible example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
\cite{greenwood_financial_1989}
# Partie 2
bla bla
and here is the content of the references.bib file:
#article{greenwood_financial_1989,
title = {Financial Development, Growth and the Distribution of Income},
url = {https://www.nber.org/papers/w3189},
number = {3189},
journaltitle = {NBER Working Paper Series},
date = {1989},
author = {Greenwood, Jeremy and Jovanovic, Boyan}
}
Does anybody have a solution?
Here's the solution that combines this answer on doing something similar with bibtex and this one on the TeX required to do it in biblatex, plus #Ralf's comment about adding lang: fr
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
lang: fr
---
In my document, I used :
header-includes:
- \usepackage[french]{babel}
And your Contents section also changes.
I had a similar problem I wanted to place the bibliography above a supplemental section and placing <div id = "refs"></div> where you want the references successfully repositioned the section. I also had no problem renaming the section by simply changing the # title above that section. This did work for PDF output as well as HTML despite appearing to be an HTML only solution, though I was also using the markdown flavored ([#Smith2019]) references in the body of my document I don't know if using the LaTeX style will affect things.
I am trying to generate dynamic PDF reports from Rmarkdown with dynamic titles. To do this I use the function rmarkdown::render() in my R script and I pass in the argument params the title parametre as set.title = title.
The YAML of my Rmarkdown script I have the next code:
author: "Author test"
date: "`r Sys.setlocale('LC_TIME','C');format(Sys.Date(),'%B %d, %Y')`"
output:
pdf_document:
toc: yes
toc_depth: 5
keep_tex: yes
html_document:
theme: united
toc: yes
classoption: table
header-includes:
- \usepackage{array}
- \usepackage{float}
- \usepackage{xcolor}
- \usepackage{caption}
- \usepackage{longtable}
#- \usepackage{mulicol}
params:
set.title: title
title: "`r params$set.title`"
Once I run my code everything goes well and generate the different pdfs that I expect, the problem is that neither of these PDFs show the title, author and date. I am working with version 1.8 of rmarkdown package.
Can anyone help me with this issue?
For closing the conversation of this question I write how has been solved this question.
At the beginning I was thinking this issue was related with the code in YAML (where the title was informed from parameters) but eventually I discovered that there was nothing to do that. The problem was that I was using a the function cat() in the varible title that I pass as a parametre and this function changes the value of variable title into NULL.
For knowing exactly all the explanation about how to write dynamic titles in rmarkdown documents redirect yourself to the next entrance: Setting document title in Rmarkdown from parameters
I defined keywords in the .Rmd file, but they are not visible in the output PDF.
Current Output
Expected results
Current .Rmd
First lines of .Rmd file looks as follows:
---
title: "No keywords within the output file"
abstract: "This is sample text for abstract. Generally speaking, I would like to show keywords list below an abstract (as in case of the linked example)"
keywords: "keywordA, keywordB"
author: "Mateusz Kędzior"
output:
bookdown::pdf_document2:
keep_tex: true
number_sections: yes
toc: false
base_format: rticles::elsevier_article
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Elsevier article
This is an R Markdown document.
I'm trying to prepare an Elsevier article.
I wonder if base_format is actually doing any work in your example (the output looks the same with and without base_format). Since base_format is an argument to pdf_book, consider changing your YAML header to
---
title: "No keywords within the output file"
author:
- name: "Mateusz Kędzior"
abstract: "This is sample text for abstract. Generally speaking, I would like to show keywords list below an abstract (as in case of the linked example)"
keywords: "keywordA, keywordB"
output:
bookdown::pdf_book:
keep_tex: true
number_sections: yes
toc: false
base_format: rticles::elsevier_article
---
which gives you the following output:
Alternatively, add keywords to the abstract:
abstract: "This is sample text for abstract. Generally speaking, I would like
to show keywords list below an abstract (as in case of the linked example) \\par
\\textbf{Keywords:} a, b"
to get