For html_document or pdf_document, there have been solutions to suppress automatic table name and number, [for example,] (How to suppress automatic table name and number in an .Rmd file using xtable or knitr::kable?).
However, adding the following in the YAML section
header-includes:
- \usepackage{caption}
and the following before the code chunk
\captionsetup[table]{labelformat=empty}
does not work for html_document2.
Knitted from the following .rmd file, the automatic table name and number "Table 1.1: " cannot be disabled in the output html file. Thanks in advance for help!
---
title: "Suppress automatic table name and number"
author: Generated by bookdown
output:
bookdown::html_document2: default
header-includes:
- \usepackage{caption}
---
# https://bookdown.org/yihui/rmarkdown-cookbook/cross-ref.html
\captionsetup[table]{labelformat=empty}
```{r myirischunk, results = 'asis', tab.cap = NULL, echo = TRUE}
print(knitr::kable(head(iris), caption = "Table 1.a - First own table name"))
print(knitr::kable(tail(iris), caption = "Table 1.b - Last own table name"))
Related
Basically i want to build a random multiple choice question generator with R Markdown. For this task there need to be equations in the code chunks of the markdown.
The following works like a charm and gives the equation "greekbeta = 1"
---
title: "test"
author: "me"
output:
word_document: default
---
```{r eval=TRUE, echo=FALSE,results = "asis"}
"$\beta = 1$"
```
In contrast, this will not work when some other math symbol is used, for example:
---
title: "test"
author: "me"
output:
word_document: default
---
```{r eval=TRUE, echo=FALSE,results = "asis"}
"$\sum_{n=1}^{\infty}$"
```
After pressing knit, an error occurs (unfortunately the error message is in german, basically this: "'\s' is an unknown escape-sequence within the string starting with "$/s"").
I am very puzzled by this, especially because for example \frac{1}{2} works, but \hat{x} does not. Equations in the "normal" markdown text are no problem at all. But for my task, the equations have to be in the code chunk sections.
Does someone has a workaround for this problem? I tried using "$\hat{x}$" or even "$$\hat{x}$", but the error message is still the same.
I am using pandoc 2.11.4, R 4.1.0 and knitr 1.33
Use cat() and escape the escapes.
---
title: "test"
author: "me"
output:
word_document: default
---
```{r eval=TRUE, echo=FALSE,results = "asis"}
cat("$\\beta = 1$", '\n\n')
cat("$a^2+b^2 = c^2$", '\n\n')
cat("$\\sum_{n=1}^{\\infty}x_i$", '\n\n')
```
I'm compiling a report using Papaja and Rmarkdown, and I want to highlight various text throughout. Doing so with latex or pure Rmarkdown is easy, but I'm receiving an "undefined control sequence" error when I compile the report to PDF using Papaja's application of Knitr.
A similar question about text highlighting within a single Rmarkdown file was answered here: RMarkdown / pandoc fails to knit Pdf with latex color commands. I'd like to know if an answer exists for multiple Rmarkdown files using Papaja.
I'll include a minimal example below.
1) File called papaja_file.Rmd
---
# https://crsh.github.io/papaja_man/index.html
title : "Some Title"
shorttitle : "HEADER"
author:
- name : "Name R Here"
affiliation : "1"
corresponding : yes # Define only one corresponding author
address : "Include addresss"
email : "randomemail#usa.edu"
affiliation:
- id : "1"
institution : "Any University"
author_note: |
....
abstract: |
Text here for abstract.
keywords : "Keyword1, keyword2, keyword3"
bibliography : ["references.bib"]
figsintext : no
figurelist : no
tablelist : no
footnotelist : no
lineno : yes
lang : "english"
class : "man"
output : papaja::apa6_pdf
---
```{r load_packages, include = FALSE}
library("papaja")
```
```{r analysis_preferences}
# Seed for random number generation
set.seed(42)
```
```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.path = 'figures/', echo = TRUE, warning = FALSE, message = FALSE)
```
```{r child = 'child_document.Rmd'}
```
\newpage
# References
```{r create_references, echo = F}
r_refs(file = "references.bib")
```
\setlength{\parindent}{-0.5in}
\setlength{\leftskip}{0.5in}
Notice that it references a single child Rmarkdown document.
2) The child document with text, called child_document.Rmd
---
output:
pdf_document:
includes:
in_header: preamble.tex
---
One sentence without highlighting. \hl{Another with highlighting.}
3) The preamble, called preamble.tex
\usepackage{color}
\usepackage{soul}
\definecolor{lightblue}{rgb}{0.90, 0.95, 1}
\sethlcolor{lightblue}
Knitting the main papaja file produces the error. Removing the \hl command within the child document allows the pdf to compile without issue.
Result after putting YAML header within the main papaja document rather than the child:
The YAML header in your child document is not evaluated, c.f.
The master document, for example, consists of the YAML front matter and includes the children, which are themselves R Markdown documents without a YAML front matter.
https://crsh.github.io/papaja_man/tips-and-tricks.html#splitting-an-r-markdown-document
But you can include your preamble.tex in you master file using:
output:
papaja::apa6_pdf:
includes:
in_header: preamble.tex
c.f. https://github.com/rstub/stackoverflow/commit/a92a67d4721ee9c06e995b08adbf8cb89daebcb4
Result:
I am working on RMarkdown to generate a report that includes an appendix after references. I have written the appendix on a different RMarkdown file and adapted my principal file to compile it. This is the code for my principal Rmd file that generates report:
---
bibliography: bb.bib
fontsize: 11pt
nocite: '#*'
output:
pdf_document:
includes:
after_body: Demo2.Rmd
keep_tex: yes
link-citations: true
---
\newpage
\section{Testing}\label{sec1}
```{r}
summary(cars)
```
\section{Demo}
This was done using #shiina and we will use some info from Section \ref{sec1} to do.
```{r}
summary(iris[,1:2])
```
\section{References}
The file bb.bib contains next references:
#article {shiina,
author = {Shiina, Takayuki and Birge, John R.},
title = {Stochastic unit commitment problem},
journal = {International Transactions in Operational Research},
volume = {11},
number = {1},
publisher = {Blackwell Publishing},
pages = {19--32},
year = {2004},
}
#book{groewe2001,
title={Stochastic unit commitment in hydro-thermal power production planning},
author={Gr{\"o}we-Kuska, N. and R{\"o}misch, W.},
year={2001},
series = { Preprints aus dem Institut f{\"u}r Mathematik },
publisher = { Humboldt-Universit{\"a}t zu Berlin, Institut f{\"u}r Mathematik },
}
Finally, my appendix Rmd file, Demo2.Rmd, contains this structure:
\appendix
\section*{Appendix}
\section{Additional info}
In this section we also follow #shiina to explain concepts.
Compilation works fine and generate document but issues are appearing in the appendix section. I used a reference with #shiina to cite something, but I am getting this output in the final report:
The circle in black shows that citation from bibliography is not working. Instead of #shiina, it should appear Shiina and Birge (2004). I have tried replacing Rmd file with a TeX file but it did not work.
Is it any way to correct that?, I do not know if after_body needs to be adjusted or what to do.
So, I did actually find a solution that does use some minor trickery.
---
bibliography: bb.bib
fontsize: 11pt
nocite: '#*'
output:
pdf_document:
keep_tex: true
includes:
after_body: Demo2.tex
link-citations: true
---
```{r,include=FALSE}
library(tidyverse)
rmarkdown::render('Demo2.Rmd')
a <- readChar('Demo2.tex', file.size('Demo2.tex'))
a <- a %>% str_remove('[[:space:]]*\\\\hypertarget[[\\w\\W]]+\\z') %>%
str_remove('\\A[[\\w\\W]]+begin.document.')
writeChar(a, 'Demo2.tex',eos = NULL)
```
\newpage
\section{Testing}\label{sec1}
```{r}
summary(cars)
```
\section{Demo}
This was done using #shiina and we will use some info from Section \ref{sec1} to do.
```{r}
summary(iris[,1:2])
```
\section{References}
And your Appendix-file:
---
bibliography: bb.bib
fontsize: 11pt
output:
pdf_document:
keep_tex: yes
link-citations: true
---
\appendix
\section*{Appendix}
\section{Additional info}
In this section we also follow #shiina to explain concepts.
# References
results in:
The way it works is to render the Demo2.Rmd- file before rendering the actual file and to keep the associated .tex- file.
Then the non included R-chunk cuts of all the parts we don't want to have at the end of the main file and overwrites the Demo2.tex-file.
What remains is the exact tex-code you need to have your references working.
Feels pretty dirty, but should work.
I am preparing R markdown document and I would like to display postgre sql codes nicely in R markdown document of course the codes should only be displayed not runned. How can I do that? . Below I put some code examples.
Thank you.
title: "POSTGRE sql "
output:
html_document: default
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r1, eval=F}
with data as (select * from (values
('03-05-2019'::date,'{"color": true,"view": [181] ,"school":
[805,812,852,856,857]}'::jsonb),
('06-08-2019'::date,'{"color": false,"view": [184,185],"school":
[805,855,859]}'::jsonb),
('04-07-2019'::date,'{"color": true,"view": [184,185,189],"school":
[855,859]}'::jsonb)
) as v(published_date,attributes))
```
In the header add this to your output
output:
html_document:
highlight: pygments
and in the body use this line
{r, engine = 'sql', eval = FALSE}
I am not sure the major differences in SQL and PostgreSQL, but the syntax highlighting does work.
Here is a link to show other languages you can use with pygments
http://pygments.org/languages/
I want to knit a pdf-document but the keywords don't appear in the final document. Can someone say me what I'm doing wrong?
---
title: "title"
subtitle: "subtitle"
author: "author"
date: "09 04 2019"
output:
pdf_document:
keywords: "word1, word2, word3"
footerdate: yes
abstract: 'Insert abstract here'
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Introduction
When knitting to PDF, keywords are sent to the file metadata but are not actually visible in the file. Source
You can customize the template for PDF generation or render Rmd files with base_format: rticles::elsevier_article.
However, there is another way to show keywords on the PDF just by adding few codes to the Rmd file:
Add a LaTeX code to provide the \keyword command (\providecommand{\keywords}[1]{\textbf{\textit{Keywords---}} #1}) into YAML's header-includes key;
Add keywords in the text section using the LaTeX command
---
title: "title"
subtitle: "subtitle"
author: "author"
date: "09 04 2019"
output:
pdf_document:
# keywords: "word1, word2, word3" # <- You don't have to add your keywords here since they only appear as the 'invisible' metadata of PDF
footerdate: yes
abstract: 'Insert abstract here'
header-includes:
- |
```{=latex}
\providecommand{\keywords}[1]{\textbf{\textit{Keywords---}} #1}
```
---
```{=latex}
\keywords{word1, word2, word3}
```
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Introduction