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$set(echo = TRUE)
```
```{r1, eval=F}
with data as (select * from (values
('03-05-2019'::date,'{"color": true,"view": [181] ,"school":
[805,812,852,856,857]}'::jsonb),
('06-08-2019'::date,'{"color": false,"view": [184,185],"school":
[805,855,859]}'::jsonb),
('04-07-2019'::date,'{"color": true,"view": [184,185,189],"school":
[855,859]}'::jsonb)
) as v(published_date,attributes))
```
In the header add this to your output
output:
html_document:
highlight: pygments
and in the body use this line
{r, engine = 'sql', eval = FALSE}
I am not sure the major differences in SQL and PostgreSQL, but the syntax highlighting does work.
Here is a link to show other languages you can use with pygments
http://pygments.org/languages/
Related
Basically i want to build a random multiple choice question generator with R Markdown. For this task there need to be equations in the code chunks of the markdown.
The following works like a charm and gives the equation "greekbeta = 1"
---
title: "test"
author: "me"
output:
word_document: default
---
```{r eval=TRUE, echo=FALSE,results = "asis"}
"$\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$", '\n\n')
```
is it possible to include an inline (internal document) hyperlink in the YAML title block of a RMarkdown document? Or is there a R package that allows this?
Below is what I am trying to do:
---
title: blah {#one1} and so on {#two2}
...
---
# Bibliography
1. Reference note to [explain](#one1) in title
2. Reference note to [explain](#two2) in title
Thank you.
The title is parsed as markdown, so you can use regular markdown link syntax in order to get the behavior you want.
---
title: 'There is a link in this title...[LINK](#anchor)'
author: "Jason Punyon"
date: "6/16/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Bibliography
<p id='anchor'>Here's where I went!</p>
You could also just put the link in manually...
---
title: 'There is a link in this title...LINK'
author: "Jason Punyon"
date: "6/16/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Bibliography
<p id='anchor'>Here's where I went!</p>
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 generating a PDF document using Knitr. I am calling my r script from a separate file. Everything prints out fine in the PDF, but when I output a table using Stargazer, knitr generates a new page in the PDF document with "asis" printed on the page. I included a screen shot. Any ideas why this is happening?
My code chunk:
---
title: "PALS Biomarker Analysis"
author: "Daniel Parker"
date: "November 20, 2017"
output: pdf_document
header-includes:
- \usepackage{caption}
---
\captionsetup[table]{labelformat=empty}
```{r echo=FALSE}
library(knitr)
read_chunk('11-20-17 PALS Analysis V3.R')
```
```{r eighth, echo = FALSE, results="asis"}
<<linear_model_one>>
```
If I remove the results="asis" the table does not print correctly.
Try changing this code
```{r eighth, echo = FALSE, results="asis"}
<<linear_model_one>>
```
to this (remove the double quotes surrounding asis)
```{r eighth, echo = FALSE, results='asis'}
<<linear_model_one>>
```
I've been looking at the diagrammeR package (http://rich-iannone.github.io/DiagrammeR/) to generate diagrams in rMarkdown. This works great when rendering the documents in HTML; now the question I have is whether there is a possibility to output the document as MS Word document?
For example, consider this:
---
title: "Test"
author: "Test"
date: "Monday, May 18, 2015"
output: html_document
---
```{r, echo=FALSE, warning=FALSE}
if (!require("DiagrammeR")) library("DiagrammeR")
```
Check out this diagram:
```{r, echo=FALSE, results='asis'}
DiagrammeR::grViz("
digraph rmarkdown {
node [shape = box ]
'A' -> 'B'
}
")
```
Using HTML as output format works like a charm. But, when I switch to MS Word, all I get is:
Error: Functions that produce HTML output found in document targeting docx output.
Please change the output type of this document to HTML.
Any ideas would be appreciated.
Many thanks, Philipp
trelliscope is useful: https://github.com/tesseradata/trelliscope
After installing http://phantomjs.org/download.html,
You can generate word doc file by:
---
title: "Test"
author: "Test"
date: "Monday, May 18, 2015"
output: word_document
---
```{r include=FALSE}
if (!require("DiagrammeR")) library("DiagrammeR")
library(trelliscope)
```
Check out this diagram:
```{r, include=FALSE}
p = DiagrammeR::grViz("
digraph rmarkdown {
node [shape = box ]
'A' -> 'B'
}
")
widgetThumbnail(p, paste0(getwd(), "/hoge.png"))
```
Here is the screenshot. It looks perfect :)